Biology Commons^™

Maxent Ecological Niche Models For Alternanthera Philoxeroides, Amynothrips Andersoni, And Agasicles Hygrophila, Samuel A. Schmid, Andrés F. Sánchez-Restrepo, Alejandro J. Sosa, Gray Turnage, Gary N. Ervin

CAS Publications

Alternanthera philoxeroides is an aquatic invasive weed from South America with a long history of biological control. The well-studied Agasicles hygrophila (alligatorweed flea beetle) successfully controls Al. philoxeroides in some parts of its invaded range, but Ag. hygrophila is unsuitable in other areas due to its intolerance to cold temperatures. An understudied biological control agent, Amynothrips andersoni (alligatorweed thrips) has shown greater tolerance to cold temperatures, but no research has been conducted to determine its ecological niche with respect to Al. philoxeroides. Additionally, climate change is predicted to shift the ecological niches of species globally, and these changes must be …

Male Beetle Courtship Dance Analysis By Deeplabcut Technology, Andrea Newbrough

Undergraduate Theses, Professional Papers, and Capstone Artifacts

No abstract provided.

Microbiological Investigation Of Local Native Clays And Samples From The Scripps Ceramic Studio, Kelly Fuller

Scripps Senior Theses

This study explores the relationship between microorganisms and clay using samples currently being utilized in the Lincoln Ceramics Studio at Scripps College. Clay science spans disciplines, from geology and soil science to industrial material development and artistic practices. Although biological processes have been thought to effect clay properties such as plasticity and malleability, the interplay between microorganisms and clay minerals has not been thoroughly investigated in the scientific community. Drawing from diverse disciplines, this research investigates the microbial ecology of clay bodies to unveil potential innovations in ceramics production. In this experiment, colony-forming unit (CFU) assays were performed in both …

Hamstring And Quadriceps Activation During Single Leg Hopping At Varying Frequencies: Electromyography Analysis, Jemma Bosselman

Scripps Senior Theses

Identification of knee motor control strategy is salient both for biomechanical understanding of the lower limb and for medical applications. Integral to knee function are the quadriceps and hamstring, an antagonistic muscle pair. Sub-optimal relative activation of the pair can increase injury potential. Muscle activation patterns are largely activity specific, necessitating muscle control research across various tasks. Single leg hopping has been sparsely studied, particularly for muscle activation in relation to hopping frequency. This project thus aimed to determine the effect of single leg hopping frequency on quadriceps and hamstring activation using surface electromyography (EMG), with the vastus lateralis (VL) …

Complete Genome Sequence Of Microbacterium Foliorum Phage Curie, A Podovirus Isolated From Soil In Spokane, Washington, Emma N. Horton, Kathryn T. Cook, Kyra G. Cronin, Avery T. Haag, Sierra M. Salter, Nicole A. Stojanovic, Zoe E. Fry, Brian M. Connolly, Rebekah F. Hare, Ann-Scott H. Ettinger, Marianne K. Poxleitner, Kirk Anders

Biology Faculty Scholarship

Bacteriophage Curie is a podovirus that infects Microbacterium foliorum. The Curie genome spans 16,810 bp, has 90 bp terminal inverted repeats, and includes 23 protein-coding genes. Its genome architecture resembles phage PineapplePizza and other phi29-like phages. Together, Curie and PineapplePizza form a new actinobacteriophage Cluster GI.

Persistence Of Wastewater-Associated Antibiotic Resistant Bacteria In River Microcosms, Aoife P. Mahaney

Theses and Dissertations

The spread of antibiotic-resistant bacteria (ARB) associated with wastewater is a significant environmental concern, but little is known about the persistence and proliferation of these organisms in receiving water bodies after discharge. To address this knowledge gap, we performed a series of microcosm experiments in which river water was amended with either untreated or treated wastewater, and the abundance of viable ciprofloxacin-, Bactrim-, and erythromycin-resistant bacteria was monitored for 72 hours.

