Digital Commons Network^™

Eggers, Daryl K., San Jose State University

Emeritus and Retired Faculty Biographies

University of California, San Francisco, Pharmacology, PhD 1997

University of California, Berkeley, Chemical Engineering, MS 1987

Rose-Hulman Institute of Technology, Chemical Engineering, BS 1981

Immune Checkpoint Inhibitors: A Narrative Review On Pd-1/Pd-L1 Blockade Mechanism, Efficacy, And Safety Profile In Treating Malignancy, Ian Brandon

All Publications

Checkpoint inhibitors have been implicated in the treatment of several cancers due to their ability to exploit the immune system's regulatory pathways. This article serves to emphasize the importance of these immunotherapeutic agents and provide further insight into their mechanisms, efficacies, and safety profiles. The main agents in question include programmed cell death protein 1 (PD-1) and programmed death ligand 1 (PD-L1). Several literature sources were found to assess the use of these inhibitors in cancers involving the lung, breast, and skin. Several peer-reviewed systematic reviews and the outcomes of clinical trials are combined within this article to support the …

Genome-Wide Screening Identifies Trim33 As An Essential Regulator Of Dendritic Cell Differentiation, Ioanna Tiniakou, Pei-Feng Hsu, Lorena S Lopez-Zepeda, Görkem Garipler, Eduardo Esteva, Nicholas M Adams, Geunhyo Jang, Chetna Soni, Colleen M Lau, Fan Liu, Alireza Khodadadi-Jamayran, Tori C Rodrick, Drew Jones, Aristotelis Tsirigos, Uwe Ohler, Mark T Bedford, Stephen D Nimer, Vesa Kaartinen, Esteban O Mazzoni, Boris Reizis

Faculty, Staff and Student Publications

The development of dendritic cells (DCs), including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs), is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected Flt3L-driven DC differentiation using CRISPR-Cas9-based screening. Genome-wide screening identified multiple regulators of DC differentiation including subunits of TSC and GATOR1 complexes, which restricted progenitor growth but enabled DC differentiation by inhibiting mTOR signaling. An orthogonal screen identified the transcriptional repressor Trim33 (TIF-1γ) as a regulator of DC differentiation. Conditional targeting in vivo revealed an essential role of Trim33 in the development of all DCs, but not of monocytes …

In Silico And In Vitro Study Of Isoquercitrin Against Kidney Cancer And Inflammation By Triggering Potential Gene Targets, Safia Iqbal, Md Rezaul Karim, Shahnawaz Mohammad, Jong Chan Ahn, Anjali Kariyarath Valappil, Ramya Mathiyalagan, Deok-Chun Yang, Dae-Hyo Jung, Hyocheol Bae, Dong Uk Yang

Faculty, Staff and Student Publications

Kidney cancer has emerged as a major medical problem in recent times. Multiple compounds are used to treat kidney cancer by triggering cancer-causing gene targets. For instance, isoquercitrin (quercetin-3-O-β-d-glucopyranoside) is frequently present in fruits, vegetables, medicinal herbs, and foods and drinks made from plants. Our previous study predicted using protein-protein interaction (PPI) and molecular docking analysis that the isoquercitrin compound can control kidney cancer and inflammation by triggering potential gene targets of IGF1R, PIK3CA, IL6, and PTGS2. So, the present study is about further in silico and in vitro validation. We performed molecular dynamic (MD) simulation, gene ontology (GO), Kyoto …

Diverse Habitats Shape The Movement Ecology Of A Top Marine Predator, The White Shark Carcharodon Carcharias, Oliver J. D. Jewell, Taylor K. Chapple, Salvador J. Jorgensen, Paul Kanive, Jerry H. Moxley, James R. Tweedley, Scot Anderson, Barbara A. Block, Adrian C. Gleiss

Marine Science Faculty Publications and Presentations

An animal's movement is influenced by a plethora of internal and external factors, leading to individual- and habitat-specific movement characteristics. This plasticity is thought to allow individuals to exploit diverse environments efficiently. We tested whether the movement characteristics of white sharks Carcharodon carcharias differ across ontogeny and among habitats along the coast of Central California. In doing so, we elucidate how changes in internal state (physiological changes coinciding with body size) and external environments (differing seascapes and/or diel phases) shape the movement of this globally distributed predator. Twenty-one white sharks, from small juveniles to large adults, were equipped with motion-sensitive …

