Life Sciences Commons^™

Characterization Of Phytoplankton-Excreted Metabolites Mediating Carbon Flux Through The Surface Ocean, Yuting Zhu, Hanna S. Anderson, Eli Salcedo, Samuel E. Miller, Krista Longnecker, Melissa C. Kido Soule, Sheean T. Haley, Gretchen J. Swarr, Rogier Braakman, Sonya T. Dyhrman, Elizabeth B. Kujawinski

Chemistry & Biochemistry Faculty Publications

The marine labile dissolved organic carbon (DOC) pool is a dynamic reservoir of thousands of molecules that cycles approximately one-quarter of Earth’s primary production within days to weeks. After excretion by phytoplankton and other microbes, metabolites are rapidly consumed, resulting in low standing concentrations (picomolar to low nanomolar). Despite the decades-long search for labile DOC sources and molecular identities, marine phytoplankton exometabolomes are not well characterized, largely due to difficulties in measuring small polar molecules in saline water. Here, we profiled the exometabolomes of six axenic phytoplankton species representing key functional groups including a diatom (Thalassiosira pseudonana CCMP1335), a …

The Coral Microbiome Under Climate Change: Shifting Symbiotic Interactions, Katherine E. Parker, Kate M. Quigley

Biological Sciences Faculty Publications

Host–microbe symbioses are central to organismal health, yet these complex partnerships are often strongly shaped by the environment. Climate change is increasingly altering environmental conditions, disrupting the balance of host–microbe interactions and pushing them along a continuum from mutualism (both partners benefit) toward parasitism (one partner gains at the other’s expense). Reef-building corals provide a clear example of this vulnerability, as the coral holobiont, an ecological unit comprising diverse photosynthetic algal symbionts (Symbiodiniaceae) and other microbial partners, depends largely on these mutualistic interactions for nutrition, immunity, and stress tolerance. Increasingly, evidence suggests that under heat stress, the algal symbionts retain …

[Review Of The Book A Conspectus Of The North American Isoetaceae, By D. F. Brunton, J. T. Kartesz, M. Nishino, And P. C. Sokoloff]., Lytton John Musselman

Biological Sciences Faculty Publications

Isoetes (Isoetaceae; Lycopodiopsida; quillworts) constitutes a highly successful, cosmopolitan genus with over 200 species. Isoetes is derived from isos Greek for equal and eter for year, referring to the typically long persisting leaves of the sole genus in this ancient plant family. The leaves resemble a ‘quill-of-feather,’ hence the common name ‘Quillworts,’ wort, from old Germanic wurti, meaning plant. In large measure due to its simple form, inconspicuous appearance and negligible economic value, it represents one of the least studied and least collected of all North American genera. Isoetes constitutes a taxonomically enigmatic group with numerous polyploid species that arose …

Mitochondrial Genome Of The Indo-Pacific Mesophotic Coral Leptoseris Columna (Scleractinia: Agariciidae) Assembled Using Pacbio Long-Read Sequencing, Nomita Rani Adhikary, Daniel J. Barshis, J. Antonio Baeza

Biological Sciences Faculty Publications

Leptoseris columna, a mesophotic coral species belonging to the family Agariciidae, is distributed throughout the Indo-Pacific region. This species is considered as of "Least concern" by the IUCN, yet, faces multiple local and global stressors. To support conservation plans, this study sequenced and characterized the complete mitochondrial genome of L. columna. The complete mitochondrial genome of Leptoseris columna was assembled using PacBio long-reads with a coverage of 459× per bp. The AT-rich mitochondrial genome of Leptoseris columna is 18,546 bp long and comprises 13 protein-coding genes (PCGs), 2 transfer RNA genes (trnM and trnW), and 2 ribosomal RNA …

