Digital Commons Network^™

Overnight Rice Fermentation: An Analysis Of The Physicochemical Changes In White, Brown, And Enriched Rice Varieties, Kavin Sivakumar

Master's Theses

Fermentation refers to the activity of microorganisms breaking down substrates, resulting in changes to a food product. One fermented food practice from the Indian subcontinent is overnight fermented rice. The traditional preparation consists of covering cooled cooked rice in water and leaving it at room temperature to ferment overnight. The objective of this project was to investigate overnight rice fermentation through quantifying its physicochemical changes. The study utilized three types of rice: white, enriched white, and brown. Mixtures of cooked rice and water at a 1 gram: 2 milliliter ratio were fermented at 29 degrees Celsius and 60% humidity for …

Observations Of Currents, Waves, And Turbulence Within A Giant Kelp Forest In Stillwater Cove, Carmel, California, Logan A. Grady

Master's Theses

Nutrient distribution and propagule dispersal within Giant kelp (Macrocystis pyrifera) forests are significantly influenced by turbulence. In-situ measurements of turbulence within giant kelp forests are limited and driving mechanisms are primarily informed by controlled-flume experiments. This study investigates relationships between currents, surface gravity waves, and turbulence within a kelp forest through deployment of moored instrumentation and kelp surveys in Stillwater Cove, California during summer of 2022. Oceanographic conditions were primarily driven by coastal upwelling and a semi-diurnal internal tide, which was associated with cooling events and enhanced onshore velocity within the kelp forest during rising tides. Estimates of gradient Richardson …

Seasonal Dynamics Of The Introduced Sponge Hymeniacidon Perlevis In The Elkhorn Slough, California, Usa, Jackson Hoeke

Master's Theses

Hymeniacidon perlevis is a cosmopolitan sponge with a seasonal life cycle We investigated seasonal and interannual dynamics of H. perlevis in Elkhorn Slough estuary, where it is an introduced species, and explored correlations between sponge cover and environmental conditions. We used sponge cover to estimate the potential effects H. perlevis on its environment and how those could vary across its seasonal life cycle. We found that successful recruitment is currently restricted to the upper estuary and while it varies annually, the frequency and density of sponge recruits have generally increased from 2007 to 2023. A seasonal life cycle was confirmed …

Image Segmentation By Convolutional Neural Networks In Coral Resilience Research, Jennifer Benbow

Master's Projects

As ocean temperatures rise, coral bleaching is becoming more frequent and severe. Selective breeding experiments show promise for enhancing coral resilience, but scaling these projects is hindered by the labor-intensive nature of taking numerous time series measurements as corals grow. Automating this process with computer vision is one solution to this bottleneck, and to our knowledge, no such tool exists at present. To fill this gap, we have trained a set of machine learning models, based on the Mask R-CNN framework, for segmenting juvenile corals in lab-based coral resilience research. This work shows that retraining the Mask R-CNN architecture through …

The Debate On Nil: Progress For Female Collegiate Sports?, Stephanie Andrada

Master's Theses

In this study, seven female collegiate athletes from three different women’s sports teams (basketball, gymnastics, and volleyball) from a mid-major, Division-I college were interviewed. The study analyzed the lived experiences that NIL has on these specific female athletes in these particular women’s sports using a qualitative methodology. Three research questions were posed:

1. In what ways does the commercialization of college sports influence the NIL opportunities for these female athletes?
2. Could NIL perpetuate an uneven playing field for these female athletes in competition for limited resources?
3. To what degree do these female college athletes feel that NIL presents opportunities for equitable …

Behavorial Response Of Diving Northern Elephant Seals (Mirounga Angustirostris) When Exposed To Predator Calls, Daphne M. Shen

Master's Theses

Understanding how marine mammals respond to and recover from acoustic stressors is crucial if underwater noise increases. The use of an animal-borne biologger that combines a speaker with a motion sensor allows for the collection of whole-dive and fine-scale data over repeated exposures under identical experimental parameters. This study determined whether northern elephant seals (Mirounga angustirostris), a model for deep-diving marine mammals, exhibited a stereotypical behavioral response when exposed to killer whale whistles, an acoustic stressor. I examined changes in dive characteristics, measured duration of altered response, and observed behavior in response to repeated exposures. When exposed to the playback …

