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2019

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Timing And Potential Drivers Of Symbiont Selection In The Early Life Stages Of The Massive Starlet Coral Siderastrea Siderea, Sarah G. Koerner Jul 2019

Timing And Potential Drivers Of Symbiont Selection In The Early Life Stages Of The Massive Starlet Coral Siderastrea Siderea, Sarah G. Koerner

HCNSO Student Theses and Dissertations

The ability of corals to build reefs can be attributed to their relationship with single-celled algae of the familySymbiodiniaceae.Through the process of photosynthesis, these algae can provide their coral hosts with over 90% of their daily energy requirements. Most coral species acquire multiple species of symbionts from the surrounding water during their larval stage or immediately after settling. However, over time, the coral will select a dominant symbiont speciesthat can depend on the local environment. Until this study, the size or age of the coral at which this transition from multiple Symbiodiniaceaespecies to one dominant species occurs has remained …

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Shallow- Water Hardbottom Communities Support The Separation Of Biogeographic Provinces On The West- Central Florida Gulf Coast, Shelby Eagan Jul 2019

Shallow- Water Hardbottom Communities Support The Separation Of Biogeographic Provinces On The West- Central Florida Gulf Coast, Shelby Eagan

HCNSO Student Theses and Dissertations

Several studies have found separation of biogeographic provinces on the West Florida Shelf (WFS), but the location of this separation differs depending on different organisms with faunal boundaries proposed at Apalachicola, Cedar Key, Anclote Key. Tampa Bay, Charlotte Harbor, Cape Romano, or Cape Sable. Biogeographic boundaries can be gradual over a given space and are often species-specific. Analyses of marine benthic mapping and community characterization of Florida’s West-central coast shallow water (depth) hardbottom habitats indicate a major shift in the benthos across Tampa Bay. Quantitative benthic surveys of 29 sites yielded a total of 4,079 individuals of nine stony coral …

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Desperate Coral Larvae? Behavioral Responses To Settlement Cues In Aging Agaricia Agaricites Larvae, Helena Sasha Fulmore Jul 2019

Desperate Coral Larvae? Behavioral Responses To Settlement Cues In Aging Agaricia Agaricites Larvae, Helena Sasha Fulmore

HCNSO Student Theses and Dissertations

The global stressors of ocean warming and acidification, as well as local stressors such as eutrophication, overfishing, and coastal construction, have all contributed to the severe decline in coral populations worldwide. Recovery of coral reefs depends partly on recruitment, which relies on the response of larvae to settlement cues indicative of habitat quality; however, it remains unclear whether recruitment in disturbed areas will be compromised. Specifically, as reefs become more disturbed and dominated by macroalgae, it is important to understand larval behavior in response to changes in habitat quality. In this study, we first assessed the settlement success of newly …

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Investigating Changes In The Chemical Composition Of Wood Upon Digestion By Wood-Boring Bivalves Of The Sub-Family Xylophagaidae, And Potential Implications For Marine Biogeochemical Cycles, Briony Cope Jul 2019

Investigating Changes In The Chemical Composition Of Wood Upon Digestion By Wood-Boring Bivalves Of The Sub-Family Xylophagaidae, And Potential Implications For Marine Biogeochemical Cycles, Briony Cope

The Plymouth Student Scientist

The sub-family of molluscs Xylophagaidae are the primary degraders of wood in the oceans. They are part of an opportunistic ecosystem, which survives on temporary falls of large organic matter, such as carcasses and wood debris. After digesting the wood with the help of symbiotic bacteria, Xylophagaidae excrete a pulp like substance, which lines the walls of their burrows. The nutrients in the broken down wood becomes accessible to other forms of life, and growing populations create anoxic environments, which encourage chemoautotrophic activity. This research aims to identify the role that Xylopohagaidae play in the biogeochemical cycles of certain elements, …

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Species Distribution Model Of Cetaceans In Relation To Environmental Factors At Two Locations In The North Atlantic, Laura Adams Jul 2019

Species Distribution Model Of Cetaceans In Relation To Environmental Factors At Two Locations In The North Atlantic, Laura Adams

The Plymouth Student Scientist

Cetaceans in the North Atlantic are under threat from the increasing pressure and demand placed on the sea by humans. In order to conserve cetacean populations, legislative acts such as the EC Habitats Directive (Council Directive 92/43/EEC) are calling for protected areas to be established. Species distribution models have been used in this study as a tool to outline habitat preference of cetaceans in the Celtic Sea and eastern North Atlantic, helping to determine the boundaries for protected areas. Remotely-sensed environmental data was analysed against visual boat survey data using boosted regression tree modelling. A review of the literature emphasised …

