Integrative Biology Commons^™

Nasp: An Accurate, Rapid Method For The Identification Of Snps In Wgs Datasets That Supports Flexible Input And Output Formats, Jason Sahl, Darrin Lemmer, Jason Travis, James Schupp, John Gillece, Maliha Aziz, +Several Additional Authors

Environmental and Occupational Health Faculty Publications

Whole-genome sequencing (WGS) of bacterial isolates has become standard practice in many laboratories. Applications for WGS analysis include phylogeography and molecular epidemiology, using single nucleotide polymorphisms (SNPs) as the unit of evolution. NASP was developed as a reproducible method that scales well with the hundreds to thousands of WGS data typically used in comparative genomics applications. In this study, we demonstrate how NASP compares with other tools in the analysis of two real bacterial genomics datasets and one simulated dataset. Our results demonstrate that NASP produces similar, and often better, results in comparison with other pipelines, but is much more …

Do Novel Weapons That Degrade Mycorrhizal Mutualisms Explain Invasive Species Success?, Philip L. Pinzone Mr.

Biology Theses

Invasive plants often dominate novel habitats where they did not co-evolve with local species. Several hypotheses suggest mechanisms that explain increased exotic plant success, including 'novel weapons' and 'degraded mutualisms'. Japanese knotweed (Fallopia japonica) and European buckthorn (Rhamnus cathartica) are widespread plant invaders in North America that can dominate ecosystems. The goal of this study is to test whether these impacts are more consistent with novel weapons or degraded mutualism hypotheses. I examine tree seedling recruitment, (germination and initial survival) growth, (biomass) and mycorrhizal invasion (AMF content) as a function of F. japonica and R. cathartica …

Venom Peptides Lasioglossin Ii And Mastoparan B As Escherichia Coli Atp Synthase Inhibitors, Rafiat Ajoke Bello

Electronic Theses and Dissertations

The inhibitory effects on Escherichia coli ATPase activity by two venom peptides, lasioglossin II and mastoparan B. Membrane bound F₁F_O ATP synthase was isolated from E. coli strain pBWU13.4/DK8 and treated with varied concentrations of lasioglossin II and mastoparan B. Lasioglossin II caused very low inhibition of ATPase activity, but the inhibition profile of mastoparan B was suggestive of an interesting biological effect. A relatively shorter total length, a smaller net positive charge, and a reduced amphipathic character of both peptides, as compared to previously tested antimicrobial peptides, may account for the limited degree of inhibition observed …

The Effects Of 4-Nonylphenol On The Immune Response Of The Pacific Oyster, Crassostrea Gigas, Following Bacterial Infection (Vibrio Campbellii), Courtney Hart

Master's Theses

Endocrine disrupting chemicals (EDCs) are compounds that can interfere with hormone signaling pathways and are now recognized as pervasive in estuarine and marine waters. One prevalent EDC in California’s coastal waters is the xenoestrogen 4-nonylphenol (4-NP), which has been shown to impair reproduction, development, growth, and in some cases immune function of marine invertebrates. To further investigate effects of 4-NP on marine invertebrate immune function we measured total hemocyte counts (THC), relative transcript abundance of immune-relevant genes, and lysozyme activity in Pacific oysters (Crassostrea gigas) following bacterial infection. To quantify these effects we exposed oysters to dissolved phase …

The Effects Of Δ9-Tetrahydrocannabinol (Thc) On Development And Hyperekplexia In Embryonic Zebrafish Model, Olivia Christine Mistretta

Master of Science in Integrative Biology Theses

Marijuana is one of the most commonly used illicit drugs around the world. It has gained attention as an alternative medicine to many different disorders. Though initially investigated in modern medicine for its analgesic and antiemetic properties, cannabis has been recently found to benefit numerous neurological disorders. Though there are over 100 different cannabinoids produced by the cannabis plant, Δ⁹ – tetrahydrocannabinol (THC) has been shown to the most efficacious phytocannabinoid in neurological disorders. THC has been shown in numerous previous studies to be effective at treating spasticity caused by multiple sclerosis and spinal cord injury, as well as …

Opn-A Induces Muscle Inflammation By Increasing Recruitment And Activation Of Pro-Inflammatory Macrophages., Gina M Many, Yasuyuki Yokosaki, Kitipong Uaesoontrachoon, Peter P Nghiem, Luca Bello, Sherry Dadgar, Ying Yin, Jesse M Damsker, Heather B Cohen, Joe N Kornegay, Marcas M Bamman, David M Mosser, Kanneboyina Nagaraju, Eric P Hoffman