Evaluating The Effectiveness Of Dormant Season Grazing To Reduce Cheatgrass And Its Effect On Biodiversity, Curtis L. Drake

Theses and Dissertations

Invasion of cheatgrass (Bromus tectorum L.) into sagebrush steppe communities threatens the survival of these at-risk ecosystems. One tool available to combat cheatgrass invasion is dormant season grazing. This study investigates the effectiveness of dormant season cattle grazing to reduce cheatgrass abundance in two high-elevation sagebrush steppe communities in southeastern Idaho, as well as the impact of dormant season grazing on plant species biodiversity. Our experiment utilized a randomized complete block design with four grazing treatments – ungrazed, fall-grazed, spring-grazed, and a combination of spring- and fall-grazed. We used an ANOVA standard least squares procedure to determine differences in biodiversity …

Association Of F. Alocis And D. Pneumosintes With Periodontitis Disease Severity And Red Complex Bacteria, Hawaabi F.M. Shaikh, Pratima U. Oswal, Manohar Suresh Kugaji, Sandeep S. Katti, Kishore Gajanan Bhat, Eswar Kandaswamy, Vinayak M. Joshi

School of Dentistry Faculty Publications

Oral biofilms are considered the principal etiological agent in the development of periodontitis. Novel species that may contribute to periodontitis and dysbiosis have been identified recently. The study aims to evaluate the presence of F. alocis and D. pneumosintes in healthy and diseased patients and their association with clinical parameters and with red complex bacteria. The study included 60 subjects, with 30 patients each in the healthy and periodontitis groups. The clinical parameters were noted, and samples were subjected to DNA extraction followed by a polymerase chain reaction. Statistical analysis was performed using the Graph Pad Prism software. Results: F. …

Truman Scholar Travels Globe To Study Conservation, Erin Garrett

University of Mississippi News

OXFORD, Miss. – From across the world, University of Mississippi biology major Christian Boudreaux received a life-changing Zoom call from Chancellor Glenn Boyce last week. Despite Zanzibar's spotty internet service, the message was clear: Boudreaux had won a coveted Truman Scholarship.

Capn2 Correlates With Insulin Resistance States In Pcos As Evidenced By Multi-Dataset Analysis, Xi Luo, Yunhua Dong, Haishan Zheng, Xiaoting Zhou, Lujuan Rong, Xiaoping Liu, Yun Bai, Yunxiu Li, Ze Wu

Faculty, Staff and Student Publications

OBJECTIVE: IR emerges as a feature in the pathophysiology of PCOS, precipitating ovulatory anomalies and endometrial dysfunctions that contribute to the infertility challenges characteristic of this condition. Despite its clinical significance, a consensus on the precise mechanisms by which IR exacerbates PCOS is still lacking. This study aims to harness bioinformatics tools to unearth key IR-associated genes in PCOS patients, providing a platform for future therapeutic research and potential intervention strategies.

METHODS: We retrieved 4 datasets detailing PCOS from the GEO, and sourced IRGs from the MSigDB. We applied WGCNA to identify gene modules linked to insulin resistance, utilizing IR …

Application Of High-Deflection Strain Gauges To Characterize Spinal-Motion Phenotypes Among Patients With Clbp, Spencer Alan Baker

Theses and Dissertations

Chronic low back pain (CLBP) is a nonspecific and persistent ailment that entails many physiological, psychological, social, and economic consequences for individuals and societies. Although there is a plethora of treatments available to treat CLBP, each treatment has varying efficacy for different patients, and it is currently unknown how to best link patients to their ideal treatment. However, it is known that biopsychosocial influences associated with CLBP affect the way that we move. It has been hypothesized that identifying phenotypes of spinal motion could facilitate an objective and repeatable method of determining the optimal treatment for each patient. The objective …