Larval Genomics As A Viable, Fisheries-Independent Tool For Investigating Population Structure In Tropical Pacific Tunas, Jacob E. Jaskiel, Hannah E. Aichelman, Giulia Anderson, Louw Claassens, James E. Fifer, Christina M. Hernandez, Alexa K. Huzar, Joel K. Llopiz, Jan W. Witting, Sean P. Mullen, Randi D. Rotjan

Biological Sciences Faculty Publications

Understanding how dispersal, life history, and environmental variability shape genetic connectivity in the open ocean remains a central challenge in evolutionary biology. Highly migratory marine predators like tunas have traditionally been considered genetically homogeneous across ocean basins, yet emerging genomic evidence suggests that cryptic population structure can persist even in species with high gene flow and large effective population sizes. We used 2bRAD sequencing of 348 larval and subadult skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares), and bigeye tuna (T. obesus) collected from the central Pacific across 7 years of sampling to examine species boundaries, …

A Re-Evaluation Of Atlantic Bluefin Tuna (Thunnus Thynnus) Spawning Distribution In The Western Atlantic Ocean, David E. Richardson, Katrin E. Marancik, Malgorzata Adamus, Elizabeth A. Broughton, Robert K. Cowen, Trika Gerard, Christina M. Hernández, John J. Hoey, Joel K. Llopiz, Molly E. Lutcavage, Estrella Malca, Debra L. Palka, Lourdes Vásquez-Yeomans, Harvey J. Walsh, C. Michelle Willis, Glenn A. Zapfe

Biological Sciences Faculty Publications

There is currently a lack of consensus on the spatial, seasonal and decadal-scale patterns of Atlantic bluefin tuna (Thunnus thynnus) spawning in the western Atlantic Ocean. We compiled ichthyoplankton and reproductive data to characterize bluefin spawning patterns and the uncertainty in these patterns. Ichthyoplankton data indicates that bluefin spawn in the Gulf of America/Gulf of Mexico, northwest Caribbean Sea, north of the Bahamas, along the inshore edge of the Florida Current off the Carolinas and in the western Slope Sea. Reproductive studies identified these same spawning areas, as well as the Windward Passage and waters east of the …

Land Use Influences Dissolved Organic Matter Composition In The U.S. Coastal Critical Zone Network, Aleksandar I. Goranov, Elizabeth V. Whitney, Brian R. Moyer, Katherine L. Tully, Patrick G. Hatcher, Yu-Ping Chhin

Chemistry & Biochemistry Faculty Publications

Coastal watersheds are highly productive biogeochemical systems supporting robust coastal fisheries and contributing significantly to the marine gross primary production flux. These ecosystems are comprised of civil infrastructure, farms, forests, and marshes, and their diversity is reflected in the quantity and quality of dissolved organic matter (DOM). Here, we assess the role of farming in influencing DOM from surface waters of six coastal tidal creeks adjacent to forest and farm sites in the US Critical Zone Network. Molecular fingerprinting using electrospray ionization - Fourier transform - ion cyclotron resonance - mass spectrometry revealed that farm-influenced DOM was enriched in nitrogen-, …

Lingnan Gardeners Newsletter (No. 77) = 彩園通訊 (第77期), Lingnan Gardeners, Centre For Cultural Research And Development, Lingnan University

Lingnan Gardeners Newsletter 嶺南彩園通訊

No abstract provided.

Systematics Of Disk-Winged Bats (Thyroptera), Courtney L. Klumpp

Capstone Showcase

This thesis investigates the evolutionary relationships among disk-winged bats in the genus Thyroptera, a small group of Neotropical bats known for the adhesive suction disks on their wings and feet that allow them to roost inside tightly rolled leaves. The distinctive morphology and behavior of these bats have not been extensively documented, and their phylogenetic relationships remain only partially resolved. The goal of this research is to better understand how these species are related to one another and to determine whether the five recognized species of Thyroptera form a single monophyletic group. To address this question, morphological and genetic …

Building A Cell Specific System For In Vivo Rna Imaging Of The Endogenous Actin Gene In C. Elegans, Jasmine A. Huerta Canete