Genomics and Precision Medicine Faculty Publications

New Findings

• What is the central question of this study? What is the functional relevance of OPN isoform expression in muscle pathology?
• What is the main finding and its importance? The full‐length human OPN‐a isoform is the most pro‐inflammatory isoform in the muscle microenvironment, acting on macrophages and myoblasts in an RGD‐integrin‐dependent manner. OPN‐a upregulates expression of tenascin‐C (TNC), a known Toll‐like receptor 4 (TLR4) agonist. Blocking TLR4 signalling inhibits the pro‐inflammatory effects of OPN‐a, suggesting that a potential mechanism of OPN action is by promoting TNC–TLR4 signalling.

Although osteopontin (OPN) is an important mediator of muscle remodelling in health …

Comparisons Of The Socio-Behavioral Differences Between Chimpanzees (Pan Troglodytes) And Bonobos (Pan Paniscus), Investigating The Impact Of A Naturally Occurring Polymorphic Microsatellite Deletion In The 5’ Flanking Region Of Arginine Vasopressin Receptor 1a (Avpr1a) On Gene Expression And Sociality Within The Pan Genus, Robert E. Evans

Master of Science in Integrative Biology Theses

Among the great apes, chimpanzees are unique in having a polymorphic deletion of a ~350bp microsatellite containing region (DupB) in the 5’ flanking region of the arginine vasopressin receptor 1a (AVPR1a) gene. This results in three genotypes (DupB+/+, DupB+/- and DupB-/-) of AVPR1a in chimpanzees. Variations in the length of microsatellites 5’ of AVPR1a have been associated with social behaviors (pair-bonding, paternal care, degree of social interest) and differential levels of expression of AVPR1a in the brains of voles. The polymorphic DupB microsatellite in chimpanzees allows the investigation of microsatellite variation 5’ of AVPR1a in higher order primates. We hypothesized …

Distances Between Species In Food Webs: Evaluating Alternative Metrics' Predictive Power, Molly C. Johnson

Master of Science in Integrative Biology Theses

The complexity of ecological systems makes it difficult to predict how one species will react to the disturbance of another. Complex systems of species’ interactions can be described as ecological networks. One way in which ecological networks can give information concerning one species’ response to the perturbation of another is through the quantification of species’ proximity to one another in the network. In this study, we evaluate communicability, a topological metric that accounts for all of the direct and indirect interactions between species in a food web without additional information concerning the strengths of species interactions. Communicability is then compared …

Induced Phytoextraction Of Lead From Contaminated Soils By Panicum Virgatum, Enhanced With Edta, Citric Acid, Benomyl, Propiconazole And Nitric Oxide, Adrianna E. Beavers

Master of Science in Integrative Biology Theses

Soil lead (Pb) contamination represents a major environmental and public health risk. Conventional Pb remediation methods are typically expensive and risk further environmental damage. Phytoextraction has emerged as an alternative heavy metal remediation method with the potential for reducing both economic cost and negative environmental effects. For this study, North American native switchgrass (Panicum virgatum) was chosen due to its ability to achieve high biomass yields across a variety of climates and environmental conditions. The switchgrass plants in this study were treated with chemical chelates, fungal suppressants, and nitric oxide (NO) donors with the intent of optimizing Pb …

The Effects Of Amphetamine Exposure On Neurodevelopment And Behavior In Early Life Stages Of Danio Rerio, Jennifer D. Bullard

Master of Science in Integrative Biology Theses

Amphetamines are frequently prescribed to young children for attention deficit hyperactivity disorder (ADHD). Due to the recent rise in ADHD diagnoses and the resulting increase in amphetamine intake in children, we investigated how amphetamine exposure impacts the development of stereotyped behaviors and the neural circuit that governs these behaviors. The zebrafish (Danio rerio) was used as our model organism because of the extensively studied developmental milestones these fish provide. Using escape responses as a behavior model, we exposed embryos to three doses of amphetamine (10 μg/ml, 20 μg/ml, and 30 μg/ml) environmentally during the first 48 hours of …

Conservation Genetics And Mark-Recapture Monitoring Of The Rare Pigeon Mountain Salamander (Plethodon Petraeus) Within A Highly Restricted Range, Kate Donlon

