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Impacts Of Viral Infection By Ma-Lmm01 On Microcystin Production By Microcystis Aeruginosa, Amber Elizabeth Haley

Senior Honors Theses and Projects

Increasing global temperatures and nutrient availability from anthropogenic sources have contributed to climate change and pollution in waterways. Environmental changes have promoted annual harmful algal blooms (HABs), which have the potential to lead to conditions that negatively affect aquatic ecosystems and organisms that depend on them. HABs can impact water quality through the release of soluble toxins (e.g., microcystin), produced by cyanobacteria that can bypass standard drinking water processing protocols. It has been suggested that viral infections of cyanobacteria may contribute to increased production and release of microcystins. In this project, two hypotheses were assessed: 1) virus-mediated lysis releases toxins …

Sexism And Racism In Stem: A Bleak History And A Bright Future, Abigail Hoskins

Senior Honors Theses and Projects

Women and people of color have faced discrimination throughout history, and this inequity persists today. This results in low numbers of women and people of color in STEM and leads to stereotypes and bias as well as harassment, financial disparities, and erasure of their contributions. Current initiatives promote equality and equity in STEM, such as protests against discriminatory practices and after-school programs encouraging youth from marginalized groups to participate in STEM, but these are not enough. Institutional and structural changes and solutions that address the intersectional needs of women and people of color are necessary to ensure equity and equality …

Potential Effects Of Road Proximity On Zooplankton Communities And Water Quality In Lakes In The Northwest Territories, Marie N. Hannan

Theses and Dissertations (Comprehensive)

Studies conducted along Canada’s Dempster Highway in the Northwest Territories have shown that road dust can affect water quality in roadside lakes, leading to higher calcium, conductivity, and pH levels. These water quality changes have the potential to affect important members of the lower aquatic food web, such as zooplankton.

For my thesis research, I had two main objectives: 1) To determine if changes in water chemistry caused by deposition of road dust affects zooplankton communities; and 2) To examine if the type of roadside vegetation influences the effects of road dust on aquatic habitats. To achieve these objectives, I …

The Effect Of Alkalinity On Lampricide Effectiveness And Gill Physiology In Invasive Sea Lamprey (Petromyzon Marinus), Alexandre J. Walsh

Theses and Dissertations (Comprehensive)

The pesticides, 3-trifluoromethyl-4-nitrophenol (TFM) and niclosamide are used to control populations of invasive sea lamprey (Petromyzon marinus) in the Laurentian Great Lakes of North America. Added to streams infested with larval sea lamprey, the effectiveness of these pesticides, commonly called lampricides, are strongly influenced by water pH, with greater toxicity for both TFM and niclosamide in lower pH than higher pH water. However, the TFM and niclosamide sensitivity of sea lamprey are also greater in poorly buffered, low alkalinity water than in high alkalinity water but it is unclear why. One goal of my thesis was to propose …

Temperature Regulation Of Pipecolic Acid-Mediated Plant Systemic Immunity In Arabidopsis Thaliana, Alyssa Shields

Theses and Dissertations (Comprehensive)

Significant crop losses are caused by pathogenic infections annually, which are exacerbated by increasing global temperatures due to climate change. One way by which plants respond to pathogenic attacks is through the activation of pattern-triggered immunity (PTI), effector-triggered immunity (ETI), and systemic acquired resistance (SAR), which lead to production of the central defence phytohormone salicylic acid (SA). Accompanying SA release is the putative mobilization of pipecolic acid (Pip), which acts as an immune regulatory plant metabolite that works with and independently from SA. As demonstrated in the model plant Arabidopsis thaliana following infection with the model bacterial pathogen Pseudomonas syringae …

Characterization Of The Clostridioides Difficile Glycosyl Hydrolase Ccsz, Brian Lowrance

Theses and Dissertations (Comprehensive)

