Marine Biology Commons^™

With Love, ; An Interdisciplinary And Intersectional Look At Why Creativity Is Essential, Theo Starr Gardner

Whittier Scholars Program

My Whittier Scholars Program self-designed major, Teaching Creativity, is a mixture of Art, Literature, and Education classes. My research and praxis classes have been focused on the ‘how?’s and 'why?’s of creativity, so it felt only right that my project should be a constructivist, generative project. The project I have been working on throughout my time at Whittier, and that has just fully come to fruition on April 11th, 2024, was a solo art gallery/open mic event entitled ‘With Love,’. With Love, was conceptually inspired by the research I’ve conducted on creativity and creative arts education over the past few …

Protective Responses Of The Intestinal Epithelial Cell Line Ht-29 Cells Exposed To Dephosphorylated Salmonella Flagellin [Research Note], Heyeon Baik, Jaiesoon Cho

The Philippine Agricultural Scientist

This study aimed to describe the effects of Salmonella Typhimurium flagellin (SFL) dephosphorylated by sweet potato purple acid phosphatase (PAP) on the protective responses of the intestinal epithelial cell line HT-29 cells. The enzyme was reported to display a broad substrate specificity for various organic phosphorylated conjugates and phosphoproteins. Dephosphorylation of SFL by sweet potato PAP decreased to 35% in the presence of 0.05 mM vanadate as compared with the negative control (p < 0.05). Intact SFL and the SFL treated with sweet potato PAP did not remarkably induce the activation of caspase-3 in HT-29 cells at all the tested levels of the substrate. Intact SFL maximally induced the release of IL (interleukin)-8 in HT-29 cells at 1000 ng/mL (p < 0.05). However, the SFL treated with the enzyme inhibited the release of IL-8 at over 100 ng/mL of the substrate as compared with intact SFL, resulting in an approximately 8-fold decrease even at 1000 ng/mL (p < 0.05). The SFL treated with the enzyme decreased the activation of the total ERK1/2 in the cells to 1.9 and 1.7–fold at 10 and 1000 ng/mL of the substrate, respectively, as compared with intact SFL (p < 0.05). In conclusion, sweet potato PAP could be a promising tool for controlling excessive inflammation during Salmonella infection in animal husbandry, and the enzyme could be a safe alternative that can overcome the drawbacks of chemotherapy.

Multi-Omics Reveals Largely Distinct Transcript- And Protein-Level Responses To The Environment In An Intertidal Mussel, Lani U. Gleason, Florian J. Fekete, Richelle L. Tanner, W. Wesley Dowd

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between …

Draft West Coast Rock Lobster Resource Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries management papers

Harvest strategies for Western Australia’s (WA) aquatic resources are formal documents developed by the Department of Primary Industries and Regional Development (DPIRD, the Department) to support decision-making processes that ensure the outcomes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002a) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). Harvest strategies are a key component of all contemporary fishery management systems and a requirement for certification under the Marine Stewardship Council (MSC). The objectives of ESD are reflected in the objectives of the Fish Resources Management Act 1994 (FRMA) and the Aquatic Resources Management Act …

South Coast Offshore Crustacean Resource Of Western Australia Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries management papers

Harvest strategies for aquatic resources in Western Australia (WA) that are managed by the Department of Primary Industries and Regional Development (DPIRD, the Department) are formal documents that ensures decision-making processes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA) and the Aquatic Resources Management Act 2016 (ARMA), which is anticipated replace the FRMA once enacted. At this point, the Fish Resources Management Regulations 1995 (FRMR) is also anticipated to …

Population Genomics, Ecology And Conservation Of Asterias Sea Stars In The North Atlantic, Melenia I. Giakoumis

Dissertations, Theses, and Capstone Projects

Uncovering how species respond to environmental change is a central question in biology (Ehrlén & Morris 2015; Habibullah et al. 2022). It is the key to elucidating the past, understanding the present and predicting the future of species’ population dynamics. This dissertation investigates the influence of environmental change on intertidal species’ distributions and genomics at several timescales, with implications for conservation.