Master of Science in Integrative Biology Theses

Globally, amphibian species are experiencing declines at an alarming rate largely due to habitat loss, disease and climate change. Species with limited ranges are at an elevated risk of a significant decline in population numbers and extinction because of the inability to avoid and recover from these impacts. Long-term management plans are critical for conservation of species with small ranges; however, the knowledge required to develop effective plans is absent from the literature for many species. One such species is the Pigeon Mountain Salamander. The distribution of the Pigeon Mountain Salamander, Plethodon petraeus, is restricted to roughly 17 kilometers …

Small Packages, Big Returns: Uncovering The Venom Diversity Of Small Inverebrate Conoidean Snails, J. Gorson, M. Holford

Publications and Research

Venomous organisms used in research were historically chosen based on size and availability. This opportunity-driven strategy created a species bias in which snakes, scorpions, and spiders became the primary subjects of venom research. Increasing technological advancements have enabled interdisciplinary studies using genomics, transcriptomics, and proteomics to expand venom investigation to animals that produce small amounts of venom or lack traditional venom producing organs. One group of non-traditional venomous organisms that have benefitted from the rise of -omic technologies is the Conoideans. The Conoidean superfamily of venomous marine snails includes, the Terebridae, Turridae (s.l), and Conidae. Conoidea venom is used for …

Histological And Molecular Analysis Of A Progressive Diffuse Intrinsic Pontine Glioma And Synchronous Metastatic Lesions: A Case Report., Javad Nazarian, Gary E Mason, Cheng Ying Ho, Eshini Panditharatna, Madhuri Kambhampati, Louis Gilbert Vezina, Roger J. Packer, Eugene I Hwang

Genomics and Precision Medicine Faculty Publications

There is no curative treatment for patients with diffuse intrinsic pontine glioma (DIPG). However, with the recent availability of biopsy and autopsy tissue, new data regarding the biologic behavior of this tumor have emerged, allowing greater molecular characterization and leading to investigations which may result in improved therapeutic options. Treatment strategies must address both primary disease sites as well as any metastatic deposits, which may be variably sensitive to a particular approach.In this case report, we present a patient with DIPG treated with irradiation and serial investigational agents. The clinical, pathological and molecular phenotypes of both the progressive primary tumor …

Home-Field Advantage? Evidence Of Local Adaptation Among Plants, Soil, And Arbuscular Mycorrhizal Fungi Through Meta-Analysis, Megan A. Rúa, Anita Antoninka, Pedro M. Antunes, V Bala Chaudhary, Catherine Gehring, Louis J. Lamit, Bridget J. Piculell, James D. Bever, Cathy Zabinski, James F. Meadow, Marc J. Lajeunesse, Brook G. Milligan, Justine Karst, Jason D. Hoeksema

Integrative Biology Faculty and Staff Publications

BACKGROUND: Local adaptation, the differential success of genotypes in their native versus foreign environment, arises from various evolutionary processes, but the importance of concurrent abiotic and biotic factors as drivers of local adaptation has only recently been investigated. Local adaptation to biotic interactions may be particularly important for plants, as they associate with microbial symbionts that can significantly affect their fitness and may enable rapid evolution. The arbuscular mycorrhizal (AM) symbiosis is ideal for investigations of local adaptation because it is globally widespread among most plant taxa and can significantly affect plant growth and fitness. Using meta-analysis on 1170 studies …

Mapping Morels: Predicting The Locations Of Morchella Species Through Environmental Factors Using The Gis System, Emily M. Stanevicius

Celebration of Learning

Morel mushrooms, Morechella esculenta and M. deliciosa, are known delicacies across the globe, ranging from exquisite dishes in French cuisine to Eastern palates such as Japanese Matsutake. According to literature, true morels diverged as their own genus about 129 million years, again which has led to the development of more than 177 species and have been part of the human diet since their beginning. However, the elusiveness of morels has contributed to the mushrooms infamy for rarity, and has even been known to sell for more than $40 per pound. This project seeks to aid in the search for morels …

The Role Of Daf-19 In Non-Ciliated Neurons: How Is Neural Development Regulated By Different Daf-19 Isoforms?, Zabdiel Ek Vazquez