Bacteria inhabit many of the harshest environments on Earth; persisting and thriving in conditions thought to be unsuitable for life. One common strategy to withstand these environments is the formation of a biofilm. Biofilm composition varies greatly, depending on the underlying community that produces it. Cellulose, a polymer consistently prevalent in biofilms, has been identified as a virulence factor in many pathogens and is suspected to be involved in pathogenesis by Clostridioides difficile. C. difficile is the #1 cause of hospital acquired diarrhea, which can range from mild to life-threatening infections. Biofilm formation is hypothesized to be involved in …

Reappraising The Evolutionary History Of The Largest Known Gecko, The Presumably Extinct Hoplodactylus Delcourti, Via High-Throughput Sequencing Of Archival Dna, Matthew P. Heinicke, Stuart V. Nielsen, Aaron M. Bauer, Ryan Kelly, Anthony J. Geneva, Juan D. Daza, Shannon E. Keating, Tony Gamble

Biological Sciences Faculty Research and Publications

Hoplodactylus delcourti is a presumably extinct species of diplodactylid gecko known only from a single specimen of unknown provenance. It is by far the largest known gekkotan, approximately 50% longer than the next largest-known species. It has been considered a member of the New Zealand endemic genus Hoplodactylus based on external morphological features including shared toe pad structure. We obtained DNA from a bone sample of the only known specimen to generate high-throughput sequence data suitable for phylogenetic analysis of its evolutionary history. Complementary sequence data were obtained from a broad sample of diplodactylid geckos. Our results indicate that the …

Strong Dispersal Limitation Of Microbial Communities At Shackleton Glacier, Antarctica, Nathan P. Lemoine, Byron J. Adams, Melisa A. Diaz, Nicholas B. Dragone, Andre L.C. Franco, Noah Fierer, W. Berry Lyons, Ian Hogg, Diana H. Wall

Biological Sciences Faculty Research and Publications

Microbial communities can be structured by both deterministic and stochastic processes, but the relative importance of these processes remains unknown. The ambiguity partly arises from an inability to disentangle soil microbial processes from confounding factors, such as aboveground plant communities or anthropogenic disturbance. In this study, we characterized the relative contributions of determinism and stochasticity to assembly processes of soil bacterial communities across a large environmental gradient of undisturbed Antarctic soils. We hypothesized that harsh soils would impose a strong environmental selection on microbial communities, whereas communities in benign soils would be structured largely by dispersal. Contrary to our expectations, …

Excess Dietary Sugar Alters Colonocyte Metabolism And Impairs The Proliferative Response To Damage, Ansen H.P. Burr, Junyi Ji, Kadir Ozler, Heather L. Mentrup, Onur Eskiocak, Brian Yueh, Rachel Cumberland, Ashley V. Menk, Natalie Rittenhouse, Christopher Marshall, Pailin Chiaranunt, Xiaoyi Zhang, Lauren Mullinax, Abigail Overacre-Delgoffe, Vaughn S. Cooper, Amanda C. Poholek, Greg M. Delgoffe, Kevin P. Mollen, Semir Beyaz, Timothy W. Hand

Biological Sciences Faculty Research and Publications

Background & Aims

The colonic epithelium requires continuous renewal by crypt resident intestinal stem cells (ISCs) and transit-amplifying (TA) cells to maintain barrier integrity, especially after inflammatory damage. The diet of high-income countries contains increasing amounts of sugar, such as sucrose. ISCs and TA cells are sensitive to dietary metabolites, but whether excess sugar affects their function directly is unknown.