Both types of wastewater amendments increased the initial abundance of ARB compared to microcosms containing only river water. The increase was greatest with untreated wastewater, but that effect decreased …

Assessing The Feasibility Of Seaweed Farm-Offshore Wind Co-Location In New Jersey, Brianna Delaney Reynolds

Theses, Dissertations and Culminating Projects

New Jersey’s offshore wind energy sector may provide an opportunity to advance the seaweed farming industry through ocean multi-use. Yet, opportunities, constraints, and knowledge gaps for seaweed farm-offshore wind co-location remain largely uninvestigated. Here, I determine the suitability of native seaweed species for offshore cultivation in New Jersey and conduct a quick scoping review (QSR) to assess the knowledge base surrounding seaweed farm-offshore wind multi-use. Saccharina latissima and Fucus vesiculosus were identified as native species with commercial value for cultivation in New Jersey. Yet, offshore waters at the location of a wind development site had insufficient nutrients to meet the …

Characterizing The Role Of Temperature On West Nile Virus Evolution And Vector-Virus Interactions, Rachel Lucy Fay

Legacy Theses & Dissertations (2009 - 2024)

West Nile virus (WNV) is the most common mosquito-borne disease in the contiguous U.S. WNV is a member of the Flaviviridae family which is group of single stranded positive sense RNA genome viruses. It is commonly vectored by Culex mosquitoes and is found in a transmission cycle between its amplifying hosts of birds. Incidental hosts of WNV include people and animals. WNV is known to cause flu-like illness and in rare cases can become neuroinvasive. There are currently no approved therapeutics on the market for WNV. Since the beginning of the 20th century the earth’s average temperature has increased by …

Loss Of Courtship Suppression Memory In A Drosophila Melanogaster Model Of Alzheimer’S Disease, Eric Robles, Johannes Berlandi, Chris Ellis, Tianyi Wu, Astrid Jeibmann, Fang-Ju Lin

Biology

Alzheimer’s disease (AD) is the most prevalent and lethal neurodegenerative disease. Memory loss and motor dysfunction are accompanied by pathological hallmarks like neurofibrillary tangles or amyloid plaques. In this study, courtship suppression assay was used to assess learning and memory of a transgenic Drosophila melanogaster (the fruit fly) line expressing human Amyloid beta 42 (Aβ42). At young age (4–6 days old), both parental control and AD flies displayed lower courtship indices during training after being rejected by previously mated females. However, in the subsequent testing phase, young AD flies showed compromised recall memory, unlike that of parental controls. Neither control …

A Tale Of Two Turtles: Sympatry Of Two Lotic Musk Turtle Species In The Pascagoula River Drainage, Grover J. Brown, Brian R. Kreiser

Research, Publications & Creative Work

Competition and hybridization between closely related species have remained topics of interest for decades. The ranges of the Razorback Musk Turtle (Sternotherus carinatus) and Stripe-necked Musk Turtle (Sternotherus peltifer) are mostly non-overlapping, but they are sympatric in south and central Mississippi, USA. In allopatry, each species fills the niche of a lotic, bottom-walking musk turtle and each can range in habitat from small, montane headwater streams to large, muddy bayous in the coastal plain. Using environmental, morphological, and genetic data, we assessed whether the two species exhibit different habitat associations, differ in morphology, and maintain reproductive isolation in sympatry. The …

Combination Of Hdac And Fyn Inhibitors In Synovial Sarcoma Treatment, Kyra Parker, Yanfeng Zhang, Gavin Anchondo, Ashlyn Smith, Sergio Guerrero Pacheco, Tadashi Kondo, Le Su

Research, Publications & Creative Work

The SS18-SSX fusion protein is an oncogenic driver in synovial sarcoma. At the molecular level, SS18-SSX functions as both an activator and a repressor to coordinate transcription of different genes responsible for tumorigenesis. Here, we identify the proto-oncogene FYN as a new SS18-SSX target gene and examine its relation to synovial sarcoma therapy. FYN is a tyrosine kinase that promotes cancer growth, metastasis and therapeutic resistance, but SS18-SSX appears to negatively regulate FYN expression in synovial sarcoma cells. Using both genetic and histone deacetylase inhibitor (HDACi)-based pharmacologic approaches, we show that suppression of SS18-SSX leads to FYN reactivation. In support …

