Life Sciences Commons^™

Unseen Science: Modern Discoveries Too Far Away Or Tiny For Human Eyes, Lucy Huang

Capstones

As science has progressed, scientists have realized that evidence goes beyond the realms of physical sight. Whether it is too small or difficult to find, scientists have developed different ways to get around this problem. We see this in cancer genomics and in extrasolar planetary research. Scientists use what they know and what they measure to validate their work.

https://lucy-huang-9tge.squarespace.com/

Transcription Activator Like Effector Nucleases (Talens): A New, Important, And Versatile Gene Editing Technique With A Growing Literature, Philip Barnett

Publications and Research

Transcription activator like effector nucleases (TALENs) is a new and powerful technique in genetic engineering that can delete deleterious genes or add beneficial genes to organisms. It is being widely studied to improve crops and livestock, and is also being investigated clinically. Comparing the details of how both TALENs and its competitor, CRISPR-Cas9, function, reveals the potential advantages of TALENs. The growing literature, besides covering the scientific and technical aspects of TALENs, also includes pertinent information on regulatory aspects and the public’s perception and acceptance of TALENs.

Genetic Diversity Of Kemp's Ridley (Lepidochelys Kempii) Sea Turtles On South Padre Island, Texas, Hilary R. Frandsen

Theses and Dissertations

In 2010, researchers observed an abrupt decline in nesting numbers of the Kemp’s ridley following 35 years of positive growth. In wake of this halt, and subsequent lowered nesting averages, evaluation of the genetic diversity of remaining individuals is relevant to investigate the plausibility of a genetic bottleneck, and determine the reproductive stability of the Kemp’s ridley.

Here, I evaluate the genetic diversity within a sampling of the Kemp’s ridleys on South Padre Island using two methods: targeting the mitochondrial control region and targeting the complete mitochondrial genome. Opportunistic samples were donated from juvenile ridleys on the East coast, and …

Glutamylation Regulates Transport, Specializes Function, And Sculpts The Structure Of Cilia, Robert O'Hagan, Malan Silva, Ken Cq Nguyen, Winnie Zhang, Sebastian Bellotti, Yasmin Ramadan, David Hall, Maureen M. Barr

Department of Biology Faculty Scholarship and Creative Works

Ciliary microtubules (MTs) are extensively decorated with post-translational modifications (PTMs), such as glutamylation of tubulin tails. PTMs and tubulin isotype diversity act as a “Tubulin Code” that regulates cytoskeletal stability and the activity of MT-associated proteins such as kinesins. We previously showed that, in C. elegans cilia, the deglutamylase CCPP-1 affects ciliary ultrastructure, localization of the TRP channel PKD-2 and the kinesin-3 KLP-6, and velocity of kinesin-2 OSM-3/KIF17, while a cell-specific α-tubulin isotype regulates ciliary ultrastructure, intraflagellar transport, and ciliary functions of extracellular vesicle (EV)-releasing neurons. Here, we examine the role of PTMs and the Tubulin Code in the cililary …

Uncovering Tasselsheath3. A Genomic And Phenotypic Analysis Of A Maize Floral Mutant., Thompson Zhang

Masters Theses

In the modern era, maize has become the most successful crop grown in the United States. According to the USDA over 90 million acres of land are planted to corn and 96.2% of the U.S feed grain production is made up of the cereal. Part of the success of maize is due to its floral architecture, and its pollination technique in which the flower opens, exposing stamens containing pollen into the air. A unique organ called the lodicule functions as a release mechanism, forcing the flower to open. Lodicules from grasses and eudicot petals are homologous, yet there is little …

Dorsal And Ventral Color Patterns In A South Georgia Population Of Agkistrodon Piscivorus Contanti, The Florida Cottonmouth, David L. Bechler, Joseph A. Kirkley Mr., John F. Elder