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Students’ Perceptions Of Religious Practices And Spiritual Maturity Within Pentecostalism: A Case Study, Sheila Jackson Jul 2019

Students’ Perceptions Of Religious Practices And Spiritual Maturity Within Pentecostalism: A Case Study, Sheila Jackson

CUP Ed.D. Dissertations

The purpose of this qualitative case study was to explore how 10 Pentecostal-Charismatic college students perceived the influence of Pentecostal-Charismatic religious practices on their spiritual maturity in Florida. All Christian denominations are distinctive and identified by name, style of leadership, doctrine, beliefs, practices, and spiritual activity. One of Pentecostals distinctive beliefs, adherents are taught from scripture that the initial evidence of being baptized in the Holy Spirit—speaking in tongues (e.g., Acts 2:4, 10:45–46). To explore this phenomenon, the researcher interviewed college students and a campus pastor, and students responded to a spiritual maturity index as a questionnaire to determine the …

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Protecting Stone Heritage In The Painted Desert: Employing The Rock Art Stability Index In The Petrified Forest National Park, Arizona, Kaelin M. Groom, Niccole Villa Cerveny, Casey D. Allen Jul 2019

Protecting Stone Heritage In The Painted Desert: Employing The Rock Art Stability Index In The Petrified Forest National Park, Arizona, Kaelin M. Groom, Niccole Villa Cerveny, Casey D. Allen

KIP Articles

Located in northeastern Arizona (USA), Petrified Forest National Park (PEFO) presents a unique story of both geologic and human history. Though perhaps most well-known for its abundant petrified wood and being part of the Painted Desert, visitors are often surprised when they discover PEFO hosts many ancient petroglyph sites. Over the years, many attempts have been made to record the petroglyph sites, but nothing has been done to assess their geomorphic stability. To address this shortcoming, we employed the Rock Art Stability Index (RASI) to assess geologic stability and (potential) deterioration of rock art sites in PEFO. Used for more …

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The Rise Of Citizen Science In Health And Biomedical Research, Andrea Wiggins, John Wilbanks Jul 2019

The Rise Of Citizen Science In Health And Biomedical Research, Andrea Wiggins, John Wilbanks

Information Systems and Quantitative Analysis Faculty Publications

Citizen science models of public participation in scientific research represent a growing area of opportunity for health and biomedical research, as well as new impetus for more collaborative forms of engagement in large-scale research. However, this also surfaces a variety of ethical issues that both fall outside of and build upon the standard human subjects concerns in bioethics. This article provides background on citizen science, examples of current projects in the field, and discussion of established and emerging ethical issues for citizen science in health and biomedical research.

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The Design And Implementation Of Aida: Ancient Inscription Database And Analytics System, M. Parvez Rashid Jul 2019

The Design And Implementation Of Aida: Ancient Inscription Database And Analytics System, M. Parvez Rashid

School of Computing: Dissertations, Theses, and Student Research

AIDA, the Ancient Inscription Database and Analytic system can be used to translate and analyze ancient Minoan language. The AIDA system currently stores three types of ancient Minoan inscriptions: Linear A, Cretan Hieroglyph and Phaistos Disk inscriptions. In addition, AIDA provides candidate syllabic values and translations of Minoan words and inscriptions into English. The AIDA system allows the users to change these candidate phonetic assignments to the Linear A, Cretan Hieroglyph and Phaistos symbols. Hence the AIDA system provides for various scholars not only a convenient online resource to browse Minoan inscriptions but also provides an analysis tool to explore …