Occupancy Of The Little Grass Frog (Pseudacris Ocularis), An Overlooked Longleaf Endemic, In A Managed Landscape, Anna M. Humphrey

Theses, Dissertations and Capstones

Amphibians are declining globally, with many declines associated with habitat loss. The longleaf pine (Pinus palustris) ecosystem historically covered most of the southeastern United States and supports a host of endemic amphibians. This ecosystem has declined by over 97% in the last two hundred years and many associated species have declined with it. The Little Grass Frog (Pseudacris ocularis) is a longleaf pine endemic anuran that has been understudied and under-surveyed; almost no information is known on the ecology of this species and no population studies have been conducted. My goals were to create an acoustic …

9s1r Nullomer Peptide Induces Mitochondrial Pathology, Metabolic Suppression, And Enhanced Immune Cell Infiltration, In Triple-Negative Breast Cancer Mouse Model, Nilufar Ali, Cody Wolf, Swarna Kanchan, Shivakumar R. Veerabhadraiah, Laura Bond, Matthew W. Turner, Cheryl L. Jorcyk, Greg Hampikian

Biology Faculty Publications and Presentations

Nullomers are the shortest strings of absent amino acid (aa) sequences in a species or group of species. Primes are those nullomers that have not been detected in the genome of any species. 9S1R is a 5-aa peptide prime sequence attached to 5-arginine aa, used to treat triple negative breast cancer (TNBC) in an in vivo mouse model. This unique peptide, administered with a trehalose carrier (9S1R-NulloPT), offers enhanced solubility and exhibits distinct anti-cancer effects against TNBC. In our study, we investigated the effect of 9S1R-NulloPT on tumor growth, metabolism, metastatic burden, tumor immune-microenvironment (TME), and transcriptome of aggressive mouse …

Applied Soft Classes And Fuzzy Confusion In A Patchwork Semi-Arid Ecosystem: Stitching Together Classification Techniques To Preserve Ecologically-Meaningful Information, Josh Enterkine, T. Trevor Caughlin, Hamid Dashti, Nancy F. Glenn

Biology Faculty Publications and Presentations

Dryland ecosystems have complex vegetation communities, including subtle transitions between communities and heterogeneous coverage of key functional groups. This complexity challenges the capacity of remote sensing to represent land cover in a meaningful way. Many remote sensing methods to map vegetation in drylands simplify fractional cover into a small number of functional groups that may overlook key ecological communities. Here, we investigate a remote sensing process that further advances our understanding of the link between remote sensing and ecologic community types in drylands. We propose a method using k-means clustering to establish soft classes of vegetation cover communities from detailed …

Genomic Surveillance Of Sars-Cov-2 Sequence Variants At Universities In Southwest Idaho, Jennifer R. Chase, Laura Bond, Daniel J. Vail, Milan Sengthep, Adriana Rodriguez, Joe Christianson, Stephanie F. Hudon, Julia Thom Oxford

Biology Faculty Publications and Presentations

Although the impact of the SARS-CoV-2 pandemic on major metropolitan areas is broadly reported and readily available, regions with lower populations and more remote areas in the United States are understudied. The objective of this study is to determine the progression of SARS-CoV-2 sequence variants in a frontier and remote intermountain west state among university-associated communities. This study was conducted at two intermountain west universities from 2020 to 2022. Positive SARS-CoV-2 samples were confirmed by quantitative real-time reverse transcription-polymerase chain reaction and variants were identified by the next-generation sequencing of viral genomes. Positive results were obtained for 5355 samples, representing …

An Aggregation Of The Pandalid Shrimp, Heterocarpus Ensifer, On Deep Reef Habitats Of The West Florida Slope, Eastern Gulf Of Mexico, Steve W. Ross