Environmental changes have occurred throughout history, on a geological scale, and have shaped the global patterns of species’ distributions and population sizes. Biologists have long studied how geological history has shaped species distributions (Sanmartín 2012) in both terrestrial (Liu …

Predicting Marine Teleost Responses To Ocean Warming And Pollution, Akila Harishchandra

Electronic Theses and Dissertations

Ocean warming and pollution are two detrimental anthropogenic factors causing rapid marine ecosystem degradation recorded in the past decades. These factors alter the marine environment intolerable for many marine species, forcing them to either adapt or shift their contemporary habitat ranges to reduce the extinction risk embedded with environmental degradation. Estimating marine species’ habitat range shifts, and their potential for developing adaptive mechanisms are critical for ecosystem conservation and management, human health risk assessment, and climate change vulnerability assessments. Given that, for the first chapter of this thesis, we focused on developing a species distribution model (SDM) integrating marine species …

Du Undergraduate Showcase: Research, Scholarship, And Creative Works, Caitlyn Aldersea, Justin Bravo, Sam Allen, Anna Block, Connor Block, Emma Buechler, Maria De Los Angeles Bustillos, Arianna Carlson, William Christensen, Olivia Kachulis, Noah Craver, Kate Dillon, Muskan Fatima, Angel Fernandes, Emma Finch, Colleen Cassidy, Amy Fishman, Andrea Francis, Stacia Fritz, Simran Gill, Emma Gries, Rylie Hansen, Shannon Powers, Jacqueline Martinez, Zachary Harker, Ashley Hasty, Mykaela Tanino-Springsteen, Kathleen Hopps, Adelaide Kerenick, Colin Kleckner, Ci Koehring, Elijah Kruger, Braden Krumholz, Maddie Leake, Lyneé Alves, Seraphina Loukas, Yatzari Lozano Vazquez, Haley Maki, Emily Martinez, Sierra Mckinney, Mykaela Tanino-Springsteen, Audrey Mitchell, Kipling Newman, Audrey Ng, Megan Lucyshyn, Andrew Nguyen, Stevie Ostman, Casandra Pearson, Alexandra Penney, Julia Gielczynski, Tyler Ball, Anna Rini, Christina Rorres, Simon Ruland, Helayna Schafer, Emma Sellers, Sarah Schuller, Claire Shaver, Kevin Summers, Isabella Shaw, Madison Sinar, Claudia Pena, Apshara Siwakoti, Carter Sorensen, Madi Sousa, Anna Sparling, Alexandra Revier, Brandon Thierry, Dylan Tyree, Maggie Williams, Lauren Wols

DU Undergraduate Research Journal Archive

DU Undergraduate Showcase: Research, Scholarship, and Creative Works

Margalefidinium Polykrikoides Cyst Resuspension In The Lafayette River, A Sub-Tributary Of The Chesapeake Bay, Gabrielle Greaney, Eduardo Perez Vega, Katherine Crider, Dreux Chappell, Kimberly Powell, Richard Hale, Peter Bernhardt, Margaret Mulholland

Undergraduate Research Symposium

Harmful Algal Blooms are a collection of algae in a body of water that can cause serious environmental issues and health problems in both people and aquatic organisms. Dinoflagellates are microscopic, unicellular, and eukaryotic organisms that are well known for forming harmful algal blooms because of eutrophication. Coastal Virginia suffers from HABs in the Chesapeake Bay and its tributaries. A common species of dinoflagellate, known as Margalefidinium polykrikoides exists in the Chesapeake Bay. The purpose of this study is to determine if sediment resuspension produced by wind generated surface gravity waves cause cysts (dinoflagellate resting stages) to be suspended into …

Host-Microbe Interactions In Non-Native Estuarine Anemones: Biogeography And Temperature, Parker K. Lund