Differential Gene Expression Analysis Of Zebrafish Embryos Exposed To Simulated Microgravity And Insights Into Cellular Effects, Nicholas Lien

Master's Projects

Spaceflight consists of many dangers which adversely affects the health of astronauts through hazards such as microgravity and cosmic radiation. One area that is still poorly understood is how spaceflight impacts human reproductive health. This study aims to shed insight into how microgravity may impact the development of embryos. Differential gene expression analysis was performed via Jupyter Notebook and SLURM scripts and run on SJSU’s HPC server as a method of implementing NASA GeneLab’s RNA-Seq Consensus Pipeline. Data for this project utilized RNA-Seq files for early-stage embryonic zebrafish (Danio rerio), stored under GLDS-373. Gene Set Enrichment Analysis was performed to …

Understanding How The Relative Abundance Of Candida Species Impacts Transcriptional Regulation In Coculture Biofilms, Diksha Kool

Master's Projects

ABSTRACT Candida albicans and Candida glabrata are common fungal species that can change from commensal to pathogen due to their ability to form robust biofilms. Candida species are the leading cause of life-threatening conditions like Candidemia, and the existing treatments for biofilm-related infections are suboptimal. Research shows that the relative abundance of the two Candida species promotes biofilm formation, enhances pathogenicity, and increases antibiotic resistance. Thus, focusing on the importance of coculture, this paper utilizes RNA sequencing to investigate the gene expression leading to biofilm development in coculture through a time-series study.

Metagenomic Analysis Of Microbial 18s Eukaryotes Communities And Environmental Factors In The Western Antarctic Peninsula Waters During Austral Summers, Idan Siman-Tov

Master's Projects

Little is known about the environmental factors that impact eukaryotic microbial populations in the Western Antarctic Peninsula. Metagenomic and environmental data have been collected over the course of three consecutive austral summers in the Western Antarctic Peninsula off Palmer Station. More than 13 million 18S rRNA eukaryotic sequences have been taxonomically identified and categorized from the Antarctic water samples collected. Here we will investigate the environmental factors that affect eukaryotic organism populations, as well as possible indicator species that could provide insight as to the status of other eukaryotic species. Due to climate change, understanding these factors and identifying status …

Mirna-Seq Analysis Pipeline And R Shiny App, Alexis Torres

Master's Projects

ABSTRACT Thrombosis in the internal jugular vein (IJV) has been identified as a risk factor for astronauts undergoing spaceflight, following a 2019 study in which one astronaut developed a thrombus, and several others experienced stagnant or retrograde blood flow. To better understand this phenomenon, a model that simulates the effects of microgravity on blood flow in the IJV is being developed. mRNA and microRNA NGS sequencing will be used to study the transcriptome of human umbilical vein endothelial cells (HUVEC) in simulated microgravity conditions. A microRNA sequencing (miRNA-seq) pipeline has been developed to quantify the miRNA sequencing results. A graphical …

Mrna-Sequencing Pipeline And Pathway Analysis To Determine The Effects Of Bisphenol A On Fragile X Syndrome In Drosophila Melanogaster, Rashi Raghulan

Master's Projects

Neurological disorders (NDDs), like Fragile X Syndrome (FXS), are becoming more prevalent. One outstanding question in the field is how genetic risk factors for NDDs, like Fmr1, converge with environmental risk factors like bisphenol A (BPA). Our research compares and contrasts the different molecular impacts of BPA exposure in wild-type and FXS flies using mRNA-sequencing analysis. This analysis identifies the mutation in the Fmr1 gene is shown to have a stronger effect on the Drosophila than the presence of BPA, resulting in significant differential gene expression that perturbed several neurological pathways. Moreover, numerous genes responsible for genetic human diseases have …

The Impact Of Bisphenol A And Its Analogues On Neurodevelopmental Transcriptomes In Drosophila Melanogaster, An Nguyen