Gulf and Caribbean Research

Heterocarpus ensifer A. Milne—Edwards (1881) (Crustacea: Pandalidae), armed nylon shrimp, is widely distributed in the western and eastern North Atlantic Ocean. In the western Atlantic this shrimp occurs from off North Carolina to Brazil and in the Gulf of Mexico (GOM), western Bahamas, and Caribbean Sea at depths of 170—885 m. Despite its widespread occurrence, ecology or biology information for this species are sparse, and in situ observations of abundance, behavior and habitat preferences are particularly lacking. During extensive submersible and ROV observations on and near deep—reefs in the north—central and eastern GOM, a remarkably large aggregation of H. ensifer …

Reaching Across The Divide: Tools For Bridging Structural And Viral Genomics Using A Combination Of Biophysical Principles And Machine Learning, Diana Yvette Lee

CGU Theses & Dissertations

Bacteriophages are the most ubiquitous biological entity on the planet, but most viruses found in nature cannot be cultured in the laboratory and encode genes whose sequences lack similarity with current nucleotide and protein databases. New predictive methods are thus necessary to determine the phenotype of viruses. In this work, we leverage the physical geometrical constraints of viruses to quantify the correlation between the geometric and genomic characteristics of tailed phages, and predict physical features such as architecture and genome length of uncultured viruses using allometric models and machine learning algorithms. Here, we present a model to predict the T-number …

Characterization Of Nuclear Microsatellites In Marchantia Polymorpha (Liverwort) With Additional Trans-Specific Analyses, Nicole Rodriguez Ortiz, Niharika Sharma, Tian Xiong Zheng, James J. Campanella

Department of Biology Faculty Scholarship and Creative Works

Microsatellites are present in mitochondria, chloroplast, and nuclear DNA, but nuclear microsatellites are more useful genetic tools than those in plastids or mitochondria. Plastid and mitochondrial microsatellites have been identified in the model plant Marchantia polymorpha (liverwort), but no laboratory has published information on nuclear microsatellite loci. The aim of this study was to detect novel nuclear markers in the most commonly employed liverwort species, design PCR primers that would allow amplification, and characterize the subsequently generated loci. We detected 18 polymorphic nuclear loci in M. polymorpha, amplifiable by PCR across all chromosomes. Additionally, trans-specific amplification of the eighteen loci …

C. Compactum Acts As A Comprehensive Climate Archive And Ecological Foundation In The Labrador Sea, Sadie Heckman

CMC Senior Theses

Clathromorphum compactum, a species of crustose coralline algae (CCA), is incredibly valuable for the future of high latitude ocean health, both as a comprehensive archive of changing ocean conditions, and ecologically as a foundational species for promoting biodiversity. Previous work establishes C. compactum as an effective climate proxy, and its life history provides several advantages for this use. C. compactum grow in nongeniculate, generally radial formations on hard substrates, over a wide distribution in mid-to-high latitude oceans and at subtidal depth ranges. Indeterminate growth leads to extreme longevity in C. compactum (Halfar et al., 2008), and growth rates are relatively …

Embryonic Exposure To Sodium Perchlorate Disrupts Organ Development In Mice, Kyle Bouten

All Graduate Theses, Dissertations, and Other Capstone Projects

Perchlorate is an endocrine disrupting compound (EDC) commonly used for its oxidative properties. Perchlorate has been detected in many industrialized countries in drinking water, soil, foods, and breast milk. Perchlorate competitively inhibits the uptake of iodide into the thyroid follicles via the sodium/iodide symporter (NIS), thus reducing thyroid hormone synthesis. Perchlorate has many conflicting results in the toxicological effects that perchlorate has on organ development in model fishes, but much less work has been done on mammals. In the present study, I examined the morphological effects of environmentally relevant concentrations (0, 10, and 100ppm) of sodium perchlorate on the thyroid, …

Dna Barcoding Reveals A New Population Of The Threatened Atlantic Forest Frog Sphaenorhynchus Canga, Diego J. Santana, Andre Yves, Elvis A. Pereira, Priscila S. Carvalho, Lucio M. C. Lima, Henrique C. Costa, Don Shepard

