Life Sciences Commons^™

Effects Of Low Dose Caffeine On Post-Exercise Heart Rate Variability: A Double-Blind Placebo-Controlled Trial, Cagney T. Sargent, Tareq K. Shahbal, Andres E. Carrillo, Tania Amorim, Jason R. Edsall, Emily J. Ryan, Edward J. Ryan

International Journal of Exercise Science

International Journal of Exercise Science 15(2): 103-112, 2022. Caffeine may impact post-exercise heart rate variability (HRV); although, studies have yielded inconsistent findings. We examined the effects of low dose caffeine on post-exercise HRV. Healthy, college-aged adults [n = 18; age: 22.1 ± 2.6 years; BMI: 26.9 ± 4.3 kg/m²; estimated maximal oxygen consumption (VO₂max): 45.1 ± 8.3 ml∙kg^-1∙min^-1] participated in a repeated-measures, double-blind, placebo-controlled trial. During the experimental trials, participants were fitted with a heart rate monitor and a mouthpiece with a one-way nonrebreathing valve and then rested for 10 min …

Forces At The Feet, Gait Timing, And Trunk Flexion/Extension Excursion While Walking With A Gear Belt Or Gear Vest Load, Shane S. Maher, Laura L. Dill, Jennifer L. Hein, Jeff A. Nessler, Deanna J. Schmidt

International Journal of Exercise Science

International Journal of Exercise Science 15(1): 36-44, 2022. Law enforcement personnel often carry gear loads, which have a history of causing low back pain. The aim of this study was to evaluate the differences in gait and trunk posture for gear load carried on a gear belt and a gear vest. Twenty-nine participants performed load carriage in three conditions: a no load control trial (C), a symmetrically loaded gear belt (GB), and an anterior-loaded gear vest (ALV). Gear conditions had 9.07 kg of additional mass. Motion capture and insole force sensors were used to collect data while participants walked on …

2021 - The Second Annual Fall Symposium Of Student Scholars

Symposium of Student Scholars Program Books

The full program book from the Fall 2021 Symposium of Student Scholars, held on November 18, 2021. Includes abstracts from the presentations and posters.

Arginine-Rich Polypeptides Are Potent Inhibitors Of Human Papillomavirus Infection And Powerful Tools To Investigate Viral Attachment And Entry, Jesse Mckay Young

Biomedical Sciences ETDs

HPV is the most common sexually transmitted infection. It is estimated that 80% of sexually active adults will contract an HPV infection. Thus, there is a significant need for low-cost and easily distributable HPV antivirals that can be used alongside vaccines to combat infection. Herein I have identified protamine sulfate (PS) as a potent microbicide against HPV infection. PS was agnostic to genotype and efficacious pre and post HPV exposure. PS application topically reduced HPV internalization by altering epidermal growth factor receptor (EGFR) signaling and suppressed EGFR-stimulated HPV entry. Our preliminary data also suggest that heparin binding epidermal growth factor …

Β-Hydroxy-Β-Methylbutyrate Supplementation Promotes Antitumor Immunity In An Obesity Responsive Mouse Model Of Pancreatic Ductal Adenocarcinoma, Michael F. Coleman, Kristyn A. Liu, Alexander J. Pfeil, Suhas K. Etigunta, Xiaohu Tang, Salvador Fabela, Et. Al.

Michigan Tech Publications, Part 1

Pancreatic cancer (PDAC) is a deadly disease, exacerbated by obesity, which lacks effective therapeutic interventions. Most PDAC has a limited response to immune- and chemotherapy. Treating PDAC is made additionally challenging by the rapid emergence of muscle wasting and cachexia, which predict poor response to several therapies. We have found that dietary supplementation with β-hydroxy-β-methylbutyrate promotes immunosurveillance in PDAC tumors and protects muscle. This dietary supplement has the potential to be an important adjuvant in PDAC therapy, opening the doors to immunotherapy response.