Methods

Here, we used a combination of 3-dimensional colonoids and a mouse model of colon damage/repair (dextran sodium sulfate colitis) to show the direct effect of sugar on the transcriptional, metabolic, and regenerative functions of crypt ISCs and TA cells. …

Effects Of Bacillus Thuringiensis Israelensis (Bti) And Mosquito Larvae On Invasive Mosquito Egg-Laying Behavior, Zachary Runkle

Capstone Showcase

Invasive Aedes mosquitoes, including Asian tiger mosquitoes (Aedes albopictus) and Asian bush mosquitoes (Aedes japonicus), oviposit eggs in natural and artificial sites containing stagnant water. Aedes species exhibit versatility in novel ecological environments, including flexibility in oviposition site selection and overall habitat conditions, demonstrating their continued pertinence in human society. I examined the effects of the biopesticide BTI and Aedes larvae on oviposition habitat selection in Aedes albopictus and Aedes japonicus mosquitoes by observing the number of eggs oviposited. A total of 6552 and 1362 eggs were collected in experiments one and two, respectively. Females consistently …

College Of Natural Sciences 2022 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

This is the 2022 issue of the annual College of Natural Sciences year-end publication.

Contents:
[Page] 2 Dean's message
[Page] 3 Department highlights
[Page] 4 Overview of Bold & Blue Campaign
[Page] 5 Dr. Edward Hogan recognition & endowment
[Page] 6 Career milestones
[Page] 7 Student travel and research
[Page] 8 $11 million COBRE grant
[Page] 9 Professional Science Masters & Research highlights
[Page]10 Outreach highlights throughout the state
[Page] 11 2022 events recap – join us in 2023!
[Page] 12 Updates on our VR initiative
[Page] 14 Overview of awards and recognitions from 2022

Genetic Evaluation Of The Current Distribution And Possible Diffrentations Between Lasiurus Borealis And Lasiurus Frantzii In Southwestern North America, Zeinab M. Haidar

Cal Poly Humboldt theses and projects

Several recent accounts of overlap and historic misidentifications regarding two species of the genus Lasiurus, Western red bat (Lasiurus frantzii) and Eastern red bat (Lasiurus borealis), have cast doubt on our understanding of their distribution, assumed spatial allopatry, and interactions in the United States Southwest. With the use of morphometrics and genetic sequencing, utilizing tissue collected from specimens throughout California and adjoining states, we have reassessed the current distribution, best practices for field identification, and genetic differentiation between both species. Appropriate species classification by region was achieved utilizing mitochondrial DNA, targeting the cytochrome c oxidase …

Are Biodiverse Communities More Resistant To Invasion? A Case Study With Marine Fouling Communities, Taylor Robert Bruntil

Cal Poly Humboldt theses and projects

The theory of biotic resistance predicts that more diverse communities should be less susceptible to invasion by novel species, but given the opposing results of multiple observational and experimental studies in marine systems, it is unclear how changes in environmental conditions can affect invasion success in communities that differ in diversity. I used marine fouling communities to test how the diversity of the species present in an initial community (hereafter termed “resident species”) affected the establishment and growth of all species not present in the initial communities (hereafter termed “novel species”) at two locations at the Eureka Public Marina, in …

Community Ecology And Disease Dynamics In Pacific Oysters: Unraveling Microbiome-Pathogen Interactions In The Wild, Victoria E. Cifelli

Cal Poly Humboldt theses and projects

In the context of multispecies microbial assemblages, disruptions can occur when there are alterations in host conditions, such as the onset of a disease. Notably, viruses have the potential to reshape a host's microbial community. However, the role of the host's habitat and environment, which could be pivotal in communities with shifting niche space and habitat filters, is often overlooked in host-microbe-pathogen interactions. Recognizing the importance of these factors, I employed a field-based approach to understand microbial community dynamics in the presence of disease. To address the influence of geographical location, I conducted an analysis involving healthy and infected oysters …

Meiotic Recombination In Zea Mays And Its Contribution To Genetic Diversity, Jasmine Elizabeth Freeman

Graduate Theses, Dissertations, and Problem Reports (ETD)

Meiotic recombination plays a vital role in shaping genome evolution by introducing genetic diversity necessary for natural selection. Recombination rates exhibit extensive variation within and between species, occurring in specific regions known as hotspots and coldspots along individual chromosomes. Maize, with its well-characterized genome, provides an excellent model for studying the nonrandom pattern of meiotic recombination. While retrotransposon activity contributes to significant intergenic variation in maize inbred lines, the genic space remains conserved in terms of gene order and sequence. To investigate recombination activity in the Bz1/Sh1 region, the maize haplotypes W22 and B73, which share genetic backgrounds but differ …