Shots Fired, Shots Refused: Scientific, Ethical & Legal Challenges Surrounding The U.S. Military's Covid-19 Vaccine Mandate, Shawn Mckelvy, L. William Uhl, Armand Balboni

St. Mary's Law Journal

The COVID-19 pandemic provided uncertain and challenging circumstances under which to lead a nation and the military that protects it. Those in charge and in command faced unique challenges—scientific, ethical, and legal—at our various levels of government to both keep people safe while keeping government and society functioning. While there were many successes to celebrate, there are also many criticisms for how this “whole-of-government approach” may have degraded some of our most cherished liberties along the way. The authors focus on the U.S. military’s vaccine mandate and propose military leaders may have failed to fully consider the evolving science, weigh …

Serum Neuroactive Metabolites Of The Tryptophan Pathway In Patients With Acute Phase Of Affective Disorders, Yanli Li, Leilei Wang, Junchao Huang, Ping Zhang, Yanfang Zhou, Jinghui Tong, Wenjin Chen, Mengzhuang Gou, Baopeng Tian, Wei Li, Xingguang Luo, Li Tian, L Elliot Hong, Chiang-Shan R Li, Yunlong Tan

Faculty, Staff and Student Publications

BACKGROUND: Many studies showed disrupted tryptophan metabolism in patients with affective disorders. The aims of this study were to explore the differences in the metabolites of tryptophan pathway (TP) and the relationships between TP metabolites and clinical symptoms, therapeutic effect in patients with bipolar disorder with acute manic episode (BD-M), depressive episode (BD-D) and major depressive disorder (MDD).

METHODS: Patients with BD-M (n=52) and BD-D (n=39), MDD (n=48) and healthy controls (HCs, n=49) were enrolled. The serum neuroactive metabolites levels of the TP were measured by liquid chromatography-tandem mass spectrometry. Hamilton Depression Scale-17 item (HAMD-17) and Young Mania Rating Scale …

Combined Deletion Of Men1, Atrx And Pten Triggers Development Of High-Grade Pancreatic Neuroendocrine Tumors In Mice, Mary Esmeralda Fuentes, Xiaoyin Lu, Natasha M Flores, Simone Hausmann, Pawel K Mazur

Faculty, Staff and Student Publications

Pancreatic neuroendocrine tumors (PanNETs) are a heterogeneous group of tumors that exhibit an unpredictable and broad spectrum of clinical presentations and biological aggressiveness. Surgical resection is still the only curative therapeutic option for localized PanNET, but the majority of patients are diagnosed at an advanced and metastatic stage with limited therapeutic options. Key factors limiting the development of new therapeutics are the extensive heterogeneity of PanNETs and the lack of appropriate clinically relevant models. In that context, genomic sequencing of human PanNETs revealed recurrent mutations and structural alterations in several tumor suppressors. Here, we demonstrated that combined loss of MEN1, …

Restore Texas Land: A Proposal To Utilize Emission Reduction Credits To Fund The Railroad Commission Of Texas' Well Plugging Initiative, George Coates Roberts

St. Mary's Law Journal

No abstract provided.

Understanding The Mechanism Behind Hfip's Effect On Diastereomeric Separation Of Oligonucleotides, Ian Neidigh

Honors Theses

The goal of this research was to determine the mechanism behind 1,1,1,3,3,3-hexafluoroisopropanol's (HFIP0 ability to suppress the separation of oligonucleotide diastereomers. This was accomplished by selecting different molecules that were like HFIP but differed in specific ways such as polarity, number and type of halogen(s), alcohol group location, carbon chain length, hydrophobicity, and chao/kosmotropicity. These molecules replaced HFIP in an IPRP chromatography method to determine if splitting of the diastereomers was observed and then they would becompared to HFIP's effect. Viscosity tests were to run to acquire quantitative data to determine chao/kosmotropicity. No decisive trend among a single factor was …

My Journey In Researching Depression Among Black People: Experiences Of A Researcher In A Sensitive Study, Brightness L. Kgatla

