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Changes In The Microbiome Of The Sea Anemone Exaiptasia Diaphana During Bleaching From Short-Term Thermal Elevation, Jamison R. Sydnor, Jamie Lopez, Gordon V. Wolfe, Lisa Ott, Cawa Tran

Biology: Faculty Scholarship

We examined the response of microbial communities in the model sea anemone Exaiptasia diaphana (Aiptasia) to short-term thermal elevation. Through 16S rRNA gene sequencing, we characterized the microbiomes of symbiotic (with algal symbionts) and aposymbiotic (bleached) anemones under ambient (27°C) and heat-stressed (34°C) conditions for 8-10 days, using both replicated endpoint and non-replicated time-course approaches. Consistent with prior studies, we observed a stable abundance of bacteria from the families Alteromonadaceae and Rhodobacteraceae, though with wide variation among individual anemones. We observed that symbiotic state conferred a larger impact on the microbiome than heat stress, implying the microbiome may play a …

Proposing An Rna Interference (Rnai)-Based Treatment For Human Immunodeficiency Virus (Hiv) By Analyzing The Post-Transcriptional Gene Targeting Of Sars-Cov-2, Hepatitis C Virus, And A549 Lung Cancer Cells, Arjun Jagdeesh

UROP Posters

Human Immunodeficiency Virus (HIV) is a retrovirus that infects CD4+ T cell lymphocytes in humans, leading to the development of Acquired Immunodeficiency Syndrome (AIDS) if left untreated. While current treatment methods, including antiretroviral combination treatments, effectively limit HIV replication, HIV can evade these treatments due to its high mutation rate. Long-term antiretroviral treatment can also be toxic to patients, meaning patients would benefit from a new mechanism of HIV treatment. RNA interference (RNAi) is an antiviral pathway found in mammals, plants, and insects that involves a small-interfering RNA that is incorporated into a protein complex called the RNA-induced Silencing Complex …

Sense And Sensitivity: Spatial Structure Of Conspecific Signals During Social Interaction, Keshav Ramachandra

Graduate Theses, Dissertations, and Problem Reports (ETD)

Organisms rely on sensory systems to gather information about their environment. Localizing the source of a signal is key in guiding the behavior of the animal successfully. Localization mechanisms must cope with the challenges of representing the spatial information of weak, noisy signals. In this dissertation, I investigate the spatial dynamics of natural stimuli and explore how the electrosensory system of weakly electric fish encodes these realistic spatial signals. To do so In Chapter 2, I develop a model that examines the strength of the signal as it reaches the sensory array and simulates the responses of the receptors. The …

Endogenous Antioxidant Response And Lipid Peroxidation Levels In Muscle Tissue Of The Cownose Ray (Rhinoptera Bonasus), Bailey Berry

College of Graduate Studies: Theses & Dissertations

Oxidative stress is the result of an imbalance between reactive oxygen species (ROS) and antioxidant response within cells. ROS generation is a natural consequence of ETC activity within the mitochondria and is associated with aerobic metabolism. Oxidative stress data on elasmobranch muscle is limited, with previous studies primarily focusing on mammalian and teleost muscle. Elasmobranch skeletal muscle is generally composed of large proportions of white muscle fibers (anaerobic), low proportions of red muscle fibers (aerobic), and low proportions of pink muscle fibers (anaerobic). The cownose ray, a benthopelagic batoid species, presents an interesting model of study because it contains relatively …

Loggerhead Sea Turtle (Caretta Caretta) Nesting Experience, Seasonal Variation, And Hatching Success On A Georgia Barrier Island, Luke Sundquist

College of Graduate Studies: Theses & Dissertations

Loggerhead sea turtles nest commonly on the Georgia barrier islands and serve critical roles in human cultures, coastal economies, and multiple ecosystems. However, their global populations are declining and dependent on conservation efforts and informed management of natural and anthropogenic threats. Nesting offers a unique opportunity to research and protect this valuable marine species in terrestrial habitats. Microsatellite DNA sampling from eggshells can consistently identify nesting females from eggshells, allowing tracking of nesting behaviors for large populations over multiple years. Using this novel technology, we compared maternal investment and nest site-selection between first-time nesting neophytes and experienced remigrants. We sampled …