Biological Sciences Faculty Publications and Presentations

Species identification plays a significant role in biodiversity conservation. As many species remain unrecognized, particularly in neotropical hotspots like the Brazilian Atlantic Forest (AF), novel molecular techniques are being widely employed to bridge this gap. In this study, we used DNA barcoding and phylogenetic tools to identify a new population of Sphaenorynchus canga in the central region of the Brazilian AF. Our results extend the species’ known distribution by approximately 200 km to the south, encompassing a different mountain range than its type locality (Serra do Espinhaço). This disjunct distribution, while not uncommon among amphibians, suggests a historical connection between …

Myxomycetes Of Subantarctic Macquarie Island, Steven L. Stephenson

Biological Sciences Faculty Publications and Presentations

An expedition to subantarctic Macquarie Island was carried out during the period of late January to early May of 1995 with the objective of documenting myxomycete biodiversity. Collecting on the island yielded 412 field collections, with another 14 collections were obtained with the use of the moist chamber culture technique. A total of twenty-six species representing 13 genera was recorded. This is the largest set of data yet available on the myxomycetes associated with any high-latitude area of the Southern Hemisphere. Prior to the expedition, only a single species was known from Macquarie Island. The purpose of this paper is …

Sun Damages And Preventative Measures For Keratinocyte Carcinomas, Alex Kandolin

Biology and Microbiology Graduate Students Plan B Research Projects

UV rays from the sun cause damage to our genomic DNA and in turn have the ability to cause cancer. Protection methods such as sunscreen have been used for many years, however, the introduction of polyphenols and topical creams have brought new hope to skin protection. Polyphenols are a new method using an internal approach that directly targets the damaged DNA using different mechanisms through food. When used in addition to sunscreen, the chances of skin cancer are greatly reduced. Additionally, but using topical cream such as 5-fluorouracil can be an approach to already existing lesions caused from UV radiation. …

Regulation Of Inflammatory Signaling By The Gut Microbiome, Caden Johnson

Biology and Microbiology Graduate Students Plan B Research Projects

The human gut contains trillions of bacteria that play a key role in gastric homeostasis. Commensal bacteria play a critical role in the formation of the gastrointestinal barrier that prevents invasion of other pathogenic bacteria and also serves as a secondary metabolism system that aids in the synthesis of dietary fibers into many essential nutrients such as vitamins, sugars, and especially short chain fatty acids (SCFAs) in the anaerobic conditions in the large intestine. These SCFAs assist in regulating immune tolerance to commensal bacteria of the gut and promote an anti-inflammatory state important to lowering the incidence of inflammatory disorders …

Treatment-Related Adverse Effects In African Cancer Patients: A Systematic Review, Gabriel T. Fagbenro

Biology and Microbiology Graduate Students Plan B Research Projects

Treatment associated with cancer comes with serious adverse effects which affect patients’ physiological functioning, worsen financial toxicity, reduce quality of life, and increased risk of treatment discontinuation. There is dearth of evidence on prevalence and pattern of side effects among African patients receiving cancer-directed therapies. Primary research studies reporting side effects of non-surgical interventions among patients in African countries were selected for review. The most prevalent side effects included nausea, vomiting, and loss of appetite (chemotherapy); radiation dermatitis and mucositis (radiation therapy); anaemia, neutropenia/febrile neutropenia, and thrombocytopenia (chemoradiation), and cardiotoxicity (immunotherapy). Oncologists need to pre-empt and provide necessary prophylactic and …

Leveraging High Resolution Classifications And Random Forests For Hindcasting Decades Of Mesic Ecosystem Dynamics In The Landsat Time Series, N. E. Kolarik, N. Shrestha, T. Caughlin, J. S. Brandt