Cal Poly Humboldt theses and projects

Non-native species are increasing in prevalence around the world, resulting in negative economic and ecological impacts. However, the broad distributions of non-native species also offer a system for investigating the response of host-associated microbial communities to environmental factors across a range of ecological scales. At the broadest scale, I investigated the geography of microbial communities in the non-native estuarine anemone Diadumene lineata on the west coast of the United States of America. Across latitudes, microbial community composition was very similar and displayed a high percentage of Klebsiella spp. at all sites. However, the communities in California tended to exhibit higher …

Identification Of Novel Biosynthetic Gene Clusters Encoding For Polyketide/Nrps-Producing Chemotherapeutic Compounds From Marine-Derived Streptomyces Hygroscopicus From A Marine Sanctuary, Hannah Ruth Flaherty

Honors Theses and Capstones

Nearly one out of six deaths in 2020, around ten million people, were caused by cancer, making it a leading cause of death worldwide (WHO, 2022). This major public health issue, in addition to the rise of multidrug-resistant (MDR) pathogens, provides a high demand for the discovery of new pharmaceutical drugs to be used clinically to treat these conditions. The Streptomyces genus accounts to produce 39% of all microbial metabolites currently approved for human health, indicating its potential as an important species to study for antimicrobial and anticancer agents. The long linear genome of Streptomyces contains specialized sequences known as …

Disparate Population And Holobiont Structure Of Pocilloporid Corals Across The Red Sea Gradient Demonstrate Species-Specific Evolutionary Trajectories, Carol Buitrago-López, Anny Cárdenas, Benjamin C.C. Hume, Thierry Gosselin, Fabian Staubach, Manuel Aranda, Daniel J. Barshis, Yvonne Sawall, Christian R. Voolstra

Biological Sciences Faculty Publications

Global habitat degradation heightens the need to better understand patterns of genetic connectivity and diversity of marine biota across geographical ranges to guide conservation efforts. Corals across the Red Sea are subject to pronounced environmental differences, but studies so far suggest that animal populations are largely connected, excepting evidence for a genetic break between the northern-central and southern regions. Here, we investigated population structure and holobiont assemblage of two common pocilloporid corals, Pocillopora verrucosa and Stylophora pistillata, across the Red Sea. We found little evidence for population differentiation in P. verrucosa, except for the southernmost site. Conversely, S. …

Caribbean Reef-Building Coral-Symbiodiniaceae Network: Identifying Symbioses Critical For System Stability In A Changing Climate, Shaman Patel

All HCAS Student Capstones, Theses, and Dissertations

Increasing global ocean temperatures and frequency of marine heatwaves pose dire consequences for coral reefs. High temperatures often lead to disruptions in coral symbiosis resulting in coral bleaching, increasing the mortality of corals. However, corals can potentially avoid bleaching peril by associating with thermally tolerant symbionts. Here we provide a tool for understanding symbiosis network stability of Caribbean reef-building corals. We created a network of Caribbean hermatypic corals and their associated Symbiodiniaceae phylotypes. A bleaching model was applied to this network to test for resilience and robustness (R50) to thermal stress. It was also layered with trait data for coral …

Chemosensory Receptors In Berghia Stephanieae: Bioinformatics And Localization, Kelsi L. Watkins

Masters Theses

Chemosensation is achieved through the binding of chemical signals to chemoreceptor proteins embedded in the membranes of sensory neurons. The molecular identity of these receptors, as well as the downstream processing of chemosensory signals, has been well studied in arthropods and vertebrates. However, very little is known about molluscan chemosensation. The identity of chemoreceptor proteins in the nudibranch mollusc Berghia stephanieae are unknown. Data from other protostome and molluscan studies suggest Berghia may use ionotropic receptors for some forms of chemoreception. This study used a bioinformatics approach to identify potential chemosensory ionotropic receptors in the transcriptome of Berghia. A …

Determination Of Atlantic Shortfin Mako Shark (Isurus Oxyrinchus) Population Genetic Structure And Comparison Of Mitogenomic Markers, Marissa Mehlrose