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Global Spatial Risk Assessment Of Sharks Under The Footprint Of Fisheries, Nuno Queiroz, Nicolas E. Humphries, Ana Couto, Marisa Vedor, Ivo Da Costa, Ana M. M. Sequeira, Gonzalo Mucientes, Antonio M. Santos, Francisco J. Abascal, Debra L. Abercrombie, Katya Abrantes, David Acuna-Marrero, Andre S. Afonso, Darrell Anders, Gonzalo Araujo, Randall Arauz, Pascal Bach, Adam Barnett, Diego Bernal, Michael L. Berumen, Sandra Bessudo Lion, Natalia P. A. Bezerra, Antonin V. Blaison, Barbara A. Block, Mark E. Bond, Russell W. Bradford, Camrin D. Braun, Edward J. Brooks, Annabelle Brooks, Judith Brown, Barry D. Bruce, Michael Byrne, Steven E. Campana, Aaron B. Carlisle, Demian D. Chapman, Taylor K. Chapple, John Chisholm, Christopher R. Clarke, Erik G. Clua, Jesse E. M. Cochran, Estelle C. Crochelet, Laurent Dagorn, Ryan Daly, Daniel Devia Cortes, Thomas K. Doyle, Michael Drew, Clinton A. J. Duffy, Thor Erikson, Eduardo Espinoza, Luciana C. Ferreira, Francesco Ferretti, John D. Filmalter, G. Chris Fischer, Richard Fitzpatrick, Jorge Fontes, Fabian Forget, Mark Fowler, Malcolm P. Francis, Austin J. Gallagher, Enrico Gennari, Simon D. Goldsworthy, Matthew J. Gollock, Jonathan R. Green, Johan A. Gustafson, Tristan L. Guttridge, Hector M. Guzman, Neil Hammerschlag, Luke Harman, Fabio H.V. Hazin, Matthew Heard, Alex R. Hearn, John C. Holdsworth, Bonnie J. Holmes, Lucy A. Howey-Jordan, Mauricio Hoyos, Robert E. Hueter, Nigel E. Hussey, Charlie Huveneers, Dylan T. Irion, David M. P. Jacoby, Oliver J. D. Jewell, Ryan Johnson, Lance K. B. Jordan, Salvador J. Jorgensen, Warren Joyce, Clare A. Keating Daly, James T. Ketchum, A. Peter Klimley, Alison A. Kock, Pieter Koen, Felipe Ladino, Fernanda O. Lana, James S. E. Lea, Fiona Llewellyn, Warrick S. Lyon, Anna Macdonnell, Bruno C. L. Macena, Heather Marshall, Jaime D. Mcallister, Rory Mcauley, Michael A. Meyer, John J. Morris, Emily R. Nelson, Yannis P. Papastamatiou, Toby A. Patterson, Cesar Peñaherrera-Palma, Julian G. Pepperell, Simon J. Pierce, Francois Poisson, Lina Maria Quintero, Andrew J. Richardson, Paul J. Rogers, Christoph A. Rohner, David R. L. Rowat, Melita Samoilys, Jayson M. Semmens, Marcus Sheaves, George Shillinger, Mahmood S. Shivji, Sarika Singh, Gregory B. Skomal, Malcolm J. Smale, Laurenne B. Snyders, German Soler, Marc Soria, Kilian M. Stehfest, John D. Stevens, Simon R. Thorrold, Mariana T. Tolotti, Alison Towner, Paulo Travassos, John P. Tyminski, Frederic Vandeperre, Jeremy Vaudo, Yuuki Y. Watanabe, Sam B. Weber, Bradley M. Wetherbee, Timothy D. White, Sean Williams, Patricia M. Zarate, Robert Harcourt, Graeme C. Hays, Mark G. Meekan, Michele Thums, Xabier Irigoien, Victor M. Eguiluz, Carlos M. Duarte, Lara L. Sousa, Samantha J. Simpson, Emily J. Southall, David W. Sims Jul 2019

