Microbiology Commons^™

Trpv1 And Its Co‑Expressed Genes Are Associated With The Progression Of Hepatocellular Carcinoma, Bhuvnesh P. Sharma, Himanshu N. Singh, Sanjay Kumar, Deepak Verma, Deepak Parashar, Murali M. Yallapu, Everardo Cobos, Subhash C. Chauhan, Vivek K. Kashyap

Research Symposium

Background: Hepatocellular carcinoma (HCC) is the most common type of liver cancer. Transient receptor potential vanilloid 1 (TRPV1) is a nonselective Ca²⁺ channel protein widely expressed and plays a significant role in cancer initiation and progression. However, the biological significance of TRPV1 in HCC has not been systematically and comprehensively investigated. This study used deep data mining and transcriptomics analyses to describe the significance of TRPV1 expression and its association with HCC prognosis.

Methods: Download the RNA expression of TRPV1 from the Cancer Genome Atlas (TCGA), Genotype Tissue Expression Atlas (GTEx), Tumor Immune Estimation Resource (TIMER), and the UALCAN …

Impact Of Fresh-Cut Onion Types And Flavonoid Profiles On The Survival Kinetics Of Foodborne Pathogen During Refrigerated Storage, Veerachandra Yemmireddy, Matthew Mancias

School of Earth, Environmental, & Marine Sciences Faculty Publications

This study investigated the effect of onion flavonoid profiles on the growth, survival, and/or death kinetics of foodborne pathogens in fresh-cut onions at 4 °C. Fresh-cut white, yellow, red, and sweet onions were inoculated with separate four-strain cocktail(s) of nalidixic acid-adapted Salmonella spp., Escherichia coli O157:H7, and Listeria monocytogenes achieving a 4 to 5 log CFU g−1. The samples were stored in clam shell containers at 4 °C and 70 ± 2 % relative humidity for 14 days. Additionally, flavonoid profiles were determined on uninoculated control samples stored under similar conditions using standard chromatography techniques, with quercetin derivatives identified as …

Exploring Oxylipins In Host–Microbe Interactions And Their Impact On Infection And Immunity, Robert J. Neff, Christopher D. Radka

Markey Cancer Center Faculty Publications

Plasma lipids are essential components of biological systems, transported through interactions with proteins to maintain cellular functions. These lipids exist in various forms, such as fatty acids, glycerolipids, glycerophospholipids, sphingolipids, sterols, and prenol lipids, derived from dietary intake, adipose tissue, and biosynthesis. While the association between certain fatty acids and cardiovascular diseases has been widely recognized, polyunsaturated fatty acids (PUFAs) exhibit cardioprotective effects, reducing risks of arrhythmias and heart-related mortality. This is due to their role in the production of eicosanoids, which modulate inflammation. Chronic inflammation, particularly in obesity, is significantly influenced by fatty acids, with saturated fatty acids promoting …

Canonical And Non-Canonical Functions Of The Non-Coding Rna Component (Terc) Of Telomerase Complex, Chongwen Cao, Weiyi Gong, Yuanlong Shuai, Sara Rasouli, Qianyun Ge, Anam Khan, Aleksandra Dakic, Nagireddy Putluri, Gennady Shvets, Yun-Ling Zheng, Danyal Daneshdoust, Rani Mahyoob, Jenny Li, Xuefeng Liu

Faculty, Staff and Students Publications

The telomerase complex consists of a protein component (TERT), which has reverse transcriptase activity, and an RNA component (TERC), which serves as a template for telomere synthesis. Evidence is rapidly accumulating regarding the non-canonical functions of these components in both normal or diseased cells. An oligonucleotide-based drug, the first telomerase inhibitor, secured FDA approval in June 2024. We recently summarized the non-canonical functions of TERT in viral infections and cancer. In this review, we expand on these non-canonical functions of TERC beyond telomere maintenance. Specifically, we explore TERC's roles in cellular aging and senescence, immune regulation, genetic diseases, human cancer, …

Multiscale 3d Spatial Analysis Of The Tumor Microenvironment Using Whole-Tissue Digital Histopathology, Daniel Shafiee Kermany, Ju Young Ahn, Matthew Vasquez, Weijie Zhang, Lin Wang, Kai Liu, Zhan Xu, Min Soon Cho, Wendolyn Carlos-Alcalde, Hani Lee, Raksha Raghunathan, Jianting Sheng, Xiaoxin Hao, Hong Zhao, Vahid Afshar-Kharghan, Xiang Hong-Fei Zhang, Stephen Tin Chi Wong

Faculty, Staff and Students Publications

No abstract provided.