Georgia Journal of Science

We examined dorsal pigments and ventral patterns in the Florida Cottonmouth, Agkistrodon piscivorus conanti, in the Alapahoochee watershed, Lowndes County, Georgia. Cottonmouths darken as they age; but the process has not been quantified in the literature. Thus, we examined both graphically and statistically changes in dorsal color pattern that occurs when snout vent length (SVL) increases as well as discrete patterns involving splotching and block-like patterns, and cream to white coloration on the ventral surface, which indicate underlying genetic factors. Snakes with SVLs between approximately 26.8 and 120.3 cm possessed an array of dorsal colors involving white, tan, dark …

Assessment Of A Metaviromic Dataset Generated From Nearshore Lake Michigan, Siobhan C. Watkins, Neil Kuehnle, C Anthony Ruggeri, Kema Malki, Katherine Bruder, Jinan Elayyan, Kristina Damisch, Naushin Vahora, Paul O'Malley, Brianne Ruggles-Sage, Zachary Romer, Catherine Putonti

Catherine Putonti

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse …

Pleiotropy Of Genetic Variants On Obesity And Smoking Phenotypes: Results From The Oncoarray Project Of The International Lung Cancer Consortium, Tao Wang, Jee-Young Moon, Yiqun Wu, Christopher I. Amos, Rayjean J. Hung, Adonina Tardon, Angeline Andrew, Chu Chen, David C. Christiani, Demetrios Albanes, Erik H. F. M. Van Der Heijden, Eric Duell, Gadi Rennert, Gary Goodman, Geoffrey Liu, James D. Mckay, Jian-Min Yuan, John K. Field, Jonas Manjer, Kjell Grankvist, Lambertus A. Kiemeney, Loic Le Marchand, M. Dawn Teare, Matthew B. Schabath, Mattias Johansson, Melinda C. Aldrich, Michael Davies, Mikael Johansson, Ming-Sound Tsao, Neil Caporaso, Susanne Arnold

Internal Medicine Faculty Publications

Obesity and cigarette smoking are correlated through complex relationships. Common genetic causes may contribute to these correlations. In this study, we selected 241 loci potentially associated with body mass index (BMI) based on the Genetic Investigation of ANthropometric Traits (GIANT) consortium data and calculated a BMI genetic risk score (BMI-GRS) for 17,037 individuals of European descent from the Oncoarray Project of the International Lung Cancer Consortium (ILCCO). Smokers had a significantly higher BMI-GRS than never-smokers (p = 0.016 and 0.010 before and after adjustment for BMI, respectively). The BMI-GRS was also positively correlated with pack-years of smoking (p < 0.001) in smokers. Based on causal network inference analyses, seven and five of 241 SNPs were classified to pleiotropic models for BMI/smoking status and BMI/pack-years, respectively. Among them, three and four SNPs associated with smoking status and pack-years (p < 0.05), respectively, were followed up in the ever-smoking data of the Tobacco, Alcohol and Genetics (TAG) consortium. Among these seven candidate SNPs, one SNP (rs11030104, BDNF) …

Reevaluating The Occurrence And Phylogeny Of The Pigtoe Unionid Mussels Fusconaia Askewi, Fusconaia Lananensis, Fusconaia Flava, And Pleurobema Riddelli In Texas, Charles J. Pratt

Biology Theses

The recent development of DNA-based species classification methods has led to the revision of many morphology-based species designations as genetic data has provided new information for species delineation. Analysis of standardized DNA ‘barcoding’ gene regions has proven particularly effective in resolving the taxonomic status of taxa that display phenotypic and habitat overlap.