Global Spatial Risk Assessment Of Sharks Under The Footprint Of Fisheries, Nuno Queiroz, Nicolas E. Humphries, Ana Couto, Marisa Vedor, Ivo Da Costa, Ana M. M. Sequeira, Gonzalo Mucientes, Antonio M. Santos, Francisco J. Abascal, Debra L. Abercrombie, Katya Abrantes, David Acuna-Marrero, Andre S. Afonso, Darrell Anders, Gonzalo Araujo, Randall Arauz, Pascal Bach, Adam Barnett, Diego Bernal, Michael L. Berumen, Sandra Bessudo Lion, Natalia P. A. Bezerra, Antonin V. Blaison, Barbara A. Block, Mark E. Bond, Russell W. Bradford, Camrin D. Braun, Edward J. Brooks, Annabelle Brooks, Judith Brown, Barry D. Bruce, Michael Byrne, Steven E. Campana, Aaron B. Carlisle, Demian D. Chapman, Taylor K. Chapple, John Chisholm, Christopher R. Clarke, Erik G. Clua, Jesse E. M. Cochran, Estelle C. Crochelet, Laurent Dagorn, Ryan Daly, Daniel Devia Cortes, Thomas K. Doyle, Michael Drew, Clinton A. J. Duffy, Thor Erikson, Eduardo Espinoza, Luciana C. Ferreira, Francesco Ferretti, John D. Filmalter, G. Chris Fischer, Richard Fitzpatrick, Jorge Fontes, Fabian Forget, Mark Fowler, Malcolm P. Francis, Austin J. Gallagher, Enrico Gennari, Simon D. Goldsworthy, Matthew J. Gollock, Jonathan R. Green, Johan A. Gustafson, Tristan L. Guttridge, Hector M. Guzman, Neil Hammerschlag, Luke Harman, Fabio H.V. Hazin, Matthew Heard, Alex R. Hearn, John C. Holdsworth, Bonnie J. Holmes, Lucy A. Howey-Jordan, Mauricio Hoyos, Robert E. Hueter, Nigel E. Hussey, Charlie Huveneers, Dylan T. Irion, David M. P. Jacoby, Oliver J. D. Jewell, Ryan Johnson, Lance K. B. Jordan, Salvador J. Jorgensen, Warren Joyce, Clare A. Keating Daly, James T. Ketchum, A. Peter Klimley, Alison A. Kock, Pieter Koen, Felipe Ladino, Fernanda O. Lana, James S. E. Lea, Fiona Llewellyn, Warrick S. Lyon, Anna Macdonnell, Bruno C. L. Macena, Heather Marshall, Jaime D. Mcallister, Rory Mcauley, Michael A. Meyer, John J. Morris, Emily R. Nelson, Yannis P. Papastamatiou, Toby A. Patterson, Cesar Peñaherrera-Palma, Julian G. Pepperell, Simon J. Pierce, Francois Poisson, Lina Maria Quintero, Andrew J. Richardson, Paul J. Rogers, Christoph A. Rohner, David R. L. Rowat, Melita Samoilys, Jayson M. Semmens, Marcus Sheaves, George Shillinger, Mahmood S. Shivji, Sarika Singh, Gregory B. Skomal, Malcolm J. Smale, Laurenne B. Snyders, German Soler, Marc Soria, Kilian M. Stehfest, John D. Stevens, Simon R. Thorrold, Mariana T. Tolotti, Alison Towner, Paulo Travassos, John P. Tyminski, Frederic Vandeperre, Jeremy Vaudo, Yuuki Y. Watanabe, Sam B. Weber, Bradley M. Wetherbee, Timothy D. White, Sean Williams, Patricia M. Zarate, Robert Harcourt, Graeme C. Hays, Mark G. Meekan, Michele Thums, Xabier Irigoien, Victor M. Eguiluz, Carlos M. Duarte, Lara L. Sousa, Samantha J. Simpson, Emily J. Southall, David W. Sims

Biology Faculty Articles

Effective ocean management and conservation of highly migratory species depends on resolving overlap between animal movements and distributions and fishing effort. Yet, this information is lacking at a global scale. Here we show, using a big-data approach combining satellite-tracked movements of pelagic sharks and global fishing fleets, that 24% of the mean monthly space used by sharks falls under the footprint of pelagic longline fisheries. Space use hotspots of commercially valuable sharks and of internationally protected species had the highest overlap with longlines (up to 76% and 64%, respectively) and were also associated with significant increases in fishing effort. We …

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Mid To Late Season Weed Detection In Soybean Production Fields Using Unmanned Aerial Vehicle And Machine Learning, Arun Narenthiran Veeranampalayam Sivakumar Jul 2019

Mid To Late Season Weed Detection In Soybean Production Fields Using Unmanned Aerial Vehicle And Machine Learning, Arun Narenthiran Veeranampalayam Sivakumar

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Mid-late season weeds are those that escape the early season herbicide applications and those that emerge late in the season. They might not affect the crop yield, but if uncontrolled, will produce a large number of seeds causing problems in the subsequent years. In this study, high-resolution aerial imagery of mid-season weeds in soybean fields was captured using an unmanned aerial vehicle (UAV) and the performance of two different automated weed detection approaches – patch-based classification and object detection was studied for site-specific weed management. For the patch-based classification approach, several conventional machine learning models on Haralick texture features were …

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The Surface Sediment Carbon Content Of A North Norfolk Saltmarsh, Robert Van Ree Jul 2019