Biodiversity And Spatial Heterogeneity In Semi-Natural Grasslands In A Mountain Area In Slovakia, Masae Shiyomi, N. Gáborèík, H. Koizumi, A. Javorkova, E. Uhliarova, O. Jezikova

IGC Proceedings (1977-2023)

The spatial pattern of vegetation in the following 3 semi-natural grasslands in Banska Bystrica, Slovakia, was observed in August, 1998: (1) a grassland sown with improved herbage plants after plowing in 1991, (2) a grassland oversown with improved herbage plants in 1991, and (3) a natural grassland without any treatment at the time of establishment. A new method of measuring vegetation was adopted: in each grassland, 50 quadrats 50 cm × 50 cm, composed of 4 smaller cells 25 cm × 25 cm, were set up, and all the species in each cell were recorded. The sown grassland displayed the …

Optimum Area Of Semi-Natural Grassland To Maintain Maximum Butterfly And Avian Species Richness In Japan, A. Shoji, K. Kohyama, H. Sasaki

IGC Proceedings (1977-2023)

To evaluate the optimum area of semi-natural grassland to maintain maximum butterfly and avian species richness in Japan, digitalized grid data of butterfly and avian distribution, as well as vegetation distribution, throughout the country were used. After obtaining logistic regression models explaining the probabilities of occurrence of each species with semi-natural grassland area and latitude as variables, the optimum value was calculated. The expected maximum species richness of butterflies in the country was the highest in the case of about 40 square kilometers of semi-natural grassland per 100 square kilometers, though the value varied somewhat with latitude. The expected maximum …

Managing Grassy Woodlands: Balancing Production And Conservation Of Resources, John G. Mcivor, Neil D. Macleod, S. Mcintyre

IGC Proceedings (1977-2023)

Eastern Australian eucalypt woodlands are important agricultural areas that have been widely modified during two centuries of European-style use. Despite this they contain important natural resources including significant biodiversity. Long term sustainability of production depends on maintaining resources and management must be for both production and conservation. A research program on four properties in south east Queensland showed the properties were in generally good condition although all had some problems, and has highlighted a number of significant costs and barriers to adopting a more balanced approach to production and conservation.

Species Segregation And Functional Groups In The Hill Country Of New Zealand, I. López, I. Valentine, D. Hedderley, M. G. Lambert

IGC Proceedings (1977-2023)

In the hill country of New Zealand, the soil-sward relationship on hill microrelief was studied. Three categories of slope or microsites were distinguished: low, medium and high. The hypothesis was that soil variables of neighbouring microsites differ, and because of this, there is a segregation of species or functional groups of species between the microsites. Soil features, botanical composition and total annual yield were measured in the slope categories in two similar paddocks; one of which had received long-term phosphorus fertilisation and a non-fertilised paddock. ANOVA, cluster analysis and canonical variate analysis were performed on the data. Unsaturated hydraulic conductivity, …

Convergence Properties Of Solutions Of A Length-Structured Density-Dependent Model For Fish, Geigh Zollicoffer

Rose-Hulman Undergraduate Mathematics Journal

We numerically study solutions to a length-structured matrix model for fish populations in which the probability that a fish grows into the next length class is a decreasing nonlinear function of the total biomass of the population. We make conjectures about the convergence properties of solutions to this equation, and give numerical simulations which support these conjectures. We also study the distribution of biomass in the different age classes as a function of the total biomass.

Coyote Management In San Francisco, Matthew Greer

Master's Projects and Capstones

As cities in North America grow, coyotes have become progressively more important species in urban ecosystems. Moreover, as coyotes increasingly use these urban spaces, human-coyote conflicts have become more common, creating a need for new management strategies. This paper will explore how the city of San Francisco could create a new coyote management plan for its highly visible coyote population. San Francisco has had a persistent coyote population since the early 2000s (Todd, 2018). Currently, the coyote population is close to 100 individuals and is still growing (J. Young, Presidio Trust, pers. comm.). To explore this topic a literature review …

Joint Management Of Upland & Aquatic Habitat For The California Red-Legged Frog & California Tiger Salamander, Kyle E. Verblaauw