All HCAS Student Capstones, Theses, and Dissertations

This study provides the first genomics-level, population structure and genetic diversity assessment of the shortfin mako (Isurus oxyrinchus) shark. The assessments were based on mitogenome sequences from makos distributed throughout the Atlantic Ocean, with Pacific mako mitogenomes used as a comparative outgroup. In addition to complete mitogenome-based analyses, I assessed individual mitochondrial coding gene and non-coding (Control Region) sequences for their comparative resolution properties as markers for revealing matrilineal population structure and genetic diversity. Sequencing of 125 makos in the western and eastern Atlantic across northern and southern hemispheres yielded 92 complete mitogenomes (16,698-16,702 bp) and 33 partial …

A Genomic Investigation Of Divergence Between Tuna Species, Pavel V. Dimens

Dissertations

Effective management and conservation of marine pelagic fishes is heavily dependent on a robust understanding of their population structure, their evolutionary history, and the delineation of appropriate management units. The Yellowfin tuna (Thunnus albacares) and the Blackfin tuna (Thunnus atlanticus) are two exploited epipelagic marine species with overlapping ranges in the tropical and sub-tropical Atlantic Ocean. This work analyzed genome-wide genetic variation of both species in the Atlantic basin to investigate the occurrence of population subdivision and adaptive variation. A de novo assembly of the Blackfin tuna genome was generated using Illumina paired-end sequencing data and …

Characterizing Endogenous Dicer Products To Unravel Novel Rnai Biogenesis Pathways, Jacob Oche Peter

Dissertations

ABSTRACT

RNA interference (RNAi) is a pervasive gene regulatory mechanism in eukaryotes based on the action of multiple classes of small RNA (sRNA). Exploiting RNAi pathways in non-model systems have great potential for creating potent RNAi technologies. Here, we accessed RNAi-mediated control of gene expression in the two-spotted spider mite, Tetranychus urticae (T. urticae) using engineered dsRNA designed to modulate the host RNAi pathway and increase RNAi efficacy. Analysis of Dicer (Dcr) generated fragments revealed how exogenous RNAs access the host RNAi pathway in this animal, opening avenues for designing RNAi technology for their control. Further, some organisms …

Comparing Two Non-Invasive Methods For Assessing Marine Mammal Genetic Diversity: Environmental Dna Vs. Fecal Dna, Sydney Jackson

Honors College

As technology and science progresses, the methodology behind observing, monitoring, and sampling marine mammals advances as well. One such technique is environmental DNA or eDNA, which entails extracting organismal DNA from water samples without ever handling or disturbing the organism. It is a cost-efficient and non-invasive method that can be utilized in the sampling of seal haulout sites as is its purpose for this research. Another method, using the DNA analysis of seal fecal samples, is a less invasive method that can also be utilized to monitor and assess marine mammals. Through collecting both fecal and water samples from gray …

Temporal And Spatial Comparison Of Pseudo-Nitzschia Species Composition And Domoic Acid In Narragansett Bay, Rhode Island And The Northeast U.S. Shelf, Isabella Church, Bethany D. Jenkins

Senior Honors Projects

Diatoms are unicellular algae that make up a significant portion of phytoplankton biomass at the base of marine food webs. Narragansett Bay (NB), RI is home to several species of the diatom genus Pseudo-nitzschia (P-n), some of which are known to cause harmful algal blooms through the production of the potent neurotoxin domoic acid (DA). This toxin can lead to Amnesic Shellfish Poisoning in humans through the consumption of affected shellfish. Although the presence of P-n has been well established in NB for over 50 years, DA levels have only recently become a problem, with shellfish harvest closures …

Population Genomic Dynamics Of Mesopelagic Lanternfishes Diaphus Dumerilii, Lepidophanes Guentheri, And Ceratoscopelus Warmingii (Family: Myctophidae) In The Gulf Of Mexico, Andrea Bernard, Kimberly A. Finnegan, Tracey Sutton, Ron Eytan, Max Weber, Mahmood Shivji