Lawrence University Honors Projects

A degenerative disease-like phenotype, specifically reduction in synaptic protein levels in adult worms, is correlated with loss-of-function of the only RFX transcription factor gene, daf-19, in C. elegans. This gene encodes four known transcription factor isoforms, two of which are correlated with particular functions. The DAF-19C isoform activates genes responsible for cilia development, while DAF-19M is needed for cilia specification in males. A comparison of the transcriptome of daf-19 null and isogenic wild type adult worms suggests both positive and negative regulation of gene expression is correlated with the presence of DAF-19 proteins. We have assessed DAF-19 regulation …

Current Status Of Marker Genes Of Bacteroides And Related Taxa For Identifying Sewage Pollution In Environmental Waters, Warish Ahmed, Bridie Hughes, Valerie J. Harwood

Integrative Biology Faculty and Staff Publications

Microbial source tracking (MST) endeavors to determine sources of fecal pollution in environmental waters by capitalizing on the association of certain microorganisms with the gastrointestinal tract and feces of specific animal groups. Several decades of research have shown that bacteria belonging to the gut-associated order Bacteroidales, and particularly the genus Bacteroides, tend to co-evolve with the host, and are, therefore, particularly suitable candidates for MST applications. This review summarizes the current research on MST methods that employ genes belonging to Bacteroidales/Bacteroides as tracers or “markers” of sewage pollution, including known advantages and deficiencies of the many polymerase chain …

Rescuing Perishable Neuroanatomical Information From A Threatened Biodiversity Hotspot: Remote Field Methods For Brain Tissue Preservation Validated By Cytoarchitectonic Analysis, Immunohistochemistry, And X-Ray Microcomputed Tomography, Daniel Hughes, Ellen Walker, Paul Gignac, Anais Martinez, Kenichiro Negishi, Carl Lieb, Eli Greenbaum, Arshad Khan

Selected Works Temporary Series

Biodiversity hotspots, which harbor more endemic species than elsewhere on Earth, areincreasingly threatened. There is a need to accelerate collection efforts in these regionsbefore threatened or endangered species become extinct. The diverse geographical, ecological,genetic, morphological, and behavioral data generated from the on-site collection ofan individual specimen are useful for many scientific purposes. However, traditional methodsfor specimen preparation in the field do not permit researchers to retrieve neuroanatomicaldata, disregarding potentially useful data for increasing our understanding of braindiversity. These data have helped clarify brain evolution, deciphered relationships betweenstructure and function, and revealed constraints and selective pressures that provide contextabout the evolution …

Rescuing Perishable Neuroanatomical Information From A Threatened Biodiversity Hotspot: Remote Field Methods For Brain Tissue Preservation Validated By Cytoarchitectonic Analysis, Immunohistochemistry, And X-Ray Microcomputed Tomography, Hughes, Ellen Walker, Paul Gignac, Anais Martinez, Kenichiro Negishi, Carl Lieb, Eli Greenbaum, Arshad Khan

Departmental Papers (Biology)

Biodiversity hotspots, which harbor more endemic species than elsewhere on Earth, areincreasingly threatened. There is a need to accelerate collection efforts in these regionsbefore threatened or endangered species become extinct. The diverse geographical, ecological,genetic, morphological, and behavioral data generated from the on-site collection ofan individual specimen are useful for many scientific purposes. However, traditional methodsfor specimen preparation in the field do not permit researchers to retrieve neuroanatomicaldata, disregarding potentially useful data for increasing our understanding of braindiversity. These data have helped clarify brain evolution, deciphered relationships betweenstructure and function, and revealed constraints and selective pressures that provide contextabout the evolution …

The Function Of Shoc2: A Scaffold And Beyond, Eun Ryoung Jang, Emilia Galperin

Molecular and Cellular Biochemistry Faculty Publications

The extracellular signal-regulated kinase (ERK1/2) cascade regulates a myriad of functions in multicellular organisms. Scaffold proteins provide critical spatial and temporal control over the specificity of signaling. Shoc2 is a scaffold that accelerates activity of the ERK1/2 pathway. Loss of Shoc2 expression in mice results in embryonic lethality, thus highlighting the essential role of Shoc2 in embryogenesis. In agreement, patients carrying mutated Shoc2 suffer from a wide spectrum of developmental deficiencies. Efforts to understand the mechanisms by which Shoc2 controls ERK1/2 activity revealed the intricate machinery that governs the ability of Shoc2 to transduce signals of the ERK1/2 pathway. Understanding …