Master's Projects and Capstones

As federally and state protected amphibians, the California tiger salamander (Ambystoma californiense) and the California red-legged frog (Rana draytonii) are recipients of ample management focus. Both species face a variety of threats, including habitat loss and alteration, introduction of non-native species, spread of disease, and effects of climate change. While management plans for the California tiger salamander and California red-legged frog exist, they frequently do not consider both species in tandem and often contain multiple shortcomings. This document aims to address the shortfalls of current management by providing practical recommendations for jointly managing the upland and …

Farnesol Secretion As A Possible Driving Force For Maintaining Candida Albicans As A Diploid, Kenneth Nickerson, Cory Boone, Kory Parker

Kenneth Nickerson Papers

Candida albicans is a pathogenic dimorphic fungus which is invariably found as a diploid in patients. C. albicans secretes the sesquiterpene farnesol both as a quorum sensing molecule which blocks the yeast to hypha conversion and as a virulence factor for pathogenicity. 20-25 μM farnesol kills other competing yeasts and fungi, often by triggering apoptosis, and yet wild type diploid C. albicans tolerates 300-500 μM farnesol. The recent availability of 10 haploid strains of C. albicans (5 mating type aand 5 mating type α) allowed us to compare their production of and sensitivity to farnesol. On average, the heterozygous diploid …

A Protocol For Rapid And Parallel Isolation Of Myocytes And Non-Myocytes From Multiple Mouse Hearts., Gabriella E Farrugia, Michael A Mclellan, Kate L Weeks, Aya Matsumoto, Charles D Cohen, Crisdion Krstevski, Taylah L Gaynor, Adam C Parslow, Julie R Mcmullen, Alexander R Pinto

Faculty Research 2021

This protocol features parallel isolation of myocytes and non-myocytes from murine hearts. It was designed with considerations for (1) time required to extract cardiac cells, (2) cell viability, and (3) protocol scalability. Here, a peristaltic pump and 3D-printed elements are combined to perfuse the heart with enzymes to dissociate cells. Myocytes and non-myocytes extracted using this protocol are separated by centrifugation and/or fluorescence-activated cell sorting for use in downstream applications including single-cell omics or other bio-molecular analyses. For complete details on the use and execution of this protocol, please refer to McLellan et al. (2020).

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 …

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 …

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 …

Cgrp-Driven Lateralization Of Pain Modulation By The Central Amygdala, Heather Allen

Electronic Theses and Dissertations

The central amygdala (CeA) is a bilateral, mid limbic brain region involved in the processing of pain and emotion. Interestingly, the left and right CeA are functionally lateralized in the context of bladder pain, with the left and right CeA having opposing effects on bladder pain-like behavior. However, the specific mechanisms driving these divergent functions are unknown. Nociceptive signals from the bladder are relayed to the CeA via projection neurons in the parabrachial nucleus (PBN) that express high levels of calcitonin gene-related peptide (CGRP). In these studies, we investigated the influence of PBN CGRP signaling in the left and right …

Real-Time Monitoring Of Cell Death Progress Using Capacitance Spectroscopy, Suyang Wu

Electronic Theses and Dissertations

Biologics, including the monoclonal antibody (mAb), has experienced rapid development in the last decade. However, the price of biologics is often prohibitively high because of the low process efficiency. Delaying the inevitable cell death improves the productivity of upstream bioprocessing, whose success relies on monitoring the cell death onset that indicates the timing for preventive actions.