Spatial Processing Of Conspecific Signals In Weakly Electric Fish: From Sensory Image To Neural Population Coding, Oak Everette Milam

Graduate Theses, Dissertations, and Problem Reports (ETD)

In this dissertation, I examine how an animal’s nervous system encodes spatially realistic conspecific signals in their environment and how the encoding mechanisms support behavioral sensitivity. I begin by modeling changes in the electrosensory signals exchanged by weakly electric fish in a social context. During this behavior, I estimate how the spatial structure of conspecific stimuli influences sensory responses at the electroreceptive periphery. I then quantify how space is represented in the hindbrain, specifically in the primary sensory area called the electrosensory lateral line lobe. I show that behavioral sensitivity is influenced by the heterogeneous properties of the pyramidal cell …

Analysis Of ‘Touch’ Dna Recovered From Metal Substrates: An Investigation Into Cfdna-Metal Interactions And The Efficacy Of Different Collection Techniques On Dna Yield, Jessica E. Thornton

Graduate Theses, Dissertations, and Problem Reports (ETD)

While several improvements have been made in recent years to optimize the recovery of ‘touch’ DNA, relatively little research has been conducted to understand the relationship between ‘touch’ DNA and the binding affinity of that DNA to metal surfaces, specifically those with a significant copper presence. Furthermore, characterization of cell-free DNA (cfDNA) and its contribution to ‘touch’ samples and those cfDNA-metal interactions from objects commonly identified at crime scenes (cartridge casings, knives, doorknobs) have been lacking. Research has identified the tendency of copper ions to intercalate with DNA helices, resulting in sample degradation among other damaging conformational changes; however, while …

Effect Of Soil Transplantation On Fungal Communities During Restoration, Thomas Luehl

All Master's Theses

Ectomycorrhizal fungi are integral parts of natural ecological systems that provide access to nutrients that would otherwise be unavailable by forming symbiotic relationships with plants. Relationships with ectomycorrhizal fungi are known to improve plant growth rate, increase plant resistance to pathogens, and improve survival. Current revegetation practices often ignore this relationship between fungi and plants. During the revegetation of the Interstate 90 Keechelus Lake wildlife overcrossing (Easton, WA), soil from forest sites adjacent to the restoration area were collected and used to inoculate a set of experimental plots to determine whether ectomycorrhizal fungi would become established in the plots and …

Effects Of Solar Arrays On Southwestern Desert Thermal Landscapes: Consequences For Terrestrial Ectotherms, Adrian Slade

All Master's Theses

Solar energy development in the Southwestern United States coincides with habitat for many sensitive and endemic species, including reptiles such as Mojave Fringe-toed Lizards and Mojave Desert Tortoises who are threatened by a warming and drying climate. While utility-scale solar energy reduces carbon emissions and should ultimately benefit climate-sensitive species, it locally destroys fragile desert habitat, displaces wildlife, and has been shown to incur local air and surface temperature changes. Mitigation-based translocation of wildlife species in the face of solar development yields mixed results, and the unprecedented pace of solar expansion in the desert highlights the need for alternative practices …

Cleaning The Variable Mess: A Population Genomics Approach To Understanding The Evolutionary History Of A Complicated Plant Group, Claire Marino

Honors Theses

The Solanum dioicum clade is a group of Australian bush tomatoes consisting primarily of species native to Western Australia and the Northern Territory whose species delimitations tend to be quite unclear. Since David Symon’s monograph A Revision of the Genus Solanum in Australia was published in 1981, little additional progress has been made in clarifying these relationships. In this project, a population genomics approach was used to analyze the relationships and delimitations between three species within the S. dioicum clade: Solanum dioicum, S. carduiforme, and S. ossicruentum. The use of population genomics methods is advantageous to understanding …