Biology Faculty Publications and Presentations

Mesic ecosystems are fundamental to conservation efforts in semi-arid systems, but are threatened by climate change and development. Newer earth observation datasets, including Sentinel-1 and −2, provide opportunities to monitor mesic ecosystems at meaningful spatial scales, but are insufficient for measuring decadal-scale changes. Conversely, the Landsat time series has decades of data, but images are spatially coarse relative to many of the mesic ecosystem areas that sustain dryland systems, resulting in classifications with mixed pixels inadequate for effective monitoring. We developed a workflow that uses 10-m classifications produced from fusion of the Sentinel-1 and −2 time series (2017–2020) to estimate …

Low Spatial Habitat Overlap Of Herbivores In The High Arctic Tundra, Virve Ravolainen, Ingrid M. G. Paulsen, Isabell Eischeid, Jennifer Sorensen Forbey, Eva Fuglei, Tomáš Hájek, Brage B. Hansen, Leif Egil Loe, Petr Macek, Jesper Madsen, Eeva M. Soininen, James D. M. Speed, Audun Stien, Hans Tømmervik, Åshild Ønvik Pedersen

Biology Faculty Publications and Presentations

Herbivores play a crucial role in shaping tundra ecosystems through their effects on vegetation, nutrient cycling, and soil abiotic factors. Understanding their habitat use, co-occurrence, and overlap is therefore essential for informing ecosystem-based management and conservation. In the High Arctic, only a marginal proportion of the land area is vegetated, and climate change is impacting herbivore population sizes and their habitats. In this study, we assessed the spatial habitat overlap of a vertebrate herbivore community based on: 1) regional predictive summer habitat suitability models for the resident Svalbard reindeer (Rangifer tarandus platyrhynchus), resident Svalbard rock ptarmigan (Lagopus …

Reciprocal Inhibition And Competitive Hierarchy Cause Negative Biodiversity-Ecosystem Function Relationships, Rafael D'Andrea, Gabriel Khattar, Thomas Koffel, Veronica F. Frans, Leonora S. Bittleston, Catalina Cuellar-Gempeler

Biology Faculty Publications and Presentations

The relationship between biodiversity and ecosystem function (BEF) captivates ecologists, but the factors responsible for the direction of this relationship remain unclear. While higher ecosystem functioning at higher biodiversity levels (‘positive BEF’) is not universal in nature, negative BEF relationships seem puzzlingly rare. Here, we develop a dynamical consumer-resource model inspired by microbial decomposer communities in pitcher plant leaves to investigate BEF. We manipulate microbial diversity via controlled colonization and measure their function as total ammonia production. We test how niche partitioning among bacteria and other ecological processes influence BEF in the leaves. We find that a negative BEF can …

What Are The Best Treatment Options For Infantile Cataracts?, Breindy Hecht

The Science Journal of the Lander College of Arts and Sciences

Congenital and infantile cataracts are characterized by opacity of the ocular lens, causing decreased visual acuity and inducing amblyopia. Treatment of pediatric patients is complicated because the eye is still growing during childhood, and the mind-eye connection is developing during this time. Anything that obstructs visual input from the eye to the brain raises risks of permanent visual deficit. Treatment includes immediate cataract extraction; this is sometimes followed by intraocular implantation of an artificial lens. After surgery, treatment continues in the form of occlusive patching therapy, corrective spectacles, or cycloplegic eye drops. Oftentimes, several methods are used simultaneously for maximal …

Lead Exposure: Neurological Implications, Transmission In Utero, And Treatment, Chana Birnbaum

The Science Journal of the Lander College of Arts and Sciences

Blood lead levels are routinely measured in pediatric clinics due to the well-documented detrimental effects of lead exposure on neurodevelopment and consequently cognition. Reading difficulties, impaired detailed movement, and depressed reaction time are three areas, among others, implicated in lead toxicity (Needleman, 1990). Furthermore, lead toxicity can be of particular concern in pregnant women, as placental transmission is viable (Gundacker & Hengstschläger, 2012, as cited in Sun et al., 2018). Future research investigating the transmission of lead from mother to fetus may provide insight into the timeline of in utero lead transmission and consequently the ability to direct anti-toxicity treatment …