Dna Methylation And The Response To Infection In Introduced House Sparrows, Melanie Gibson

College of Graduate Studies: Theses & Dissertations

Epigenetics is the study of molecular modification of a genome without changing its base pairs. The most studied type of epigenetic mechanism is DNA methylation, which is capable of turning a gene “on” or “off.” Epigenetic potential is the capacity to which an individual can have methylation on its genome. The more CpGs available, the greater the epigenetic potential. In invasive species, genetic variation has been observed to be paradoxical: not much of it exists on a genomic level, but epigenetically, phenotypic variation can occur. The focus on shift in gene expression in this study is on Toll-Like Receptor 4 …

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 …

Updated Virophage Taxonomy And Distinction From Polinton-Like Viruses, Simon Roux, Matthias G. Fischer, Thomas Hackl, Laura A. Katz, Frederik Schulz, Natalya Yutin

Biological Sciences: Faculty Publications

Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of “hyperparasitism” in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and …

3d-Printed Hydrogels Dressings With Bioactive Borate Glass For Continuous Hydration And Treatment Of Second-Degree Burns, Fateme Fayyazbakhsh, Michael J. Khayat, Candy Sadler, Delbert Day, Yue-Wern Huang, Ming-Chuan Leu

Biological Sciences Faculty Research & Creative Works

Recent advances in additive manufacturing have led to the development of innovative solutions for tissue regeneration. Hydrogel materials have gained significant attention for burn wound treatment in clinical practice among various advanced dressings due to their soothing and moisturizing activity. However, prolonged healing, pain, and traumatic removal due to the lack of long-term wound hydration are some of the challenges in the treatment of second-degree burn wounds. In this study, 3D-printed dressings were fabricated using gelatin, alginate, and bioactive borate glass (BBG) using an extrusion-based bioprinter. After ionic crosslinking, the 3D-printed dressings were characterized for mechanical properties, degradation rate, hydration …

Island Meltdown: Demise Of The Abrolhos Painted Button-Quail Turnix Varius Scintillans In The Face Of Multiple Threats, Ryan Carter

Theses: Doctorates and Masters

Island avifauna suffer high rates of extinction and decline. The major threats to island birds centre around the ecological impacts of invasive predators, competitors, and grazers. The Abrolhos Painted Button-quail (Turnix varius scintillans) is a subspecies that has been determined to be the 5th most likely taxon to become extinct in Australia. T. v. scintillans historically inhabited three islands in the Houtman Abrolhos archipelago off the mid-west coast of Australia. This study aimed to 1) confirm the status of T. v. scintillans on North Island and determine the main causes of decline, 2) model habitat variables with detections from camera …

Adeno-Associated Virus 8 Delivers An Immunomodulatory Peptide To Mouse Liver More Efficiently Than To Rat Liver, Yuqing Wang, Ayrea Hurley, Marco De Giorgi, Mark R Tanner, Rong-Chi Hu, Michael W Pennington, William R Lagor, Christine Beeton

Faculty, Staff and Students Publications

Targeting the Kv1.3 potassium channel has proven effective in reducing obesity and the severity of animal models of autoimmune disease. Stichodactyla toxin (ShK), isolated from the sea anemone Stichodactyla helianthus, is a potent blocker of Kv1.3. Several of its analogs are some of the most potent and selective blockers of this channel. However, like most biologics, ShK and its analogs require injections for their delivery, and repeated injections reduce patient compliance during the treatment of chronic diseases. We hypothesized that inducing the expression of an ShK analog by hepatocytes would remove the requirement for frequent injections and lead to a …

Combating Hypertension Beyond Genome-Wide Association Studies: Microbiome And Artificial Intelligence As Opportunities For Precision Medicine, Sachin Aryal, Ishan Manandhar, Xue Mei, Beng S Yeoh, Ramakumar Tummala, Piu Saha, Islam Osman, Jasenka Zubcevic, David J Durgan, Matam Vijay-Kumar, Bina Joe