Theses and Dissertations

Messenger RNA (mRNA) plays a crucial role in protein synthesis and cellular processes, important for the development of cells such as neurons. When dysregulation occurs, it can lead to outcomes such as aberrant translation, causing neurodegenerative conditions to arise. Unfortunately, the localization of mRNA in an in vivo cell specific manner is still not understood. To address this, we decided to develop a cell-specific system to image RNA in vivo, within the organism known as C. elegans with a focus on the actin gene. The Actin gene encodes for an important cytoskeleton protein expressed ubiquitously, vital for the cell …

The Effect Of The Affordable Care Act Medicaid Expansion On The Risk Of Hospital Closure And Adolescent Hpv Immunization In Rural Counties, Juliette Des Rosiers

Scripps Senior Theses

From 2005 to 2025, over 200 rural hospitals shut their doors, often citing increased operational costs, staffing shortages, low patient volume, regulatory barriers, financial challenges exacerbated by the COVID-19 pandemic, and uncompensated care as common contributors to the closures. Rural patients are often referred by their primary care physician to a hospital for regular immunizations, since smaller clinics have less capacity to provide immunizations due to a shortage of pediatricians and limited vaccine stock. A crucial vaccine that is not required by schools and underutilized in rural areas is that against human papillomavirus (HPV), a virus that infects cutaneous and …

Seeing Through The Fuzz: Understanding Conformational Diversity In The Fuzzy Coat Of Amyloids Across Fibril Polymorphs Using Solid-State Nmr, Carah K. Allen

Scripps Senior Theses

The aggregation of α-synuclein (α-syn) into amyloid fibrils is a central pathological hallmark of Parkinson’s disease and other related synucleinopathies. Although monomeric α-syn is intrinsically disordered, the protein assembles into multiple fibril polymorphs that differ in their β-sheet core structures. Surrounding each polymorph is the “fuzzy coat,” which is a highly dynamic, intrinsically disordered region (IDR) that is not resolved by high-resolution structural techniques, such as Cryo-EM, but is thought to influence fibril interactions, propagation, and toxicity. Understanding whether different polymorphs maintain distinct fuzzy-coat conformational ensembles is therefore essential for connecting amyloid structure to biological function. To address this question, …

Indirect Effects Of Coral Bleaching On Tursiops Truncatus Diet And Foraging Behavior In Bocas Del Toro, Panama, Annabel Fiero

Scripps Senior Theses

Indirect effects, where another species or factor mediates the effects of a given species, are critical to ecosystem structure and resilience. Shifts in fish community structure, as a result of rapidly declining coral reefs in the Caribbean due to warming-induced bleaching, pose a threat to apex predators like Tursiops truncatus (bottlenose dolphins). Branching corals create habitat niches for numerous fish species. These fish rely on coral for food and habitat, and in turn provide food for upper trophic levels. Prior research has highlighted how coral bleaching will disrupt Acroporid reef building corals and fish community structure, but the effects of …

How Semiflightless Birds Adapt: A Survey From Barú, Costa Rica, Eli P. Laloudakis

Scripps Senior Theses

When we think of birds, we think of flight. Because of this, scientific research often focuses on how birds evolved flight and how their wings function during flight. However, not all birds can fly or fly well, as wings wax and wane on developmental, seasonal, and evolutionary time scales (Dial and Heers 2021). Consequently, rudimentary wings can be found in developing birds, secondarily flightless or semiflightless birds, birds that undergo simultaneous molts, and extinct theropods with “protowings” (structures that preceded fully functional wings). Secondarily flightless and semiflightless birds often evolve where there is no/low predation, abundant year-round food supply, and …

Lead Biosorption By Oceanobacillus Profundus Kbz 3-2: Strategies For Bioremediation Systems In Kabwe, Danielle S. Desmarteau