Master's Projects

Bisphenol A (BPA) is an endocrine-disrupting compound (EDC) that can act as an agonist or antagonist to interfere with multiple signaling pathways, including neurological pathways. The impact of BPA related to neurodevelopmental disorders (NDDs) is one of the biggest concerns in BPA exposure in humans. Therefore, BPA analogues are used to replace BPA in manufacturing and BPA-free products. However, most BPA analogues, including Bisphenol F (BPF) and Bisphenol S (BPS), act the same way as BPA on estrogen and androgen receptors. RNASequencing (RNA-seq) analysis was used to investigate the impact of BPA, BPF, and BPS on neurodevelopmental transcriptomes in Drosophila …

An Investigation Of Segmental Duplications Across Topologically Associating Domains, Sara Bell

Master's Projects

High-throughput chromosome conformation capture (Hi-C) reveals organization within genomes. Topologically associating domains (TADs) make up one level of organization and are identified by applying algorithms to Hi-C data. TADs have boundaries disrupted by structural variants (SVs), hypothesized to form due to recombination that occurs between segmental duplications (SDs). Little research is available about the effects of SDs at TAD boundaries. This project aimed to understand the distribution of SDs near TADs and determine any overlap between the two features. We analyzed public data and found SDs to have low breakpoint frequency and coverage at TAD boundaries. We then processed a …

Conservation And Prevalence Of Sequence Paired Sites In Humans, Punit Sundar

Master's Projects

The completion of the Human Genome Project in 2003 made it possible to leverage the power of computers to quicken biological discoveries. The human genome contains rich information relevant to the proper functions of cells that is computationally arduous and costly to investigate in a laboratory setting. Specifically, gene expression levels in cells can be impacted when functionally relevant motifs in the DNA are mutated preventing proper transcription factor binding. To study the consequences of such mutations, it is necessary to first identify such functionally relevant regions of the genome using computational approaches. A signaling pathway that is of particular …

Comparison Of An Oxford Nanopore Technologies Sequencing Platform To Existing Sequencing Methods For Differential Expression Studies, Nikola Klier

Master's Projects

As the genomics revolution continues, there is constant pressure to make sequencing technology more accessible and practical for a growing series of applications. Existing sequencing technologies are often prohibitively expensive, limiting their use for novel diagnostic and research applications. Additionally, existing technologies are often limited by short read lengths, which may present problems to certain quantitative sequencing applications. One such application is Differential Expression Analysis, in which RNA-Seq is performed in paired samples under different experimental conditions to identify differences in gene expression. In this study, an Oxford Nanopore Technologies sequencing platform was used to conduct a differential expression study …

A Lims-Less System For Genotyping Data In Marker-Assisted Selection, Alex Rios

Master's Projects

Climate change and feeding the growing human population are two tightly intertwined problems we face now. Innovations across several agricultural sectors are needed to meet these challenges as we proceed into the future. Seed companies and plant breeders are at the forefront of producing new plant varieties that must survive under the unique stresses of extreme weather patterns caused by changing climates. This project aims to provide breeders with faster marker results by streamlining the data process of marker-assisted selection (MAS). Manually managing genotyping data in MAS can take several hours or days to compile results for breeders. Although some …

Spaceflight And Differential Gene Expression Analysis Of Mice Quadriceps Exposed To Microgravity, Tommy Nguyen

Master's Projects

he trip to Mars and back is planned for the next 20 years. Improvement in technology and research has allowed data analysis, at a larger scale, on spaceflight specimen. However, research involving spaceflight is decentralized, as research is spread across laboratories with different methodologies. NASA’S GeneLab is a public repository for spaceflight-related omics data and promotes centralizing spaceflight RNA-Seq studies using NASA’s RNA-Seq pipeline. Jonathan Oribello, a SJSU’s Bioinformatics graduate and now an employee at GeneLab, has implemented Nextflow to NASA’s RNA-Seq pipeline. The Nextflow RNA-Seq pipeline was ran on San Jose State University’s College of Science High Performance Computing …

An Examination Of Bone Loss During Space Travel With Differential Gene Expression Analysis, Claudia Vo

Master's Projects

Spaceflight poses many risks to human health due to the harsh conditions of microgravity, cosmic radiation, and confinement. One of the impacts that spaceflight entails is bone loss, which is a risk to astronauts as future space missions will require long travel durations. To elucidate the role of genetics in spaceflight bone loss, in this study differential gene expression analysis was performed using Nextflow-RCP, an adaptation of NASA Genelab’s RNA-Seq Consensus pipeline. The dataset for this project was GLDS-241, which contained samples from mice femoral skin. To gain a comprehensive understanding of the genes involved in bone loss, the results …