Faculty, Staff and Students Publications

The single largest contributor to human mortality is cardiovascular disease, the top risk factor for which is hypertension (HTN). The last two decades have placed much emphasis on the identification of genetic factors contributing to HTN. As a result, over 1,500 genetic alleles have been associated with human HTN. Mapping studies using genetic models of HTN have yielded hundreds of blood pressure (BP) loci but their individual effects on BP are minor, which limits opportunities to target them in the clinic. The value of collecting genome-wide association data is evident in ongoing research, which is beginning to utilize these data …

Targeting Hiv-1 Reservoirs In T Cell Subsets, Min Li, Marietta M Budai, Min Chen, Jin Wang

Faculty, Staff and Students Publications

The HIV-1 reservoirs harbor the latent proviruses that are integrated into the host genome. It is a challenging task to eradicate the proviruses in order to achieve an HIV cure. We have described a strategy for the clearance of HIV-1 infection through selective elimination of host cells harboring replication-competent HIV (SECH), by inhibition of autophagy and promotion of apoptosis during viral re-activation. HIV-1 can infect various CD4+ T cell subsets, but it is not known whether the SECH approach is equally effective in targeting HIV-1 reservoirs in these different subsets in vivo. In a humanized mouse model, we found …

Optical Coherence Tomography For Dynamic Investigation Of Mammalian Reproductive Processes, Kohei Umezu, Irina V Larina

Faculty, Staff and Students Publications

The biological events associated with mammalian reproductive processes are highly dynamic and tightly regulated by molecular, genetic, and biomechanical factors. Implementation of live imaging in reproductive research is vital for the advancement of our understanding of normal reproductive physiology and for improving the management of reproductive disorders. Optical coherence tomography (OCT) is emerging as a promising tool for dynamic volumetric imaging of various reproductive processes in mice and other animal models. In this review, we summarize recent studies employing OCT-based approaches toward the investigation of reproductive processes in both, males and females. We describe how OCT can be applied to …

A Guide To Naming Eukaryotic Circular Rnas, Ling-Ling Chen, Albrecht Bindereif, Irene Bozzoni, Howard Y Chang, A Gregory Matera, Myriam Gorospe, Thomas B Hansen, Jørgen Kjems, Xu-Kai Ma, Jun Wei Pek, Nikolaus Rajewsky, Julia Salzman, Jeremy E Wilusz, Li Yang, Fangqing Zhao

Faculty, Staff and Students Publications

Alternative splicing of eukaryotic transcripts often leads to production of multiple mature RNAs from a single gene locus. In addition to encoding linear RNAs, genes can produce stable circular RNAs (circRNAs) that are often co-expressed with their cognate linear RNAs. Multiple distinct circRNAs are frequently generated from a gene locus via back-splicing, with each mature transcript having a potentially unique function due to its distinct combination of exons and sometimes retained introns. However, names currently given to circRNAs are often ambiguous and lack consistency across studies. Here, we call on the community to embrace standards for naming circRNAs so that …

Development Of A Peripheral Blood Transcriptomic Gene Signature To Predict Bronchopulmonary Dysplasia, Alvaro Moreira, Miriam Tovar, Alisha M Smith, Grace C Lee, Justin A Meunier, Zoya Cheema, Axel Moreira, Caitlyn Winter, Shamimunisa B Mustafa, Steven Seidner, Tina Findley, Joe G N Garcia, Bernard Thébaud, Przemko Kwinta, Sunil K Ahuja

Faculty, Staff and Students Publications

Bronchopulmonary dysplasia (BPD) is the most common lung disease of extreme prematurity, yet mechanisms that associate with or identify neonates with increased susceptibility for BPD are largely unknown. Combining artificial intelligence with gene expression data is a novel approach that may assist in better understanding mechanisms underpinning chronic lung disease and in stratifying patients at greater risk for BPD. The objective of this study is to develop an early peripheral blood transcriptomic signature that can predict preterm neonates at risk for developing BPD. Secondary analysis of whole blood microarray data from 97 very low birth weight neonates on day of …