Freshwater Unionid and Margaritiferid mussels comprise one of the most diverse aquatic taxa in North America, but are also among the most threatened, with over 70% of the approximately 300 native species considered at-risk or in decline. Although mussels face extensive threats from anthropogenic activity, conservation efforts have …

Does Baylisascaris Procyonis Phylogeny Correlate With That Of The Raccoon (Procyon Lotor), Matthew E. Ingle, Stephen G. Dunbar, Jaynee L. Bartsch, Kyle J. Culbertson, Taylor A. Fulton, Katherine R. Guffey, Aubrey J. Juris, Ashlie N. Nolan, Daniel P. Nordquist, Carrie E. Rowlands, Joshua A. Sitler

Stephen Dunbar, PhD

Baylisacaris procyonis, commonly known as the raccoon roundworm, is a parasite that inhabits the small intestine of the North American raccoon (Procyon lotor). Although humans do not typically become the definitive host, humans can become infected through handling soil containing eggs. B. procyonis can induce serious health complications in cases of human infection, including degenerative retinal and behavioral changes, coma, and even death. High prevalence of B. procyonis in a raccoon population increases the probability of transference to human hosts. In our study, we analyzed the genetic structure of B. procyonis harvested from raccoons of southwestern Ohio, and compared this …

Does Baylisascaris Procyonis Impact Raccoon (Procyon Lotor) Genetics?, Matthew E. Ingle, Stephen G. Dunbar, Jaynee L. Bartsch, Kyle J. Culbertson, Taylor A. Fulton, Katherine R. Guffey, Aubrey J. Juris, Ashlie N. Nolan, Daniel P. Nordquist, Carrie E. Rowlands, Joshua A. Sitler

Stephen Dunbar, PhD

Raccoons (Procyon lotor) are the final host for raccoon roundworms (Baylisascaris procyonis). Raccoon roundworm is the leading cause of a dangerous neurological disease, known as larva migrans encephalopathy. Phylogenetic trees illustrate co-evolutionary events between species living in a symbiotic relationship with each other. Throughout the coevolution of host and parasite, many aspects of a population affect the way the members interact with one another and with symbiotic species. In order to evaluate the relationship between host and parasite in regards to diet, we isolated DNA from intestinal wall tissue, amplified a portion of exon 2 from MHC II, and sent …

Establishing A Lung Model For Evaluation Of Engineered Lung Microbiome Therapies, Kathryn F. Atherton, Stephen Miloro, Jenna Rickus

The Summer Undergraduate Research Fellowship (SURF) Symposium

Benzene, a toxin and carcinogen found in air polluted by cigarette smoke, car exhaust, and industrial processes, is associated with the development of leukemia and lymphoma. Other than avoiding exposure, there is no current method to deter the effects of benzene. One potential strategy to prevent these effects is to engineer the bacteria of the human lung microbiome to degrade benzene. To evaluate this novel approach, we must verify that the bacteria remain viable within the lung microenvironment. To do so, lungs were harvested from rats and swabbed to determine the contents of the original lung microbiome. Then green fluorescent …

Impact Of Home Visit Capacity On Genetic Association Studies Of Late-Onset Alzheimer's Disease, David W. Fardo, Laura E. Gibbons, Shubhabrata Mukherjee, M. Maria Glymour, Wayne Mccormick, Susan M. Mccurry, James D. Bowen, Eric B. Larson, Paul K. Crane

Biostatistics Faculty Publications

INTRODUCTION—Findings for genetic correlates of late-onset Alzheimer's disease (LOAD) in studies that rely solely on clinic visits may differ from those with capacity to follow participants unable to attend clinic visits.

METHODS—We evaluated previously identified LOAD-risk single nucleotide variants in the prospective Adult Changes in Thought study, comparing hazard ratios (HRs) estimated using the full data set of both in-home and clinic visits (n = 1697) to HRs estimated using only data that were obtained from clinic visits (n = 1308). Models were adjusted for age, sex, principal components to account for ancestry, and additional health indicators.

RESULTS …

Clinical And Experimental Studies Of A Novel P525r Fus Mutation In Amyotrophic Lateral Sclerosis, Lisha Kuang, Marisa Kamelgarn, Alexandra Arenas, Jozsef Gal, Deborah Taylor, Weiming Gong, Martin Brown, Daret St. Clair, Edward J. Kasarskis, Haining Zhu

Molecular and Cellular Biochemistry Faculty Publications

Objective: To describe the clinical features of a novel fused in sarcoma (FUS) mutation in a young adult female amyotrophic lateral sclerosis (ALS) patient with rapid progression of weakness and to experimentally validate the consequences of the P525R mutation in cellular neuronal models.