Scripps Senior Theses

Lead contamination remains a significant global public health concern, particularly in Kabwe, Zambia, the site of a former lead mining operation. Bioremediation, which utilizes biological materials and processes to remove environmental contaminants, represents a promising approach for addressing lead pollution. However, the development of effective bioremediation systems requires a detailed understanding of the mechanisms underlying metal removal and the feasibility of implementation in low-resource settings. Oceanobacillus profundus KBZ 3-2, a bacterium isolated from Kabwe mine waste, has demonstrated the ability to remove lead from aqueous environments. This study proposes to investigate the mechanism of lead biosorption by this organism, …

Assessing The Effect Of Wildfire-Specific Air Pollutants On Copd Hospitalizations In Los Angeles County, Kimberly Young

Scripps Senior Theses

As the fourth leading cause of death in the world, chronic obstructive pulmonary disorder (COPD) is one of the most severe respiratory disorders characterized by airway inflammation.  For the past two decades, climate change has exacerbated the prevalence of wildfires in California due to rising temperatures and lower precipitation. With the influx of wildfires, poor atmospheric air quality continues to be a serious health problem in the Los Angeles area, especially after the recent Eaton fire in January of 2025. My study hopes to assess whether the air pollutants particulate matter 2.5 (PM_2.5), particulate matter 10 (PM_{10 …}

Food Stamp Participation And Health Outcomes In Ca Immigrants, Esther Kang

Scripps Senior Theses

The U.S. social welfare system includes programs aiming to increase access to nutritious food to reduce nutrition insecurity. However, studies suggest that immigrants continue to face disproportionate risks of nutrition insecurity and may face barriers to enrollment due to legal status. This study, using secondary data from the 2023 California Health Interview Survey, examines the associations between food stamp participation, food insecurity, and clinical diagnosis of diabetes among adult U.S.-born, naturalized, and non-citizen adults in California. The findings suggest that those enrolled in food stamps are more likely to report food insecurity than those who are not enrolled, and that …

The Utah Reusable Root Module: Evapotranspiration Dynamics And Moisture Sensor Performance In Five-Month Reused Peat-Based Media, Claudia Garrido-Ruiz, Bruce Bugbee, Juan D. González-Teruel, Scott B. Jones

Controlled Environments

Efficient water management is essential for closed-loop food production in space applications. The Utah Reusable Root Module (URRM) is designed to support repeated cropping in the same peat-based growth media. Here, we report moisture sensor performance, nighttime-to-daytime evapotranspiration (ET) rate, yield, and water-use efficiency (WUE) in the Engineering Development Unit (EDU) using Outredgeous lettuce. Five previous crops had been planted in the same media, and this study reports growth and ET from the final crop cycle. Volumetric water content (θ_ᵥ) was monitored using two electromagnetic moisture sensors (CS650 and TEROS ONE) across five root modules (RMs) with multiple …

South Asians And Renal Disease: Traditional Food Lists For Management Of Chronic Kidney Disease, Ashwini Wagle

Open Educational Resources

The renal food list is a culturally tailored nutrition education tool designed to address the specific dietary needs of the South Asian population. It is an original intellectual work created by Ashwini Wagle, Ed.D., MS, RD, FAND, Chair and Professor, Department of Nutrition, Food Science, and Packaging at San José State University (SJSU).

An earlier version of this tool was published in 2011 with the assistance of graduate student Kalpana Balasubramanian. The development of this renal food list was strengthened by the encouragement and support of the registered dietitian community, whose contributions included verifying the accuracy of the nutritional information …

Mitochondrial Efficiency: Bridging Early-Life Environment And Organismal Performance, Kayla E. Lichtner