Open-Source, Highly Efficient, Post-Acquisition Synchronization For 4d Dual-Contrast Imaging Of The Mouse Embryonic Heart Over Development With Optical Coherence Tomography, Andre C Faubert, Irina V Larina, Shang Wang

Faculty, Staff and Students Publications

Dynamic imaging of the beating embryonic heart in 3D is critical for understanding cardiac development and defects. Optical coherence tomography (OCT) plays an important role in embryonic heart imaging with its unique imaging scale and label-free contrasts. In particular, 4D (3D + time) OCT imaging enabled biomechanical analysis of the developing heart in various animal models. While ultrafast OCT systems allow for direct volumetric imaging of the beating heart, the imaging speed remains limited, leading to an image quality inferior to that produced by post-acquisition synchronization. As OCT systems become increasingly available to a wide range of biomedical researchers, a …

Is Growth Hormone The Fountain Of Youth?, David Youlus

The Science Journal of the Lander College of Arts and Sciences

Finding the cure for aging has been a sought-after quest for as long as the world has existed. Growth hormone has been shown as a possible treatment to negate the phenotypic effects of aging. Growth hormone is released from the adenohypophysis in response to sleep, exercise and stress. This in turn stimulates insulin-like growth factor-1 (IGF-1) secretion from the liver. Growth hormone circulation decreases in volume during aging. Studies on growth hormone therapy have indicated youth-like benefits, such as the reversal of sarcopenia, improved cognitive function, and boosted immunity. However, creating an imbalance of growth hormone and insulin-like factor-1 also …

Differences In The Neurological Pathways Of Innate And Learned Fear, Efrat Jacob

The Science Journal of the Lander College of Arts and Sciences

Fear is a fundamental emotion for survival. However, not all fears are the same, leading to a necessary distinction between the two main subsections of fear; innate and learned. This research paper investigates whether the neural pathways underlying innate and learned fear are independent of each other. Using optogenetics and pharmacology, researchers have manipulated specific brain regions and circuits involved in fear processing, such as the amygdala, hypothalamus, and PAG (periaqueductal gray). By measuring the behavioral and physiological indicators of fear in rodents exposed to different types of stimuli, research suggests that there may be partial overlap between the neural …

Full Issue: Volume 17, Number 1, Fall 2023

The Science Journal of the Lander College of Arts and Sciences

Complete .pdf file of Volume 17, Number 1 of The Science Journal of the Lander College of Arts and Sciences. Published Fall 2023.

Fetal Alcohol Syndrome And Its Effects On Brain Development, Miriam Bayaz

The Science Journal of the Lander College of Arts and Sciences

Birth defects caused by maternal alcohol use during pregnancy, such as Fetal Alcohol Syndrome (FAS), are well-documented and preventable. The etiology, clinical characteristics, diagnosis, prevalence, and long-term effects of FAS are all covered in this paper’s thorough evaluation of the current state of knowledge. The teratogenic effects of alcohol on the growing fetus, as well as genetic, environmental, and maternal variables, all play a role in the complex etiology of FAS. A wide spectrum of physical, mental, and behavioral problems resulting from prenatal alcohol exposure on fetal development are discussed. FAS is characterized clinically by facial dysmorphology, growth retardation, central …

Radiation-Induced Gastrointestinal (Gi) Syndrome As A Function Of Age, Hongyan Li, Herman C. Kucharavy, Carla Hajj, Liyang Zhao, Guoqiang Hua, Ryan Glass, Phillip B. Paty, Zvi Fuks, Richard Kolesnick, Karen Hubbard, Adriana Haimovitz-Friedman