Microbial Source Tracking Protocols For Differentiation Of Fecal Bacteria From Cow, Deer, And Horse, Nika Shams, Michael Beach

Symposium of Student Scholars

Microbial source tracking (MST) attempts to identify specific animal sources of fecal contamination in the environment. While traditional fecal coliform enumeration can give a general measure of contamination, the specificity imparted by modern MST provides a more informative assessment of contaminants and their likelihood to affect human health outcomes.

We have been developing an MST system that detects DNA biomarkers from the gram-negative bacterial genus Bacteroides and the family Lachnospiraceae. They are strict anaerobes found in large quantities in the intestines of animals. Unlike E. coli or Enterococci, host-specific strains of Bacteroides and Lachnospiraceae exist. To this end, we …

Transcription Factor Binding And Discovery Of Novel Gene In The Opportunistic Human Pathogen, Pseudomonas Aeruginosa, Alaina Westee

Symposium of Student Scholars

Pseudomonas aeruginosa (PA) is a gram-negative, ubiquitously-found bacterium that primarily causes nosocomial, or hospital-borne, infections within immunocompromised patients. Therefore, it has been deemed a critical priority pathogen by the World Health Organization (WHO) and the Center for Disease Control (CDC), generating a need for research on its fundamental biology. The Van Dyke laboratory focuses on proteins called transcription factors, which promote or repress gene expression to regulate an organism’s functioning. We are specifically studying the cadmium-responsive transcription factor, CadR, due to the importance of metals in virulence and the lack of information on PA’s response to metal fluctuations. We intend …

Invasion And Metastasis In Cancer: Molecular Insights And Therapeutic Targets, Yongxing Li, Fengshuo Liu, Qingjin Cai, Lijun Deng, Qin Ouyang, Xiang H-F Zhang, Ji Zheng

Faculty, Staff and Students Publications

The progression of malignant tumors leads to the development of secondary tumors in various organs, including bones, the brain, liver, and lungs. This metastatic process severely impacts the prognosis of patients, significantly affecting their quality of life and survival rates. Research efforts have consistently focused on the intricate mechanisms underlying this process and the corresponding clinical management strategies. Consequently, a comprehensive understanding of the biological foundations of tumor metastasis, identification of pivotal signaling pathways, and systematic evaluation of existing and emerging therapeutic strategies are paramount to enhancing the overall diagnostic and treatment capabilities for metastatic tumors. However, current research is …

Machine Learning-Enhanced Surface-Enhanced Spectroscopic Detection Of Polycyclic Aromatic Hydrocarbons In The Human Placenta, Oara Neumann, Yilong Ju, Andres B Sanchez-Alvarado, Guodong Zhou, Weiwu Jiang, Bhagavatula Moorthy, Melissa A Suter, Ankit Patel, Peter Nordlander, Naomi J Halas

Faculty, Staff and Students Publications

The detection and identification of polycyclic aromatic hydrocarbons (PAHs) and their derivatives, polycyclic aromatic compounds (PACs), are essential for environmental and health monitoring, for assessing toxicological exposure and their associated health risks. PAHs/PACs are the most dangerous chemicals found in tobacco smoke, and cigarette use during pregnancy can convey these molecules to the developing fetus through the placenta. This exposure is associated with many negative health outcomes, from premature birth to sudden infant death syndrome and adverse neurodevelopmental disorders. This study demonstrates the use of surface-enhanced Raman and surface-enhanced infrared absorption spectroscopies for direct detection of PAHs/PACs in human placental …

Thermophilic Microbiota Of Fifth Water Hot Springs: A Genomic Perspective, Ethan Powers, Zack Galbraith, Trever Thurgood