The Surface Sediment Carbon Content Of A North Norfolk Saltmarsh, Robert Van Ree

The Plymouth Student Scientist

Carbon sequestration is an important aspect of mitigating climate change and its detrimental environmental and economic effects. Vegetative ecosystems such as rainforests are often praised for their ability to sequester carbon through photosynthesis, however more efficient systems for sequestering carbon such as saltmarshes are often overlooked. Carbon storage was investigated in the developing salt marsh habitats of Holkham Bay, part of the Holkham National Nature Reserve in Norfolk, England between 31/07/2017 and 03/08/2017. This was done to assess the quantity of carbon that may be lost to rising sea levels associated with climate change and be released as CO2, which …

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Occupancy Patterns Of Sea Birds In Relation To Oceanographic Conditions At Sites On The Llŷn Peninsula, Emily Goodman Jul 2019

Occupancy Patterns Of Sea Birds In Relation To Oceanographic Conditions At Sites On The Llŷn Peninsula, Emily Goodman

The Plymouth Student Scientist

With the current increase in the emergence of offshore renewable energy installations it is becoming increasingly important to monitor and study seabird populations. In order to understand the potential impacts of these installations we must first understand the spatial and temporal factors affecting seabirds site usage which may then inform future monitoring and management. In this study a series of shore based surveys were carried out to assess the occupancy patterns of seabirds in relation to oceanographic conditions at three sites along the Llŷn peninsula. One site, named Bardsey Sound is a proposed site for tidal energy extraction due to …

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Statistical Analysis Of The Effect Of Lesson And Learning Styles On The Learning And Retention Of Information Of Secondary School Chemistry Students, Lauren Barry Jul 2019

Statistical Analysis Of The Effect Of Lesson And Learning Styles On The Learning And Retention Of Information Of Secondary School Chemistry Students, Lauren Barry

The Plymouth Student Scientist

The study is an interdisciplinary study as it links to both chemistry and also social science. The project investigated the learning and recall of information of year 9 students at Richard Lander School. In total 85 students participated in this study. Two top set ability groups and two bottom set ability groups were selected by the school to participate in either a non-practical or practical lesson. The students all completed a pre-lesson test to assess their knowledge of the lesson subject (chromatography) prior to the lesson. This was used to establish that the top/bottom set ability was the same for …

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The Association Of Optimism With Sleep Duration And Quality: Findings From The Coronary Artery Risk And Development In Young Adults (Cardia) Study, Rosalba Hernandez, Thanh-Huyen T. Vu, Kiarri N. Kershaw, Julia K. Boehm, Laura D. Kubzansky, Mercedes Carnethon, Claudia Trudel-Fitzgerald, Kristen L. Knutson, Laura A. Colangelo, Kiang Liu Jul 2019

The Association Of Optimism With Sleep Duration And Quality: Findings From The Coronary Artery Risk And Development In Young Adults (Cardia) Study, Rosalba Hernandez, Thanh-Huyen T. Vu, Kiarri N. Kershaw, Julia K. Boehm, Laura D. Kubzansky, Mercedes Carnethon, Claudia Trudel-Fitzgerald, Kristen L. Knutson, Laura A. Colangelo, Kiang Liu

Psychology Faculty Articles and Research

Optimism is associated with better health outcomes with hypothesized effects due in part to optimism's association with restorative health processes. Limited work has examined whether optimism is associated with better quality sleep, a major restorative process. We test the hypothesis that greater optimism is associated with more favorable sleep quality and duration. Main analyses included adults aged 32-51 who participated in the Coronary Artery Risk Development in Young Adults (CARDIA) study (n = 3,548) during the fifth (Year 15: 2000-2001) and sixth (Year 20: 2005-2006) follow-up visits. Optimism was assessed using the revised Life-Orientation Test. Self-report measures of …

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Targeting Sporadic And Neurofibromatosis Type 1 (Nf1) Related Refractory Malignant Peripheral Nerve Sheath Tumors (Mpnst) In A Phase Ii Study Of Everolimus In Combination With Bevacizumab (Sarc016), Brigitte C. Widemann, Anglea C. Hirbe, Et Al Jul 2019

Targeting Sporadic And Neurofibromatosis Type 1 (Nf1) Related Refractory Malignant Peripheral Nerve Sheath Tumors (Mpnst) In A Phase Ii Study Of Everolimus In Combination With Bevacizumab (Sarc016), Brigitte C. Widemann, Anglea C. Hirbe, Et Al

Open Access Publications

No abstract provided.