Master’s Theses

Mitochondria operate at the forefront of organismal-environmental interactions. Despite remarkable diversity in mitochondrial function both within and among species, all mitochondria serve a universal role in facilitating the flow of energy between organisms and their environment. Energetic efficiency, the way in which organisms assimilate and transform environmental substrate into physiological currency, is a major determinant of organismal performance. Although previous studies have shown that early-life environment can have lasting effects on metabolism, the underlying mechanisms driving the emergence of mitochondrial phenotypic variation remain poorly understood. Leach’s storm-petrels (Hydrobates leucorhous) provide a valuable opportunity to investigate longitudinal hypotheses of …

Overview And Methods Of Molecular Paleontology: A Review, Shelby Touchstone

Williams Honors College, Honors Research Projects

Molecular paleontology—the study of ancient biomolecules preserved in fossils and sediments, including ancient DNA, lipids, and proteins—has motivated researchers since the 1950s, inspiring both scientific inquiry and broader cultural imagination. Think Jurassic Park. This honors thesis presents a comprehensive review of the history, current state, and methods of the field of molecular paleontology. Drawing on peer-reviewed literature and scholarly resources accessed through databases such as EBSCO and Bierce library, this review examines key techniques such as Next Generation Sequencing and amino acid racemization and will go over limitations and controversies in the field. It will also explore potential new …

Effect Of Jet Lag And Nighttime Shifts On The Circadian Rhythm Of Humans, Mahd Adrees

Williams Honors College, Honors Research Projects

This project reviews the circadian rhythm and its disruption by jet lag and nighttime shifts. It discusses the effects on melatonin, sleep quality, and physiological symptoms using articles from Google Scholar. Key studies, mechanisms, and statistics will support these points. A discussion follows, comparing and contrasting the various literature sources. This review aims to raise awareness and summarize strategies to reduce jet lag and nighttime shift effects, improving wellbeing.

Rate Response Of Curlyleaf Pondweed And Native Plants To Flumioxazin In Minnesota Lakes, Pearl J. Jensen

All Graduate Theses, Dissertations, and Other Capstone Projects

Curlyleaf pondweed (Potamogeton crispus L.) is an invasive aquatic plant present across the United States that causes significant recreational issues, outcompetes native plant species, and depletes water quality. Before senescing in mid-summer, curlyleaf pondweed forms a large number of turions that can lay dormant in the sediment for several years. Typical herbicide management of this species occurs in early spring to target the plant before turion production occurs and while native plants are dormant. Flumioxazin has shown potential in curlyleaf pondweed management in small scale studies, but its effects have not been assessed in operational management. In this study, treatments …

Ethanol And Iron Absorption Interactions Within Crayfish Invertebrate Models, James Rollman, Andrew Wissmar

Williams Honors College, Honors Research Projects

Analysis of the effects of alcohol consumption (ethyl-alcohol) on iron absorption within crayfish model. The use of tube-feeding provides a novel, more precise output, and less invasive procedure compared to the traditional approach of dissolving the target substance in tank water and measuring hemolymph changes. The project aims to determine the extent to which alcohol influences iron absorption. Ultimately, the choice of iron reflect the future potential to aid in research with genetic hemochromatosis and or Iron overload.

Physiological Development Of Hypertension As A Result Of High-Fat Diet Induced Obesity, Michael Nguyen

Williams Honors College, Honors Research Projects

This literature review focuses on the physiological development of obesity due to the consumption of diets rich in fats and the resulting pathophysiological development of hypertension. This review aims to identify causes of obesity and hypertension as well as current treatments to propose future areas of study. The literature review analyzed a wide variety of literature sources on obesity and hypertension published between the years 1995 and 2025. The review identifies high-fat diets as a cause of obesity and the resulting health effects of elevated leptin, insulin, and nervous system activity as contributors to the development of hypertension. Future areas …

Toadally Not A Frog: A Neuromuscular Physiology Study, Iris Renna

Williams Honors College, Honors Research Projects

Upper-level physiology labs in undergraduate education use freshly isolated bullfrog and/or leopard frog tissue to teach core concepts in nerve and muscle physiology. Sourcing live animals for routine educational use raises ethical and conservation concerns. Cane toads (Rhinella marina) are an invasive species that are routinely culled, can provide a potential source of laboratory animals which would remove pressure to native amphibian populations. This study tested the hypothesis that cane toads can serve as a functional substitute for bullfrogs and/or leopard frogs in the muscle and nerve physiology lab. Isolated sciatic nerve and gastrocnemius muscle preparations from cane …