Methods: We conducted sequencing of genomic DNA from the index patient and her family members. Immunocytochemistry was performed in various cellular models to determine whether the newly identified P525R mutant FUS protein accumulated in cytoplasmic inclusions. Clinical features of the index patient were compared with 19 other patients with ALS carrying the P525L mutation in the same …

Genome Wide Association And Next Generation Sequencing Approaches To Map Determinants Of Ascites In Broiler Chickens, Shatovisha Dey

Graduate Theses and Dissertations

These studies have investigated different candidate genomic regions for their contributions to ascites in broilers. Ascites syndrome is a manifestation of idiopathic pulmonary arteriole hypertension that concerns the poultry industry worldwide. Investigations have demonstrated the disease to be genetically regulated and to exhibit moderate to high heritabilities. Although previous studies have indicated a few chromosomes to be involved with ascites, no genes have been identified to date with direct links to the disease. This dissertation presents a collection of studies that determine the genomic and genetic interactions for regions on chromosome 2 and 9 for ascites phenotypes in broiler chickens. …

Consequences Of Severe Habitat Fragmentation On Density, Genetics, And Spatial Capture-Recapture Analysis Of A Small Bear Population, Sean Mccarthy Murphy, Ben C. Augustine, Wade Allen Ulrey, Joseph Maddox Guthrie, Brian K Scheick, J. Walter Mccown, John J. Cox

Forestry and Natural Resources Faculty Publications

Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agriculture expansion relegated the Highlands-Glades subpopulation (HGS) of Florida, USA, black bears (Ursus americanus floridanus) to prolonged isolation; increasing human land development is projected to cause ≥ 50% loss of remaining natural habitats occupied by the HGS in coming decades. We conducted a noninvasive genetic spatial capture-recapture study to quantitatively describe the …

Alzheimer's Disease Genetics And Abca7 Splicing, Jared B. Vasquez, James F. Simpson, Ryan Harpole, Steven Estus

Physiology Faculty Publications

Both common and rare polymorphisms within ABCA7 have been associated with Alzheimer’s disease (AD). In particular, the rare AD associated polymorphism rs200538373 was associated with altered ABCA7 exon 41 splicing and an AD risk odds ratio of ∼1.9. To probe the role of this polymorphism in ABCA7 splicing, we used minigene studies and qPCR of human brain RNA. We report aberrant ABCA7 exon 41 splicing in the brain of a carrier of the rs200538373 minor C allele. Moreover, minigene studies show that rs200538373 acts as a robust functional variant in vitro. Lastly, although the ABCA7 isoform with an extended …

Analysis Of Population Structure In A California Newt (Taricha Torosa) Metapopulation, Jessica Vincent

Mahurin Honors College Capstone Experience/Thesis Projects

As anthropogenic influences take an ever-increasing toll on the environment, understanding how environmental change affects species is paramount. Concern regarding decline in amphibian populations has spurred research examining the effects of habitat change on the dynamics of populations at landscape levels. One important goal is to understand how gene flow among populations is affected by changes in habitat. Biologists need to consider the relationship between gene flow and habitat alterations so that movements among individual breeding ponds can be maintained over time, reducing risk of local extinction events. This study focuses on patterns of gene flow among thirteen populations of …

Genetic Diversity Of Mycobacteriophages And The Unique Abilities Of Cluster K, Shea A. Morris

The Corinthian

Mycobacteriophage are a diverse set of viruses that infect a broad host range of mycobacterium. Genome analysis of this phage group reveals its diversity and provides evidence that they have experienced substantial horizontal gene transfer Collectively they have a large range of host bacteria they can infect, although each viral type may have a limited host range. However, this range is easily expanded and constantly changing in nature by mutation within and between virus types. These phages can lytically destroy their host mycobacteria, and it is this viral ability that have many mycobacteriophage researchers excited about the potential that phage …

Spokony Is A Hands-On Researcher, Teacher Of Genetics., Aldemaro Romero Jr.