Meta-Narrative Review Of Pd-L1 By Immunotherapy On Triple-Negative Breast Cancer, Hannah Lazo, Tyler Harris, Hao Truong, Alina Masroor

Research Methods Poster Session 2023

Triple-negative breast cancer (TNBC) is an aggressive form of subtype breast cancer and there are currently new treatments being discovered such as the combination of immunotherapy and chemotherapy. In immunotherapy against triple-negative breast cancer, checkpoint inhibitors like PD-1/PD-L1 treat TNBC by blocking the “off” signal that prevents T-cells from killing cancer cells. As a group, we conducted a meta-narrative review collecting results from primary sources such as clinical trials and human experimental studies to support our research question on how PD-L1 inhibitor treatments compare to other treatments in patients with TNBC. The review included articles searched from Embase, Pubmed, EMBASE, …

Emerging Applications Of 3d Engineered Constructs From Plant Seed Extracts, Sedat Odabaş, Bora Gari̇pcan, Rihab Ksouri

Turkish Journal of Biology

Seeds, by-products derived from various plants such as mango, quince, and apples, are considered waste, though they have emerging commercial potential, and have been used in biological, industrial, and physiological research. Seed-derived natural macromolecules- mainly polysaccharides, mucilage, gums, and cellulose-have physicochemical and structural diversification, giving the potential for forming gels, texturing, thickening, and providing interfacial adsorption. Seed-derived natural macromolecules have been widely used during the last few years in cell research and tissue engineering applications. Their widespread approachability and safety, high rate of biodegradability, biocompatibility, supporting cell proliferation, and extracellular matrix synthesis are the main properties making plant seed derivatives …

Linc00460 Mediates Hmga2 Expression Through Binding To Mirna-143-5p Competitively In Gastric Carcinoma, Xuqing Zhu, Yanli Xiang, Feifei Mo, Lingling Jin

Turkish Journal of Biology

Background: Compelling evidence has manifested a strong association between aberrant expression of long noncoding RNAs (lncRNAs) and gastric carcinoma (GC) development. Nonetheless, biological impacts of differentially expressed lncRNAs (DElncRNAs) on GC are not scrutinized. Methods: Bioinformatics methods were employed for differential expression analysis and target gene prediction. MTT, colony formation, and Transwell methods were implemented for GC cell proliferation, migration, and invasion assessment. Western blot was implemented to test the protein level. The binding of genes was tested with dual-luciferase and RNA binding protein immunoprecipitation (RIP) approaches. Results: Noticeably high level of LINC00460 was observed in GC tissues and cells. …

Boquila: Ngs Read Simulator To Eliminate Read Nucleotide Bias In Sequence Analysis, Ümi̇t Akköse, Ogün Adebali̇

Turkish Journal of Biology

Sequence content is heterogeneous throughout genomes. Therefore, genome-wide next-generation sequencing (NGS) reads biased towards specific nucleotide profiles are affected by the genome-wide heterogeneous nucleotide distribution. Boquila generates sequences that mimic the nucleotide profile of true reads, which can be used to correct the nucleotide-based bias of genome-wide distribution of NGS reads. Boquila can be configured to generate reads from only specified regions of the reference genome. It also allows the use of input DNA sequencing to correct the bias due to the copy number variations in the genome. Boquila uses standard file formats for input and output data, and it …

Evaluation Of Leishmanicidal Activities Of 4-Thiazolidinones Against Leishmania Major, The Causative Agent Of Human Cutaneous Leishmaniasis, Kiera Bush

All Master's Theses

The leishmaniases are a group of vector-borne parasitic diseases that affect many developing countries including parts of Africa, India, and the Middle East in addition to Southern Europe and the Americas. It is estimated that worldwide, there are about 3 million new cases of leishmaniases each year leading to as many as 50,000 fatalities annually. The parasites that cause leishmaniasis belong to the genus Leishmania spp and are transmitted by the female phlebotomine sand fly. There are three clinical forms of the infection: visceral, mucocutaneous, and cutaneous. However, the focus of this paper is on cutaneous leishmaniasis that causes skin …