Methods Of Euthanasia In Laboratory Animals, Jaiden L. Corley

Williams Honors College, Honors Research Projects

The current honors research project will focus on the current use of carbon dioxide (CO2) as a means of euthanizing laboratory mice. CO2 is commonly used as a means of euthanizing laboratory animals and has been a standard of practice for mamy years. it is regarded as fast, painless, and efficient in overwhelming the respiratory control centers of the brainstem and resulting in respiratory depression and death. However, there continues to be debate and ongoing research regarding the 'humaneness' of this approach to euthanasia, and the American Veterinary Medicine Association (AVMA) suggests the inclusion of isoflurane (a volatile anesthetic) as …

Neighborhood Socioeconomic Deprivation And Physical Activity Associate With Extracellular Vesicle Size And Cargo In A Community-Based Cohort Of Women, Yvonne Baumer, Elizabeth M. Aquino Peterson, Matthew R. Bavuso, Noel Miller, Cristhian A. Gutierrez-Huerta, Nithya P. Vijayakumar, Sam J. Neally, Kaveri Curlin, Valerie M. Mitchell, Billy S. Collins, Neelam R. Redekar, Subrata Paul, Anca D. Dobrian, Tiffany M. Powell-Wiley

Department of Biomedical and Translational Sciences Faculty Publications

African American (AA) women face disproportionate cardiovascular disease (CVD) risk due to adverse social determinants of health (SDoH), including lower socioeconomic status (SES). Physical activity (PA) and plasma extracellular vesicles (EVs) modulate CVD risk, but their relationships with SDoH remain unclear. This study examines associations between SDoH, PA, and plasma EVs in a Washington, DC-based cohort of at-risk AA women. Participants (N = 24, Age: 57 ± 12, BMI: 35 ± 6, ASCVD: 9 ± 5) joined the Step It Up Community-Engaged, Digital Health Physical Activity Intervention pilot study. EVs were isolated from fasting plasma samples. Multivariable regression, adjusted for …

Red Clover Isoflavones And Establishment In The Context Of Tall Fescue Toxicosis Mitigation In The Mid-South, Jonathan L. Stephens

Theses and Dissertations--Plant and Soil Sciences

Low levels of red clover (Trifolium pratense L.) have been shown to mitigate tall fescue (Lolium arundinaceum (Schreb.) toxicosis symptoms. This is because of the presence of plant-produced compounds known as isoflavones. Production of a red clover supplement on a commercial scale would require industrial-level processing of raw plant material into granules or pellets. The first study of this thesis evaluated the impact of drying temperature on bioavailability of isoflavones. Drying temperatures up to 104°C had minimal impact on isoflavone concentrations. Additionally, varietal differences in isoflavone concentrations were documented. The second study of this thesis evaluated optimal establishment …

Characterizing The Role Off The Sp1/Klf Transcription Factor Huckebein In The Drosophila Melanogaster Ventral Nerve Cord, Benjamin Almond

Distinguished Undergraduate Researcher Program

Over the course of embryonic development, the ectodermal cell layer gives rise to a vast array of neurons and glia patterned across the central nervous system (CNS). Neurulation and specification is achieved in the ectoderm through temporospatial patterns of transcription factor (TF) expression, many of which are conserved across evolutionary history. These conserved regulatory motifs allow the use of Drosophila melanogaster to study the mechanisms of neurodevelopment across the animal kingdom. The huckebein (hkb) gene encodes a conserved SP1/KLF TF known to play important roles in cell cycle regulation, tissue morphogenesis during tubular organ development, and gut specification in Drosophila. …