Publications and Research

“When I was very little, my parents always took

us to the American Museum of Natural History,

the Bronx Zoo, and then even just watching on TV

we would pick the shows that were about science.”

That is how Dr. Rebecca Spokony traces back her

interest in science.

A native of Brooklyn Heights, New York City,

she remembers how when her mother was an

undergraduate, she worked on fruit flies. “Even

though she did not go on to work on science after

she graduated from college, it still was important

to her, and she shared that with me, and I …

Crispr-Cas9 Nuclear Dynamics And Target Recognition In Living Cells, Hanhui Ma, Li-Chun Tu, Ardalan Naseri, Maximiliaan Huisman, Shaojie Zhang, David Grünwald, Thoru Pederson

David Grünwald

The bacterial CRISPR-Cas9 system has been repurposed for genome engineering, transcription modulation, and chromosome imaging in eukaryotic cells. However, the nuclear dynamics of clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) guide RNAs and target interrogation are not well defined in living cells. Here, we deployed a dual-color CRISPR system to directly measure the stability of both Cas9 and guide RNA. We found that Cas9 is essential for guide RNA stability and that the nuclear Cas9-guide RNA complex levels limit the targeting efficiency. Fluorescence recovery after photobleaching measurements revealed that single mismatches in the guide RNA seed sequence …

Isolation And Comparative Genomic Analysis Of Final Third Of Satis Genome, Kelly Hartigan, Nicole Curnutt, Matthew Mcdermut

Undergraduate Research Symposium Posters

A highly novel Streptomyces phage, Satis, was isolated from a direct environmental sample collected from outside Danforth House on the Washington University campus. Satis infects bacterial species Streptomyces lividans producing pinpoint, cloudy plaques less than 1mm in diameter. Electron microscope data shows rare atypical physical features. Rather than the common octahedral capsid shape, Satis has a prolate head with visible cross-linked hexagonal protein structure and average measurements of 285 nm by 47 nm with a long, flexible tail measuring 268 nm. Upon sequencing, it was found that Satis contains the longest phage genome discovered to date through the SEA-PHAGE program …

Software Development For Genome Sequence Analysis, David Farr

Symposium Of University Research and Creative Expression (SOURCE)

The cost of genome sequencing has decreased rapidly, expanding availability for many biological applications (Muir 2016). For example, researchers can now obtain genome sequences from multiple populations under different types of selection. Comparison of these sequences allows for identification of chromosome regions and specific genes associated with adaptive evolution (Kelly 2013). As an increasing number of researchers engage in this type of inquiry, many have created in-house computer scripts to analyze the raw sequence data (e.g., Kelly 2013), creating a gap in both continuity and standardization.

Using a test dataset and preliminary results from an ongoing artificial selection experiment in …

Effective Population Size, Demography, And Viability Of Eastern Massasaugas (Sistrurus Catenatus) In Southwest Michigan, Danielle R. Bradke

Masters Theses

As humans increasingly exploit natural areas, wildlife populations face a growing number of threats that often result in population decline and isolation. Small, isolated populations are vulnerable to extirpation due to both genetic and demographic factors. Yet, low detectability of many imperiled species often precludes the collection of population-level data important for assessing population viability and implementing successful conservation. The eastern massasauga (Sistrurus catenatus) is a cryptic pitviper that has been extirpated throughout much of its historic range due to agricultural conversion of wetland habitat and other synergistic threats. Consequently, this species is federally listed as threatened in both the …

Does Genotype Correlate With Phenotype? Evaluating Ruffed Lemur (Varecia Spp.) Color Vision Using Subject Mediated Automatic Remote Testing Apparatus (Smarta), Raymond Vagell

Theses and Dissertations

Ruffed lemur (Varecia spp.) color vision research was conducted using a multidisciplinary approach: psychophysics, genetic analysis, technology, and animal training. The behavioral manifestation of Varecia spp. trichromacy was shown using a touchscreen apparatus (SMARTA). Trichromats performed better than dichromats when discriminating red from green (G₂ = 78.10, p < 0.001).