The Qualitative Report

The interest in qualitative research on mental health within Black communities is rapidly growing. However, there are still debates on the conceptualization of depression among the Black community. This paper focuses on the researcher’s experiences as a young Black South African experiencing depression, and their reflections on interpretivist qualitative research focused on the realities of Black South African youth experiencing depression. The paper highlights the importance of reflexivity in a qualitative study and how the topics researched by a Black South African experiencing depression which is still considered a taboo within some parts of the Black community. If a researcher …

Identification Of Climate Change And Its Impact On Maize (Zea Mays L.) Production In Majalengka Regency, Ruminta, Maysix Lumbantobing, Fiky Yulianto Wicaksono

Jurnal Kultivasi

Maize is one of the multipurpose crop whose yields can be affected by climate change. Climate change includes increasing air temperature, increasing sea levels, and changes in rainfall can be a threat and cause a decrease in maize yields. This could be caused by climate change factors. This research aims to identify climate change and analyze the correlation between climate change and maize production in the Majalengka Regency. Maize plantations in the 26 sub-districts are still fluctuative. The method used in this research is quantitative descriptive using trend analysis and correlation. The data used include temperature, rainfall, harvested area, production, …

Growth And Yield Response Of Watani Wado Job's Tears (Coix Lacryma-Jobi L.) To The Application Frequency Of Phosphate Fertilizer And Paclobutrazol In Different Growing Seasons, Arifa Syahanna Mahdya, Rizka Farahdillah, Muhamad Kadapi, Tati Nurmala

Jurnal Kultivasi

Job's tears (Coix lacryma-jobi L.) is a carbohydrate source functional food crop that can be developed as a substitute for rice. This study aims to determine the best application frequency of phosphate (P) fertilizer and paclobutrazol for supporting the growth and yield of job's tears in both rainy and dry seasons. The research was conducted from November 2021 - November 2022 at the Ciparanje research station and Laboratory Centre Universitas Padjadjaran, Jatinangor, Sumedang. The experiment used a randomized block design (RBD) consisting of P fertilizer application frequency (once, twice, and thrice) and paclobutrazol application frequency (once, twice, and thrice) and …

Successful Shoot Tip Grafting Of Cacao (Theobroma Cacao L.) Due To The Application Of Plant Growth Regulators On Various Concentrations, Wulan Kumala Sari, Nia Putri Utami

Jurnal Kultivasi

Cacao plays an important role in the Indonesia economy. Therefore, its production and area expansion have to increase to achieve maximum cacao productivity by the quality and superior cacao clones. Shoot tip grafting is one of the propagation methods to obtain superior cacao plants by applying Plant Growth Regulators (PGRs). Research on the effect of several PGRs with various concentrations on cacao (Theobroma cacao L.) shoot tip grafting was conducted at the Integrated Innovation Farmer Group, Belubus, Sungai Talang Village, Guguak District, Lima Puluh Kota Regency, West Sumatra from February until June 2022. This study aimed to determine the interaction …

The Effectiveness Of Different Formulations Of Glyphosate Herbicides Under Simulated Rainfall Conditions In Controlling Various Weeds, Syifa Fajriani, Denny Kurniadie, Uum Umiyati

Jurnal Kultivasi

Herbicide effectiveness is affected by herbicide formulation, rainfall, and weed type. Differences in glyphosate salt formulations and 2,4 D amine mixtures may result in variations in the herbicide's ability to wash off the herbicide due to rain. The aim of this study was to assess the effectiveness of different glyphosate herbicide formulations under varying rainfall in controlling various weeds. The experiment took place in a controlled greenhouse environment, utilizing a split plot experimental design with four replications. The main plot was assigned to six different rainfall timings: 0 hours after application (HAA), 1 HAA, 2 HAA, 3 HAA, 4 HAA, …

Water, Sanitation, And Hygiene Infrastructure And Resources In Schools In Belize During The Covid-19 Pandemic, 2021-2023, Anh N Ly, Kelsey Mcdavid, Christina Craig, Dian Maheia, Yolanda Gongora, Alexandra Medley, Francis Morey, Russell Manzanero, Gerhaldine Morazan, Allison Lino, Vickie Romero, Rosalva Blanco, Kanako Ishida, Matthew Lozier, Kristy O Murray