This study proposes to develop a real-time monitoring model that quantifies the dying cell percentage in lab-scale bioreactors using capacitance spectroscopy. The capacitance spectroscopy contains cell death-related information due to various physical properties changes during the cell death process, e.g., cytoplasmic conductivity change. The …

Understanding Snow Leopard (Panthera Uncia) Population Structure, Diet, And Human-Wildlife Dimensions Using Noninvasive Genetic Approaches, Charlotte Hacker

Electronic Theses and Dissertations

Snow leopards (Panthera uncia) are a large cat endemic to the mountains of Central Asia. Despite their status as a flagship species, there are numerous knowledge gaps surrounding their population status, dietary ecology, and relationship with humans. Such knowledge gaps are prohibitive for effective conservation action for the species. Snow leopards are threatened by habitat loss, decreased prey availability, retaliatory killings, and large-scale negative impacts associated with climate change. In order to help bridge these gaps, noninvasive genetic methodologies were deployed in this work across several disciplines. Population genetic metrics were garnered at local, regional, and range-wide scales, …

Analysis Of Spore Shape Determination In Streptomyces, Ning Sun

Electronic Theses and Dissertations

Streptomycetes are Gram-positive, soil-dwelling bacteria that possess a complex life cycle with the alternation of vegetative mycelium, aerial mycelium, and spores. Streptomyces. coelicolor spore maturation is a complex process that involves spore shape metamorphosis from cylindrical pre-spores into ellipsoid spores, but the details of this process have remained enigmatic. Previously, our lab identified a novel gene ssdA that might play a role in spore shape determination using a transposon-based insertion mutagenesis in S. coelicolor. In this study, I isolated a S. coelicolor ssdA-null mutant that showed increased colony hydrophobicity and misshapen spores in sizes and shapes, confirming the …

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 …

Usp11 And Usp7 Deubiquitinases Regulate Sprtn Auto-Proteolysis And Sprtn-Mediated Dna-Protein Crosslink Repair, Megan C. Perry

Theses & Dissertations

DNA repair pathways that recognize and remove damaged DNA are vital for maintenance of genomic stability and prevention of tumorigenesis. Conversely, these pathways may be robust in tumor cells, thus diminishing the anti-cancer potential of available therapies. DNA-protein crosslinks (DPCs) are particularly deleterious DNA adducts that occur when proteins become irreversibly covalently bound to the DNA. DPCs represent a diverse group of lesions, as any protein can be crosslinked to the DNA duplex by non-specific crosslinking agents like reactive aldehydes and radiation. Additionally, functional DNA-binding proteins such as topoisomerases may become permanently crosslinked to DNA ends by abortive enzymatic processes …

Integrative Analysis Of Multi-Omics Kinome Data And Virtual Screening Of Identified Targets With Pan-Cancer Application, Siddesh Southekal

Theses & Dissertations

Cancer is a heterogeneous disease characterized by the uncontrolled growth and dissemination of abnormal cells. Unfortunately, it is also challenging to treat due to the heterogeneous nature of the tumors and the lack of known drugs that are effective against all tumor subpopulations.

The human protein kinases represent an essential and diverse family of enzymes and are often dysregulated in cancer. The human kinome comprises only around 2% of all coding genes of the human genome but phosphorylates about 30% of cellular proteins critical for regulating various biological processes such as cell proliferation, cell cycle progression, apoptosis, motility, growth, differentiation, …

Molecular Investigation Into The Biologic And Prognostic Elements Of Peripheral T-Cell Lymphoma With Regulators Of Tumor Microenvironment Signaling Explored In Model Systems, Tyler Herek

Theses & Dissertations

Peripheral T-cell lymphoma (PTCL) is heterogenous group of mature T-cell neoplasms characterized by distinctive transcriptional and genetic lesions. Herein, we investigated DNMT3A mutations in angioimmunoblastic T-cell lymphoma (AITL, n = 176) and novel molecular subtypes (i.e., PTCL-GATA3, n = 61 and PTCL-TBX21, n = 80) within PTCL- NOS and observed significant biological and prognostic differences associated with DNMT3A mutations. DNMT3A-mutated PTCL-TBX21 cases showed inferior overall survival (OS; p < 0.005), with DNMT3A mutations (DNMT3A-MT) skewed toward the methyltransferase domain and in the dimerization domain (S881-R887). Transcriptional profiling demonstrated significant enrichment of activated CD8⁺ T-cell cytotoxic gene signatures in the tumor microenvironment of DNMT3A-MT PTCL-TBX21 cases. Genome-wide methylation analysis of DNMT3A-R882/Q886 versus wild-type in PTCL-TBX21 cases demonstrated hypomethylation in target genes regulating T-cytotoxic genes, TCR …