Effective Cancer Detection Using Higher-Order Genome Architecture And Chromatin Interactions, My Chung

Master's Projects

Cancer is a complex disease which requires interactions between cell-intrinsic alterations and tumor microenvironment. The connection between epigenetics and genomic structure plays a key role in chromatin interaction which promotes enhancer-promoter interactions for transcriptional activities. Alterations of chromatin states in oncogenic signaling pathway potentially cause cancer cell-intrinsic changes and inappropriate instructions to normal cell cycles, leading to abnormal cell growth. Resulting phenotypic changes are correlated to underlying changes in higher-order chromatin structure such as topologically associating domains (TADs) and compartments. In cancer cells, TAD structure is usually altered to facilitate the communication between enhancers and promoters in addition to higher …

Mrna-Sequencing Pipeline For Differential Gene Expression Analysis, Crystal Han

Master's Projects

Endothelial cells (ECs) line the insides of blood vessels and play a key role in the coagulation and vascular repair system. Under normal circumstances, ECs are constantly expressing anticoagulants to prevent clots and maintain healthy blood flow. But when there is an injury to the vessel, endothelial cells become centrally involved in orchestrating the complex series of events that would lead to the clotting of the wound. Thus, ECs are dynamic and respond accordingly based on changes in their local environment. Unfortunately, endothelial cells can sometimes misinterpret cues from the environment and initiate coagulation when there is no vessel damage …

Transcriptional Profiling Of Neurological Development Of Drosophila Following Bisphenol A Exposure, Eden Johnson

Master's Projects

The ubiquitous environmental chemical bisphenol A (BPA) is an emerging risk factor for neurodevelopmental disorders (NDDs). BPA is an endocrine-disrupting chemical (EDC) that is thought to interfere with neuron development by changing neuronal gene expression. Impacting neurodevelopment in this manner can cause lasting changes in behavior and potentially lead to the development of NDDs. Delineating the molecular processes that incur changes in gene expression following BPA exposure will advance our understanding of how BPA impacts neurodevelopmental pathways and affects the pathophysiology of NDDs. An RNA-Sequencing (RNA-Seq) analysis pipeline was created for transcriptional profiling of neurological development in wild-type Drosophila melanogaster …

Detection Of Antibiotic Resistance Genes In The Wastewater Microbial Metagenome, Alan Caparaz Le

Master's Projects

The existential threat of emerging antibiotic resistance in microbial communities poses significant risks to public health. In particular, wastewater can serve as a point of confluence for pharmaceuticals and antibiotic-resistant bacteria from urban and agricultural settings. While this is a prime environment for genetic drift and horizontal transfer of antibiotic resistance genes (ARGs) and mobile genetic elements, it also presents an opportunity for resistome monitoring via shotgun metagenomic sequencing and downstream analysis. This project reports the application of a hybrid assembly approach for the detection of ARGs within DNA derived from a wastewater sample collected from the San José-Santa Clara …

Summer Marine Bacterial Community Composition Of The Western Antarctic Peninsula, Codey Phoun

Master's Projects

The Western Antarctic Peninsula has experienced dramatic warming due to climate change over the last 50 years and the consequences to the marine microbial community are not fully clear. The marine bacterial community are fundamental contributors to biogeochemical cycling of nutrients and minerals in the ocean. Molecular data of bacteria from the surface waters of the Western Antarctic Peninsula are lacking and most existing studies do not capture the annual variation of bacterial community dynamics. In this study, 15 different 16S rRNA gene amplicon samples covering 3 austral summers were processed and analyzed to investigate the marine bacterial community composition …

Differential Gene Expression Analysis Of Mice Thymi After Spaceflight, Roshani Codipilly

Master's Projects

With increases in space travel and a desire to inhabit the moon and Mars comes a pressing need to understand the impact of spaceflight on the body. Some effects are already known, such as reduced cardiac function and bone loss, but one area that needs to be further explored is the immune system. Differential gene expression analysis of mice thymi was performed to determine the impact of spaceflight on the immune system. The dataset that was analyzed, GLDS-289, was obtained from GeneLab, a space-omics database developed by NASA. Differential gene expression analysis was accomplished using a Nextflow implementation of GeneLab’s …