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Effects Of Turmeric (Curcuma Longa) Extract In Streptozocin‐Induced Diabetic Model, Diana G. Sami, Marwa T. Badawy, Maha E. Mansour, Ahmed Abdellatif Jul 2019

Effects Of Turmeric (Curcuma Longa) Extract In Streptozocin‐Induced Diabetic Model, Diana G. Sami, Marwa T. Badawy, Maha E. Mansour, Ahmed Abdellatif

Faculty Journal Articles

Herbal remedies have been used for centuries to ameliorate complications of diabetes mellitus (DM). The aim of this study is to compare the effects of the oral curcumin supplement versus parenteral administration of turmeric extract on diabetic complications in a streptozocin (STZ) diabetic model. STZ DM rats received low and high doses turmeric extract intraperitoneally as well as oral curcumin. Curcumin and turmeric extracts significantly reduced blood glucose and creatinine levels, but not urea, and caused an increase in uric acid. Low dose improved liver enzymes, while higher dose and oral administration caused an increase in the ALT and AST. …

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Cleavage And Sub-Cellular Redistribution Of Nuclear Pore Protein 98 By Coxsackievirus B3 Protease 2a Impairs Cardioprotection., Paul J. Hanson, Al Rohet Hossain, Ye Qiu, Huifang M. Zhang, Guangze Zhao, Cheng Li, Veena Lin, Saheedat Sulaimon, Marli Vlok, Gabriel Fung, Victoria H. Chen, Eric Jan, Bruce M. Mcmanus, David J. Granville, Decheng Yang Jul 2019

Cleavage And Sub-Cellular Redistribution Of Nuclear Pore Protein 98 By Coxsackievirus B3 Protease 2a Impairs Cardioprotection., Paul J. Hanson, Al Rohet Hossain, Ye Qiu, Huifang M. Zhang, Guangze Zhao, Cheng Li, Veena Lin, Saheedat Sulaimon, Marli Vlok, Gabriel Fung, Victoria H. Chen, Eric Jan, Bruce M. Mcmanus, David J. Granville, Decheng Yang

College of Population Health Faculty Papers

Myocarditis, inflammation of the heart muscle, affects all demographics and is a major cause of sudden and unexpected death in young people. It is most commonly caused by viral infections of the heart, with coxsackievirus B3 (CVB3) being among the most prevalent pathogens. To understand the molecular pathogenesis of CVB3 infection and provide strategies for developing treatments, we examined the role of a key nuclear pore protein 98 (NUP98) in the setting of viral myocarditis. NUP98 was cleaved as early as 2 h post-CVB3 infection. This cleavage was further verified through both the ectopic expression of viral proteases and in …

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Bilateral And Unilateral Resistance Training And Athletic Performance, Brendyn B. Appleby Jul 2019

Bilateral And Unilateral Resistance Training And Athletic Performance, Brendyn B. Appleby

Theses: Doctorates and Masters

Specificity is a key programming principle for optimal transfer of physiological adaptation of training to improved athletic performance. In resistance training, it has long been identified that the closer the mechanical specificity between the training exercise and outcome performance, the greater the transfer of improved capacity. Bilateral resistance exercises are predominately prescribed for the development of maximum strength and are well demonstrated to enhance athletic performance. However, unilateral exercises appear to demonstrate greater specificity to movements such as running and change of direction as these movements are predominantly single leg actions. Nonetheless, the unstable nature and comparatively lower magnitude of …

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Genome Characterization And Annotation Of A Cluster S Bacteriophage, Anna-Nikol Georgiev, Kathryn Myers, Kierra Jammer, Morgan Callin, Taylor Sorrel, Kari Clase, Ikenna Okekeogbu Jul 2019

Genome Characterization And Annotation Of A Cluster S Bacteriophage, Anna-Nikol Georgiev, Kathryn Myers, Kierra Jammer, Morgan Callin, Taylor Sorrel, Kari Clase, Ikenna Okekeogbu

Purdue Undergraduate Research Conference

Bacteriophages (phages) are viruses that infect their host and cannot reproduce independently outside of them. The application of bacteriophages in the biotechnology and medical sectors has recently increased, including uses as a potential antibacterial agent and CRISPR technology. In this project, the 48,667 to 58,636 base pair region (genes 87-98) of the Corazon phage genome was annotated by five student researchers at Purdue University. Corazon, a cluster S phage was isolated at Lafayette College in Easton, PA. Corazon belongs to the Siphoviridae morphotype and its genome consists of 109 genes. In this study, gene locations were called using evidence consisting …