Marine & Environmental Sciences Faculty Articles

Assessing the impacts of the Deepwater Horizon oil spill (DWHOS) on deep-sea fish assemblages of the Gulf of Mexico (GOM) has been hindered by an absence of baseline (pre-spill) data concerning the population genetic dynamics of these fishes. The lanternfishes (Myctophidae) are a speciose, yet understudied, taxonomic group, that comprise a significant portion of the global deep-sea biomass, making them integral members of meso- and bathy-pelagic food webs. Herein, we used a genomic approach (double digest restriction site associated DNA sequencing) to investigate the temporal genetic dynamics of three species of lanternfishes within the northern GOM in the region of …

Phylogenetic And Geographic Relationships Of Cheilostome Bryozoans In The Eastern Pacific, Hannah E. Lee

Cal Poly Humboldt theses and projects

The phylum Bryozoa is an incredibly diverse group of marine invertebrates with a widespread global distribution that is well suited for evolutionary studies but whose phylogenetic relationships are still poorly understood. Although recent studies on bryozoan taxonomies and phylogenies have increased, there is still a lack of assessment of species found at shallow water (<1 m) to intertidal depths. In this study, I aimed to expand the taxonomic sampling and assessment of the phylogenetic diversity of cheilostome bryozoans along the California coastline by utilizing mitochondrial DNA as well as inferring potential correlations between species presence and dispersal range both within and between rocky outer coast and sheltered harbor habitats. Illumina high-throughput sequencing was used to produce mitogenomes for cheilostome bryozoan samples collected off rocks from two rocky intertidal sites and off settlement panels from two harbor sites. Phylogenetic analyses generated evolutionary hypotheses of species relationships alongside geographic mapping of their distribution. This study identified 15 distinct species that represent 10 different families to form the first comprehensive phylogeny for multiple bryozoan families in California across a total range of approximately 973 km of coastline. Three genetically distinct species were found at multiple sites that are separated by a combination of rocky shores and sandy beaches, which indicates that the dispersal range of these species are not limited by geographic barriers along the coast of California. These results provide a future opportunity for further integration of this data with the phylogenies generated in this study to examine more robust evolutionary hypotheses for the phylogenetic and geographic relationships of Californian bryozoan species.

An Analysis Of The Spatial Genetic Structure Of A Hybrid Zone Between Two Species Of Killifish, Fundulus Heteroclitus And F. Grandis, Andrew Lee Hardy

UNF Graduate Theses and Dissertations

Hybridization offers unique insight into the evolutionary process of speciation and the forces that maintain barriers to reproduction. In northeast Florida, a hybrid zone between two species of killifish, Fundulus heteroclitus and F. grandis, has been identified near Flagler Beach, FL, although the exact boundaries of the hybrid zone remain unknown (Gonzalez et al. 2009). This study aims to determine the fine-scale spatial genetic patterns of the hybrid zone and test the hypothesis that species ranges are influenced by changes in dominant vegetation. Results from an ADMIXTURE analysis and F_ST data indicated the boundary of the area of …

Screening Ocean Samples From Georgia For The Presence Of Msx And Dermo Using Pcr And Qpcr Methods, Olivia Michelle Williams

Honors Theses and Capstones

This Senior Thesis project aimed to be able to screen samples that came in from a PhD student in Georgia for the presence of two oyster diseases, MSX and Dermo. This study was done using PCR followed by visualizing on E-gels for initial presence of disease. These were then followed by qPCR and visualization on Criterion gels. These Criterion gels were able to be analyzed in order to calculate the pg/uL of MSX and Dermo in the original ocean samples. Since the samples were sent in over the course of February-August ‘21 the presence over time was also able to …

Phylogenetic Origins And Age-Based Proportions Of Malacho (Elops Smithi) Relative To Ladyfish (Elops Saurus): Species On The Move In The Western Gulf Of Mexico, Damon Williford, Nicolette S. Beeken, Joel Anderson, Polly Hajovsky, Roberta Weixelman