Differential Gene Expression Analysis Of Rodents Exposed To Long-Term Space Flight And Insights Into Physiological Effects, Jonathan Oribello

Master's Projects

Space travel presents inherent risks to human health and a better understanding of space biology is required to mitigate harm in an oncoming age of increased space travel. Omics analysis will play a central role in better understanding human health in space. In this project, differential gene expression analysis was performed on GLDS-104, an open science dataset provided by NASA’s GeneLab. GeneLab’s RNA-Seq Consensus Pipeline was implemented using Nextflow, performed on San Jose State University’s College of Science High Performance Computing Cluster, and optimized for computational resource efficiency. Comparison of the Nextflow implemention developed in this project to GeneLab’s posted …

Meta-Analysis Of Natural Vs Pharmaceutical Interventions For Alzheimer's Disease, Tamara Vrublevskaya

Master's Projects

The purpose of this research is to present a way to compare interventions by collecting all available drug clinical trials for a disease of interest. The assessment is done using Meta-Analysis, a method for evaluating data from several studies to arrive at a combined estimate of treatment effect. The evaluation is done in R on a given set of studies to answer the question – which Alzheimer's Disease intervention (pharmaceutical vs. natural) show better outcomes and fewer adverse effects. The research covers many types of interventions across diverse patient populations. On a small subset of papers, natural treatments showed better …

Bioinformatics Metadata Extraction For Machine Learning Analysis, Zachary Tom

Master's Projects

Next generation sequencing (NGS) has revolutionized the biological sciences. Today, entire genomes can be rapidly sequenced, enabling advancements in personalized medicine, genetic diseases, and more. The National Center for Biotechnology Information (NCBI) hosts the Sequence Read Archive (SRA) containing vast amounts of valuable NGS data. Recently, research has shown that sequencing errors in conventional NGS workflows are key confounding factors for detecting mutations. Various steps such as sample handling and library preparation can introduce artifacts that affect the accuracy of calling rare mutations. Thus, there is a need for more insight into the exact relationship between various steps of the …

Regulatory Disclosure Policies And Potential Induced Changes In Behavior: An Outcome Evaluation Of Santa Clara County’S Enhanced Food Safety Program Elements, Christian Cruz

Master's Projects

Despite countless advances in food microbiology and public health regulations, foodborne illness continues to be a major strain on public health outcomes and a costly economic burden. In the United States, many agencies are responsible for ensuring the quality of food, both domestically produced and imported. States and localities are delegated the responsibility of identifying and ensuring sound practices in the latter stages of the food production process, namely the retail distribution of food products to consumers.

Regulatory policies across the nation have only recently incorporated the evidenced-based principles of hazard risk management (Law, 2003). Still, food-related acute gastrointestinal illnesses …

Santa Clara County Senior Nutrition Program Evaluation Report, Tae Hwan Ihm

Master's Projects

Santa Clara County conducts a Senior Nutrition Program (SNP) in conjunction with the City of San Jose, the Outreach Paratransit Program and local community-based organizations (CBOs) like Sourcewise (Lam, 2015). These programs combined represent a significant investment of public funds, with more than 45% of the SNP program’s funding coming from the county General Fund (Lam, 2015). Such a large financial commitment needs to demonstrate some benefit to the participants, and some positive outcomes from the current program design. This study evaluated the SNP’s effectiveness in achieving its primary goals. Primary goals of the SNP are to promote senior citizens’ …

Rna Secondary Structure Prediction Tool, Meenakshee Mali

Master's Projects

Ribonucleic Acid (RNA) is one of the major macromolecules essential to all forms of life. Apart from the important role played in protein synthesis, it performs several important functions such as gene regulation, catalyst of biochemical reactions and modification of other RNAs. In some viruses, instead of DNA, RNA serves as the carrier of genetic information. RNA is an interesting subject of research in the scientific community. It has lead to important biological discoveries. One of the major problems researchers are trying to solve is the RNA structure prediction problem. It has been found that the structure of RNA is …