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Functional Annotation Of Myasthenia Gravis Genetic Risk Variants: Results From A Genome-Wide Study, Alyssa Flint Jul 2019

Functional Annotation Of Myasthenia Gravis Genetic Risk Variants: Results From A Genome-Wide Study, Alyssa Flint

Purdue Undergraduate Research Conference

Myasthenia Gravis (MG) is an autoimmune disease of the neuromuscular junction. The purpose of this study was to analyze the biological pathways and key genetic contributors that lead to MG. In this study, we performed functional annotation of the significant variants from the results of an MG Genome-Wide Association (GWAS) study on a Southeastern European population. Furthermore, the three approaches used were positional mapping of the SNPs, pathway analysis, and eQTL mapping. The positional and eQTL mapping were performed through FUMA. We annotated the SNPs to genes based on their physical position, and for the eQTL we used data from …

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Doctor Interaction: Is There Discriminatory Treatment At Play?, Jade Meekin, Kennedy Skipper Jul 2019

Doctor Interaction: Is There Discriminatory Treatment At Play?, Jade Meekin, Kennedy Skipper

Purdue Undergraduate Research Conference

While research on healthcare disparities exist, specifically about racial disparities and pain, no studies have explored how these implicit biases impact young adults and their social interactions with their doctors. This study explored how race, age, and gender impacts the way that their medical professionals interact with their patients. A survey was sent out to many students of Purdue University where they answered various questions regarding their doctor visits. African American participants reported feeling as though their medical doctors were unwilling to pursue more extensive or serious treatment when compared to the responses of Caucasians, Asians, and other ethnicities. A …

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Investigation Of Bacteriophage Genomes, Lina Trigg, Rachel Damge, Estefania Martinez, Jenna Ischinger Jul 2019

Investigation Of Bacteriophage Genomes, Lina Trigg, Rachel Damge, Estefania Martinez, Jenna Ischinger

Purdue Undergraduate Research Conference

Bacteriophage (phage) was first found in the 1900s by Frederick Twort on accident, with the average size of a phage ranging from 3.4kb to almost 500kb (Keen 2015). Phage have become the most abundant organisms on earth and have been used for over 90 years in the treatment of bacterial infections in humans. However, there are many types of phages that are still undiscovered and researched. Discovering and annotating new phages will expand the scientific knowledge of bacteriophage and contribute to new infection treatments. In this project, the unique phage Corazon was investigated. This phage was discovered in Easton, PA …

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Corazon Genome Annotation Project, Eung Baek Kim, Eunhui Yoo, Mai Liu, Chao Fu, Yejin Jang Jul 2019

Corazon Genome Annotation Project, Eung Baek Kim, Eunhui Yoo, Mai Liu, Chao Fu, Yejin Jang

Purdue Undergraduate Research Conference

Corazon Genome Annotation Project Mycobacterium phage, Corazon, was found at Lafayette College in Easton, Pennsylvania in 2017. Its plaque was small, round and clear with siphoviridae morphology type. The approximate length of Corazon is 64931 bp with 3’ sticky overhang. The overhang had 11 base length with ‘GCGCGCAGCGC’ sequence. To perform a manual inspection of Corazon, we performed gene annotation by reviewing and revising the prediction and identifying any missing genes using DNA Annotation programs such as DNA Master, GeneMark, BLAST, Phamerator, and HHPred. We annotated the Corazon genome in three distinct steps. First, we established a relationship with our …

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Highly Efficient Selection System For Directed Evolution Of Novel Endonuclease, Paula Pandolfi Jul 2019

Highly Efficient Selection System For Directed Evolution Of Novel Endonuclease, Paula Pandolfi

Purdue Undergraduate Research Conference

Genome editing optimizes traits of interest by introducing specific changes to the genome of organisms. A novel genome editing tool, ASGARD, was developed in our laboratory as a more flexible tool for editing genomes without a binding site requirement, in contrast to the currently popular CRISPR systems (clustered regularly interspaced short palindromic repeats). Despite ASGARD’s attractive characteristics, it suffers from low efficiency and off-target activity. We aim to mutate ASGARD and design a screening system that selects for mutants that display highly efficient DNA cleavage activity with minimal off-target effects. As current methods fail to fulfill our needs, we created …

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Likelihood Of Soil Health Management Systems Users To Adopt Other Conservation Practices In The Big Pine Creek Watershed, Emma Wade Jul 2019