Metabolic Heterogeneity And The Roles Of Cody And Ccpa In Central Metabolism And S. Aureus Biofilm Formation., Logan L. Bulock

Theses & Dissertations

Staphylococcus aureus is a metabolically versatile human pathogen, causing disease in many areas of the body. Its versatility can be attributed to the fact that it utilizes a variety of tools to adapt to many different environments, including toxins to scavenge from the host and multiple transporters to compete for its preferred carbon sources. S. aureus can also survive in harsh conditions through biofilm development, which are notoriously recalcitrant to antibiotics and immune defenses. Biofilms exhibit marked heterogeneity, with division of labor for production of matrix components and differential gene expression among various niches within the biofilm.

In this study, …

Nuclear Receptor Coactivator 3 In Endoplasmic Reticulum Stress And Stress Granule Dynamics In Pancreatic Cancer, Andrew Kisling

Theses & Dissertations

Pancreatic cancer is predicted to be the second-leading cause of cancer-related deaths within the next decade. Nuclear receptor coactivator 3 (NCOA3/SRC3/AIB1) regulates an array of metabolic and signaling pathways and has been established by our group and others as a critical regulator pancreatic cancer progression and metastasis. A recent study demonstrated NCOA3 regulation by the IRE1α-XBP1 axis of the unfolded protein response (UPR), suggesting a link between NCOA3 and cellular stress management. Furthermore, NCOA3 has been shown to directly bind to a scaffolding protein of stress granules (SGs). Since SG assembly is regulated by the UPR, we hypothesized that NCOA3 …

Development Of Polymeric Cxcr4 Targeting Carriers For Sirna Delivery To Treat Acute Kidney Injury, Weimin Tang

Theses & Dissertations

Acute kidney injury (AKI) is a major kidney disease that is characterized by a sudden loss of renal function which manifests by a decrease in urine output and an increase in serum creatinine. AKI is a global healthcare burden associated with high morbidity, mortality, and increasing cost. Currently there are no effective pharmacological treatments available. Apoptosis induced by p53 has been demonstrated as an important pathological mechanism for the development of AKI. Meanwhile, CXCR4/SDF-1 axis has been associated with the inflammation during AKI, and CXCR4 is overexpressed on injured tubules. This dissertation hypothesized that polycations with CXCR4 targeting ability could …

Development Of A Muc16-Targeted Near-Infrared Antibody Probe For Fluorescence-Guided Surgery Of Pancreatic Cancer, Madeline T. Olson

Theses & Dissertations

Pancreatic cancer (PDAC) is an extremely lethal disease with an overall survival rate of 10%. Surgery remains the only potentially curative treatment option, but resections are complicated by infiltrative disease, proximity of critical vasculature, peritumoral inflammation, and dense stroma. Surgeons are limited to tactile and visual cues to differentiate cancerous tissue from normal tissue. Furthermore, translating preoperative images to the intraoperative setting poses additional challenges for tumor detection, and can result in undetected and unresected lesions. Thus, PDAC has high rates of incomplete resections, and subsequently, disease recurrence. Fluorescence-guided surgery (FGS) has emerged as a method to improve intraoperative detection …

The Rotator Cuff Tendon-To-Bone Interface: Maturation, Aging, And 3d Bioprinting For Regeneration, Xiping Jiang

Theses & Dissertations

Rotator cuff tendon injuries often occur at the tendon-to-bone interface (i.e., enthesis) area with a high prevalence for the elderly population. In addition, regeneration of the gradient structure of the enthesis is still a significant clinical challenge. Our studies aim to identify the histological, molecular, and biomechanical alterations of the rotator cuff enthesis with maturation and aging, and develop a novel therapeutic method using three-dimensional (3D) bioprinting technique to regenerate a functional enthesis. Striking variations of the entheses were observed both histologically and biomechanically during the maturation process. The histological features did not show many differences at the insertion site …