Gulf and Caribbean Research

Two species of ladyfish occur in the Gulf of Mexico (GOM), Elops saurus and Elops smithi, that are morphologically indistinguishable except for vertebral counts but can also be identified by mitochondrial DNA haplotypes. Here we expand on previous work, most of which has occurred in Florida, and examine the demography, phylogenetics, geographic distribution, and age—structure of ladyfishes in Texas estuaries. Fishery—independent gill net data demonstrated that ladyfishes increase in abundance from north to south along the Texas coast. The abundance of ladyfishes also increased in Texas waters from 1982–2021, which coincides with recent trends of warmer winters. Genetic data …

Dna Barcoding Enhances Large-Scale Biodiversity Initiatives For Deep-Pelagic Crustaceans Within The Gulf Of Mexico And Adjacent Waters, Carlos Varela

FIU Electronic Theses and Dissertations

In this dissertation I investigate the biodiversity of marine deep-water crustaceans of the Gulf of Mexico and adjacent waters, focusing on pelagic crustaceans. Taxonomic and molecular techniques were utilized to document adult and larval crustacean specimens to better under their taxonomy, life history, evolutionary relationships and cryptic biodiversity. The use of molecular techniques to study organisms from habitats with limited accessibility provides tremendous potential. With prevalent anthropogenic threats and the delicate nature of deep-water habitats, the need to improve our understanding of these systems is clear. Molecular techniques can act as a fundamental tool to complement traditional taxonomy. The application …

The Evolution Of Bioluminescence Across The Shrimp Family Sergestidae: A Genomic Skimming And Phylogenetic Approach, Charles G. Golighty Iii

FIU Electronic Theses and Dissertations

The family Sergestidae provide a unique system for studying the evolution of bioluminescence, with species possessing one of three distinct forms of photophores. This study capitalizes on molecular data to construct a genus-level phylogeny of sergestid shrimp. “Genome skimming” was implemented, capturing mitochondrial genomic data across 19 species. Additional individuals were incorporated through Sanger sequencing of four partial gene regions. The -sergestes group of genera was recovered as non-monophyletic, with the -sergia group of genera being recovered as monophyletic. Ancestral state reconstructions of light organ type indicate the organs of Pesta photophore is the ancestral state for the …

Ecological Risk Assessment For The Temperate Demersal Elasmobranch Resource, Department Of Primary Industries And Regional Development, Western Australia

Fisheries research reports

No abstract provided.

Otoliths Of South-Western Australian Fish: A Photographic Catalogue, Chris Dowling, Kim Smith, Elaine Lek, Joshua Brown

Fisheries research reports

Due to the species-specific nature of otoliths and given they are often the only part of the fish preserved when fish die, otolith catalogues can be used in numerous applications, such as diet studies in fish eating animals, including pinnipeds, fish and sea birds; archaeological purposes such as reconstructing indigenous people’s diets from otoliths found in middens or evolutionary history of fish species by comparing fossilized otoliths. Given the unique mixture of subtropical and temperate fish, including many endemic species that occur off the southwest corner of WA having a catalogue for this area is extremely important for people working …

Otoliths Of South-Western Australian Fish: A Photographic Catalogue, Chris Dowling, Kim Smith, Elain Lek, Joshua Brown

Fisheries research reports

Due to the species-specific nature of otoliths and given they are often the only part of the fish preserved when fish die, otolith catalogues can be used in numerous applications, such as diet studies in fish eating animals, including pinnipeds, fish and sea birds; archaeological purposes such as reconstructing indigenous people’s diets from otoliths found in middens or evolutionary history of fish species by comparing fossilized otoliths. Given the unique mixture of subtropical and temperate fish, including many endemic species that occur off the southwest corner of WA having a catalogue for this area is extremely important for people working …

Squid And Cuttlefish Resources Of Western Australia, Daniel Yeoh, Danielle J. Johnston Phd, David C. Harris

Fisheries research reports

No abstract provided.