Likelihood Of Soil Health Management Systems Users To Adopt Other Conservation Practices In The Big Pine Creek Watershed, Emma Wade

Purdue Undergraduate Research Conference

Since the 1970s, the hypoxic zone in the Gulf of Mexico has been growing due to fertilizer runoff and soil degradation. The hypoxic zone negatively impacts the productivity of aquatic ecosystems and threatens industries that rely on coastal areas. Soil Health Management Systems (SHMS) include farming practices that reduce nutrient runoff and downstream pollution. Farming practices impact downstream waterways, so it is important to understand what influences the adoption of conservation practices such as SHMS. A survey was developed to collect farmland owner/operator demographic information and to determine whether they adopt conservation practices. Five conservation practices were evaluated: SHMS, nutrient …

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Synthesis And Validation Of Acetyl- And Malonyl-Coa Analogs For The Study Of Substrate Specificity And Mechanism Of Acyltransferases, Jianheng Ling Jul 2019

Synthesis And Validation Of Acetyl- And Malonyl-Coa Analogs For The Study Of Substrate Specificity And Mechanism Of Acyltransferases, Jianheng Ling

Purdue Undergraduate Research Conference

Acyltransferases (AT) are seen in a wide variety of metabolic functions. These include enzymes in polyketide synthase pathways (PKSs), fatty acid biosynthesis, energy production, and secondary metabolism. The products from these enzymes often include pharmaceutically important natural products. ATs can transfer a variety of metabolites, such as acetyl, malonyl, succinyl, and larger chain fatty acyl groups using Coenzyme A (CoA). The reactivity of the thioester sulfur allows for transfer of these metabolites to secondary metabolites or enzymes. One such example of an AT is type III chloramphenicol acetyltransferase (CATIII) from E. coli. CATIII attaches the acetyl moiety of acetyl-CoA to …

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An Investigation Of A Cluster S Mycobacteriophage Genome, Corazon, Genes 4-16: Location And Function, Marina Mehling, Eli Cline, Remington Wilson, Mckenna Pineau Jul 2019

An Investigation Of A Cluster S Mycobacteriophage Genome, Corazon, Genes 4-16: Location And Function, Marina Mehling, Eli Cline, Remington Wilson, Mckenna Pineau

Purdue Undergraduate Research Conference

Mycobacteriophages are a type of virus particle that specifically attack mycobacteria. This attribute can be exploited to fight antibiotic resistance mycobacteria. As of February 2019, only 14 Cluster S types (a specific group of mycobacteriophage) have been completely sequenced and published in the Actinobacteriophage Database. The purpose of this investigation is to establish the presence, location, and function of genes within the genome of a novel bacteriophage, Corazon and add to this database. Corazon, isolated from a soil sample collected in Lafayette, Indiana, is a member of Cluster S and belongs to the Siphoviridae morphotype. It has 109 genes and …

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The Effects Of Environmental Copper Exposure On Developing Zebrafish, Christina Kaucic Jul 2019

The Effects Of Environmental Copper Exposure On Developing Zebrafish, Christina Kaucic

Purdue Undergraduate Research Conference

Copper is an essential metal that is key in many metabolic functions and is a vital cofactor in many enzymes. Copper homeostasis is dually important for optimal health. Excess copper has been associated with minor symptoms such as fatigue, weakness, and memory loss as well as with neurological disorders such as Wilson’s disease, Alzheimer’s disease and some cancers in humans. Similarly, excess copper has been shown to damage visceral organs and produce abnormal behaviors in multiple fish species including the zebrafish who has a high degree of genome sequence homology when compared to humans. For this reason, the zebrafish is …

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Uncovering The True Diversity Of Chanterelle Mushrooms In Indiana, Jairus Chittenden Jul 2019

Uncovering The True Diversity Of Chanterelle Mushrooms In Indiana, Jairus Chittenden

Purdue Undergraduate Research Conference

Chanterelles are some of the most popular wild mushrooms in Indiana and throughout the Midwest. These attractive orange and yellow fungi are a natural delicacy, and the global trade in chanterelles exceeds $1 billion per year. Like so many other clades of fungi, only a fraction of the chanterelles’ true diversity in North America is known to science. Given their economic and ecological value, I believe that chanterelles deserve a phylogenetic analysis using the full capabilities of modern DNA sequencing technology. This project will determine how many species of chanterelles there are within Indiana and how they are related to …

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