Faculty, Staff and Students Publications

Access to water, sanitation, and hygiene (WASH) resources in schools is critical for disease prevention and control, especially during public health emergencies. In Belize, systematic, national data on WASH in schools are needed to inform public health decisions and interventions. From December 2021 to January 2022, a national survey was sent electronically to government and government-aided primary and secondary schools in Belize (N = 308) to gather information on WASH services. From the survey, 12 pilot schools were selected based on the highest self-reported need for WASH resources to participate in additional evaluation and intervention, which included environmental nudges, supplemental …

Existing Challenges And Possible Pathways For Case Success In Climate Litigation With Human Rights Claims, Daniel Ziebarth

St. Mary's Law Journal

No abstract provided.

Akap12 Upregulation Associates With Pde8a To Accelerate Cardiac Dysfunction, Hanan Qasim, Mehrdad Rajaei, Ying Xu, Arfaxad Reyes-Alcaraz, Hala Y Abdelnasser, M David Stewart, Satadru K Lahiri, Xander H T Wehrens, Bradley K Mcconnell

Faculty, Staff and Students Publications

BACKGROUND: In heart failure, signaling downstream the β2-adrenergic receptor is critical. Sympathetic stimulation of β2-adrenergic receptor alters cAMP (cyclic adenosine 3',5'-monophosphate) and triggers PKA (protein kinase A)-dependent phosphorylation of proteins that regulate cardiac function. cAMP levels are regulated in part by PDEs (phosphodiesterases). Several AKAPs (A kinase anchoring proteins) regulate cardiac function and are proposed as targets for precise pharmacology. AKAP12 is expressed in the heart and has been reported to directly bind β2-adrenergic receptor, PKA, and PDE4D. However, its roles in cardiac function are unclear.

METHODS: cAMP accumulation in real time downstream of the β2-adrenergic receptor was detected for …

Influence Of Rna Circularity On Target Rna-Directed Microrna Degradation, Federico Fuchs Wightman, Jerónimo Lukin, Sebastián A Giusti, Michael Soutschek, Laureano Bragado, Berta Pozzi, María L Pierelli, Paula González, Juan P Fededa, Gerhard Schratt, Rina Fujiwara, Jeremy E Wilusz, Damián Refojo, Manuel De La Mata

Faculty, Staff and Students Publications

A subset of circular RNAs (circRNAs) and linear RNAs have been proposed to 'sponge' or block microRNA activity. Additionally, certain RNAs induce microRNA destruction through the process of Target RNA-Directed MicroRNA Degradation (TDMD), but whether both linear and circular transcripts are equivalent in driving TDMD is unknown. Here, we studied whether circular/linear topology of endogenous and artificial RNA targets affects TDMD. Consistent with previous knowledge that Cdr1as (ciRS-7) circular RNA protects miR-7 from Cyrano-mediated TDMD, we demonstrate that depletion of Cdr1as reduces miR-7 abundance. In contrast, overexpression of an artificial linear version of Cdr1as drives miR-7 degradation. Using plasmids that …

"In Our Community, We Normalize Pain": Discussions Around Menstruation And Uterine Fibroids With Black Women And Latinas, Minerva Orellana, Karen N Dsouza, Jane Q Yap, Abhirami Sriganeshan, M Elena Jones, Charis Johnson, Megan Allyse, Sateria Venable, Elizabeth A Stewart, Felicity Enders, Joyce E Balls-Berry

2020-Current year OA Pubs

BACKGROUND: Uterine fibroids are non-cancerous neoplasms that arise from the uterus affecting over 75% of women. However, there is a disparity with Black women having an increased prevalence of nearly 80%. Black women also experience increased symptom burden, including younger age at the time of diagnosis and increased number and volume of fibroids. Less is known about other ethnoracially diverse women such as Latinas and the potential cultural impacts on fibroid burden and treatment.