Immersive Learning And Participatory Engagement: Connecting In The Online Classroom Through Virtual Reality, Gesulla Cavanaugh, Helen M. Condry, Clarissa Frances Afable, Melissa Morris, Santanu De, Holly Evans Madison, Jacqueline Marshall, Chitra Paul Victor, Marsha Weiner

Biology Faculty Articles

Guided by constructivist theory, this study examines health professions student learning and engagement in the virtual classroom (VC) setting. Students (N=52) participated in a one-week VC prior to and during the COVID-19 pandemic. After participation, students were surveyed to discern their impressions of the experience, including the administration of a presence questionnaire, a key indicator of virtual environment (VE) efficacy. High student presence scores were significantly correlated with the perception that the VC facilitated learning (r = .573, p = .001). Conversely, students who perceived the course content as challenging were less likely to recommend the VC as a viable …

A Diet Comparison Of Bluegill And Bluegill X Pumpkinseed Hybrids, Russell D. Zwiers

Journal of Earth and Life Science

Bluegill Lepomis macrochirus and pumpkinseed Lepomis gibbosus commonly prey upon macroinvertebrates but have been found to show different preferences to what type of macroinvertebrates. Hybrids of the two species have been found to display physical characteristics of both parents but prey selection of the hybrids compared to the parents is unknown. Therefore, the objective of this study was to analyze the diets of bluegill and bluegill x pumpkinseed hybrids to understand what each species’ preference is when it comes to food as well as finding how a hybrid’s diet compares to the pure breed of one of the two crossed …

Effects Of Velocity And Substrate Size On The Formation Of Zebra Mussel Druses, Ian Mott

Journal of Earth and Life Science

Zebra Mussels Dreissena polymorpha are an invasive bivalve species that are highly successful at dominating new environments. These invaders have been known to colonize substrate so thoroughly that all they have to attach to are members of their own species. When large mats of interconnected mussels completely cover a riverbed, it can have a drastic effect on the surrounding environment. This study serves to create a better understanding of the hydrologic parameters needed for Zebra Mussels to create these ecosystem-transforming colonies known as druses. Data was collected on a small stretch of the Upper Mississippi River in Northern Minnesota, previously …

Estimate Of Long-Term Phytoplankton Biomass In Lake Bemidji, William J. Peterson

Journal of Earth and Life Science

Phytoplankton are photosynthetic organisms that are the base of aquatic food webs. In a dimictic temperate lake such as Lake Bemidji, the environment adjusts with the changing water temperatures and sunlight levels. The phytoplankton in a dimictic lake are adapted to subsist in long term seasonal changes but the exact change to the number of phytoplankton in unknown. The focus of this study was to estimate the biomass of phytoplankton in a long term period including winter stratification and summer peak. From a period between March 2023 and October 2023 water samples were collected from the lake in the south …

Native Amphibian Toxin Reduces Invasive Crayfish Feeding With Potential Benefits To Stream Biodiversity, Gary M. Bucciarelli, Sierra J. Smith, Justin J. Choe, Phoebe D. Shin, Robert N. Fisher, Lee B. Kats

All Faculty Open Access Publications

Background: Biodiversity is generally reduced when non-native species invade an ecosystem. Invasive crayfish, Procambarus clarkii, populate California freshwater streams, and in the Santa Monica Mountains (Los Angeles, USA), their introduction has led to trophic cascades due to omnivorous feeding behavior and a rapid rate of population growth. The native California newt, Taricha torosa, possesses a neurotoxin, tetrodotoxin (TTX), that affects freshwater animal behavior. Given P. clarkii has a limited evolutionary history with TTX, we hypothesized that TTX may affect crayfish feeding behaviors. To determine if TTX affects P. clarkii behavior, we measured cumulative movement and various feeding behaviors of P. …