Publications and Research

Previous studies show increased sensitivity of older mice (28–29 months) compared with young adult mice (3 months, possessing a mature immune system) to radiation-induced GI lethality. Age-dependent lethality was associated with higher levels of apoptotic stem cells in small intestinal crypts that correlated with sphingomyelinase activity, a source of pro-apoptotic ceramide. The objective of this study is to determine whether the cycling crypt base columnar cells (CBCs) in aging animals are specifically more sensitive to radiation effects than the CBCs in young adult mice, and to identify factors that contribute to increased radiosensitivity. Mortality induced by subtotal body radiation was …

Potential Anti-Alzheimer Properties Of Mogrosides In Vitamin B12-Deficient Caenorhabditis Elegans, Denia Cai Shi, Chunlin Long, Ella Vardeman, Edward J. Kennelly, Michael A. Lawton, Rong Di

Publications and Research

Vitamin B12 deficiency can lead to oxidative stress, which is known to be involved in neurodegenerative diseases such as Alzheimer’s disease (AD). Mogrosides are plant-derived triterpene glycosides that exhibit anti-inflammatory and antioxidant activity in animal cell lines and mouse models. Since amyloid-β toxicity is known to cause oxidative stress and damage to brain cells, we hypothesized that mogrosides may have a protective effect against AD. In this study, we investigated the potential anti-AD effect of mogrosides in vitamin B12-deficient wild-type N2 and in transgenic CL2355 Caenorhabditis elegans expressing amyloid-β peptide. Our data indicated that mogrosides have a beneficial effect on …

Quantity Of Questing Black-Legged Ticks And Associated Micro-Scale Environmental Data Collected From Four Suburban Parks Near New York City, Shipeng Sun, Chong Di, Li Li, Brian Sulkow, Weigang Qiu

Publications and Research

During 2017 and 2018, we collected the quantity of questing black-legged ticks (Ixodes scapularis), also known as deer ticks, in 124 sampling sites of 5m by 5m in four state parks—Caumsett State Historic Park, Connetquot River State Park, Rockefeller State Park, and Fire Island National Seashore—around New York City. The black-legged tick is the primary vector for the spirochete Borrelia burgdorferi, the pathogen of Lyme disease, in Northeastern United States. Using the flagging method, we collected and counted the numbers of adult and nymphal black-legged ticks at each site. Along with these quantities, we also recorded the …

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 …

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 …

Use Of Foreign Edna Tracers To Resolve Site- And Time-Specific Edna Distributions In Natural Streams, Braden A. Herman

Cal Poly Humboldt theses and projects

Substantial uncertainty in how to interpret eDNA observations motivates a need for a technique to effectively and efficiently measure of system- and time-specific eDNA distributions. Using a technique to robustly calibrate eDNA dynamics in a given system would improve established eDNA methods such as presence and absence and has the potential to refine estimates of organism abundance using eDNA concentration that are less well understood. Particles of eDNA are present in a wide variety of size and type resulting in varying transport dynamics, persistence, decay, among others. This variation likely makes eDNA transport more complex than that of conservative tracers …

Sialylation And Fucosylation Modulate Inflammasome-Activating Eif2 Signaling And Microbial Translocation During Hiv Infection, Leila B. Giron, Ceylan E. Tanes, Mariane H. Schleimann, Phillip A. Engen, Lisa M. Mattei, Altizel Anzurez, Mohammad Damra, Huanjia Zhang, Kyle Bittinger, Frederic Bushman, Andrew Kossenkov, Paul Denton, Hiroaki Tateno, Ali Keshavarizian, Mohamed Abdel-Mohsen, Alan L. Landay

Biology Faculty Publications

An emerging paradigm suggests that gut glycosylation is a key force in maintaining the homeostatic relationship between the gut and its microbiota. Nevertheless, it is unclear how gut glycosylation contributes to the HIV-associated microbial translocation and inflammation that persist despite viral suppression and contribute to the development of several comorbidities. We examined terminal ileum, right colon, and sigmoid colon biopsies from HIV-infected virally-suppressed individuals and found that gut glycomic patterns are associated with distinct microbial compositions and differential levels of chronic inflammation and HIV persistence. In particular, high levels of the pro-inflammatory hypo-sialylated T-antigen glycans and low levels of the …