Investigating The Genetic Basis For Hominoid Taillessness, Samantha M. Tickey-Mccrane, Holly Dunsworth, Johanna E. Wegener

Senior Honors Projects

Investigating the Genetic Basis for Hominoid Taillessness:

A Comparative Genetic Approach Across Ten Catarrhine Taxa

Samantha Tickey-McCrane1,2, Johanna E. Wegener2, and Holly Dunsworth1

Honors Thesis Abstract Written by Samantha Tickey-McCrane, Departments of Anthropology & Biology

Advisor: Dr. Holly Dunsworth, Department of Anthropology

How did hominoid tail loss occur? My goals are to test phylogenetic and adaptive hypotheses for tail length variation among macaques, and use those insights to reconstruct the evolution of hominoid taillessness. Further, I aim to ultimately uncover which candidate genes or pathways may be responsible for catarrhine tail loss, and what other traits may be affected by …

Genetic Polymorphisms Of The Glucocorticoid Receptor And Interleukin-8 Receptor Genes Are Related To Production Traits And Hair Coat Score In Crossbred Cattle, Avery Deaton

Animal Science Undergraduate Honors Theses

The objective of this thesis was to identify polymorphisms in the glucocorticoid receptor (GR) and interleukin-8 receptor (CXCR2) genes and to associate genotypes between the above mentioned polymorphisms and production traits in crossbred cattle. The hypothesis was that polymorphisms will exist for GR and CXCR2 genes and will be linked to production traits. Glucocorticoid receptors have been positively associated with higher milk yields, lactose content, feed intake, and feed conversion rates. Interleukin-8 genes are part of the innate immune response and help with many aspects of female reproduction health, such as protecting the embryo from the maternal immune system during …

Cost Benefit Analysis Of Genetic Markers In Cattle, Josh Crystal

Agricultural Economics and Agribusiness Undergraduate Honors Theses

Genetic sequencing in beef cattle (L. Bos Taurus) is expected to aid producers select cattle with traits that enhance profitability. Using data from experimental trials conducted with Angus, Brahman, and their reciprocal cross, this project analyzes the profitability of grazing endophyte infected tall Fescue (L. Festuca arundinacea Schreb.) vs. Bermuda grass (L. Cynodon dactylon) pasture. The study is unique in the sense that actual cow-calf breeding failure rates (open cows were not culled) were tracked from 1991 to 1997 on herds that were bred to calf in spring and either exposed to fungal endophyte (L.Acremonium coenophialum Morgan-Jones …

Hybridization Dynamics Of A Newly Discovered Parrotfish Swarm In The Tropical Eastern Pacific, Robert Barron

Honors Projects

Hybrid zones and their dynamics are important in the understanding of the genetic basis of reproductive isolation and speciation. This study seeks to investigate the hybridization dynamics of a Scarus hybrid swarm within the Tropical Eastern Pacific (TEP) that includes four phenotypically distinct species: S. perrico, S. ghobban, S. rubroviolaceus, and S. compressus. Genetic and population structure analyses of four nuclear loci and a mitochondrial locus revealed that one of the four species, S. compressus, was the result of two different hybrid crosses: S. perrico ✕ S. rubroviolaceus and S. perrico ✕ S. ghobban. A …

Attitudes Of Clinicians Towards Cardiac Surgery And Trisomy 18, Meagan Kaulfus

Dissertations & Theses (Open Access)

Trisomy 18 is an autosomal trisomy characterized by minor to major birth defects, severe disabilities, and high rates of pre- and neonatal mortality. Interventions for these infants have traditionally been withheld with focus instead on palliative support. The issues and attitudes surrounding surgical treatment of congenital heart defects, which occur in approximately 90% of infants with trisomy 18, is of our study’s interest as recent literature has indicated that cardiac surgery is being performed and may lead to improved survival compared to palliative care. In this study, the attitudes of clinicians of multiple specialties towards cardiac surgery for infants with …