METHODS: Community engagement studios were conducted to facilitate discussions with stakeholders on their uterine fibroid and menstruation experience. We recruited Black women (n = 6) diagnosed …

Heterogeneity And Plasticity Of The Naïve Cd4+ T Cell Compartment, Alia Sajani

Dartmouth College Ph.D Dissertations

Recent studies have illuminated unexpected heterogeneity in the naïve T cell compartment. Using single cell RNA sequencing of mouse naïve CD4⁺ T cells, we identified 5 unique transcriptional subsets within the naïve CD4⁺ T cell compartment. These include a quiescence cluster (T^Q) marked by Klf2, Klf6, Jun and Btg2, a memory-like cluster (T^MEM) marked by Ccr7, Il7r and Tcf7, a TCR reactive cluster (T^TCR) marked by Cd5, Cd6 and Nr4a1, an IFN responsive cluster (T^IFN) marked by Stat1, Irf7 and Ifit1 and …

Structural Basis Of Dna Crossover Capture By Escherichia Coli Dna Gyrase, Marlène Vayssières, Nils Marechal, Long Yun, Brian Lopez Duran, Naveen Kumar Murugasamy, Jonathan M Fogg, Lynn Zechiedrich, Marc Nadal, Valérie Lamour

Faculty, Staff and Students Publications

DNA supercoiling must be precisely regulated by topoisomerases to prevent DNA entanglement. The interaction of type IIA DNA topoisomerases with two DNA molecules, enabling the transport of one duplex through the transient double-stranded break of the other, remains elusive owing to structures derived solely from single linear duplex DNAs lacking topological constraints. Using cryo–electron microscopy, we solved the structure of Escherichia coli DNA gyrase bound to a negatively supercoiled minicircle DNA. We show how DNA gyrase captures a DNA crossover, revealing both conserved molecular grooves that accommodate the DNA helices. Together with molecular tweezer experiments, the structure shows that the …

Miniature Battery-Free Epidural Cortical Stimulators, Joshua E Woods, Amanda L Singer, Fatima Alrashdan, Wendy Tan, Chunfeng Tan, Sunil A Sheth, Sameer A Sheth, Jacob T Robinson

Faculty, Staff and Student Publications

Miniaturized neuromodulation systems could improve the safety and reduce the invasiveness of bioelectronic neuromodulation. However, as implantable bioelectronic devices are made smaller, it becomes difficult to store enough power for long-term operation in batteries. Here, we present a battery-free epidural cortical stimulator that is only 9 millimeters in width yet can safely receive enough wireless power using magnetoelectric antennas to deliver 14.5-volt stimulation bursts, which enables it to stimulate cortical activity on-demand through the dura. The device has digitally programmable stimulation output and centimeter-scale alignment tolerances when powered by an external transmitter. We demonstrate that this device has enough power …

Comics About Organs: Social Support And Graphic Medicine In The Awkward Yeti, Jacob Gibb

Theses and Dissertations

Comic strips have always been a medium for more than humor. Many comic strips published on social media sites address mental health issues. Despite their popularity, the field of graphic medicine, which examines the intersection of health care and comics, has seen little to no examination of how these comics function on social media. Utilizing the popular comic The Awkward Yeti, this research examines how the rhetorical devices of comics make them an ideal medium for communicating about mental health issues and providing social support to social media users. This study conducts a content analysis of 15 Instagram posts from …

Phun With Phages: Discovering Novel Bacteriophages In The Soil, Julia Kutz, Ryan Dodds, Logan Dykstra, Taylor M. Rentschler, Emma Steinhardt, Megan Vangarven, Jacie Vanderwaal, Shayler Vangelder, Byron Noordewier, Sara S. Tolsma

Celebration of Research

We used three bacterial hosts: Mycobacterium smegmatis, Microbacterium foliorum, and Gordonia terrae, to isolate novel bacteriophages from soil samples. We named these phages, created high titer lysates, and purified their DNA genomes. We have archived the high titer lysates at Northwestern College and the University of Pittsburgh. The genomes of three of our phages were sequences at the University of Pittsburgh and we will be sequencing the remaining genomes this summer. Additionally, we are planning to image our phages with transmission electron microscopy at the University of Iowa or Nebraska yet this semester.