Annual Research Symposium

Geothermal hot springs provide unique microbial habitats characterized by extreme temperatures, variable pH, and diverse geochemical conditions. This study investigates the microbial diversity of three hot spring locations in Diamond Fork Canyon, Utah—Diamond Fork Warm Springs, Fifth Water Hot Springs, and Monk’s Hollow Trailhead—using Oxford Nanopore MinION sequencing of the 16S rRNA gene. Samples were collected in triplicate and analyzed to identify the bacterial composition, with a focus on potential opportunistic pathogens. Our results revealed a diverse microbial community, including members of Pseudomonas, Comamonas, Helicobacter, and Flavobacterium, some of which are known for biofilm formation, antibiotic …

Author Correction: Orthogonal And Multiplexable Genetic Perturbations With An Engineered Prime Editor And A Diverse Rna Array, Qichen Yuan, Hongzhi Zeng, Tyler C Daniel, Qingzhuo Liu, Yongjie Yang, Emmanuel C Osikpa, Qiaochu Yang, Advaith Peddi, Liliana M Abramson, Boyang Zhang, Yong Xu, Xue Gao

Faculty, Staff and Students Publications

Correction to: Nature Communications 10.1038/s41467-024-55134-9, published online 30 December 2024

In the version of the article initially published, there were errors in Fig. 3d, where in the x-axis labels now reading “GPP-shRNA1, GPP-shRNA2, GPP-shRNA3…,” the second and third labels were duplicates of the first. The figure is amended in the HTML and PDF versions of the article.

Axl Signaling In Cancer: From Molecular Insights To Targeted Therapies, Monika Yadav, Akansha Sharma, Ketki Patne, Saba Tabasum, Jyoti Suryavanshi, Laxminarayan Rawat, Marc Machaalani, Marc Eid, Rana Singh, Toni Choueiri, Soumitro Pal, Akash Sabarwal

Department of Microbiology and Immunology Faculty Papers

AXL, a member of the TAM receptor family, has emerged as a potential target for advanced-stage human malignancies. It is frequently overexpressed in different cancers and plays a significant role in various tumor-promoting pathways, including cancer cell proliferation, invasion, metastasis, epithelial-mesenchymal transition (EMT), angiogenesis, stemness, DNA damage response, acquired therapeutic resistance, immunosuppression, and inflammatory responses. Beyond oncology, AXL also facilitates viral infections, including SARS-CoV-2 and Zika highlighting its importance in both cancer and virology. In preclinical models, small-molecule kinase inhibitors targeting AXL have shown promising anti-tumorigenic potential. This review primarily focuses on the induction, regulation and biological functions of AXL …

Ddo-Adjuvanted Influenza A Virus Nucleoprotein Mrna Vaccine Induces Robust Humoral And Cellular Type 1 Immune Responses And Protects Mice From Challenge, Victoria Gnazzo, Hanaa Saleh, Ítalo A. Castro, Adrianus C. M. Boon, Amelia K. Pinto, James D. Brien, Carolina B. López

Markey Cancer Center Faculty Publications

A challenge in viral vaccine development is to produce vaccines that generate both neutralizing antibodies to prevent infection and cytotoxic CD8+ T-cells that target conserved viral proteins and can eliminate infected cells to control virus spread. mRNA technology offers an opportunity to design vaccines based on conserved CD8-targeting epitopes, but achieving robust antigen-specific CD8+ T-cells remains a challenge. Here, we tested the viral-derived oligonucleotide DDO268 as an adjuvant in the context of a model influenza A virus (IAV) nucleoprotein (NP) mRNA vaccine in C57BL/6 mice. DDO268 when co-packaged with mRNA in lipid nanoparticles is sensed by RIG I-like receptors and …

Cardiac Surgical Bleeding, Transfusion, And Quality Metrics: Joint Consensus Statement By The Enhanced Recovery After Surgery Cardiac Society And Society For The Advancement Of Patient Blood Management, Rawn Salenger, Rakesh C Arora, Arthur Bracey, Mario D'Oria, Daniel T Engelman, Caroline Evans, Michael C Grant, Serdar Gunaydin, Vicki Morton, Sherri Ozawa, Prakash A Patel, Jacob Raphael, Todd K Rosengart, Linda Shore-Lesserson, Pierre Tibi, Aryeh Shander

Faculty, Staff and Students Publications

Background: Excessive perioperative bleeding is associated with major complications in cardiac surgery, resulting in increased morbidity, mortality, and cost.

Methods: An international expert panel was convened to develop consensus statements on the control of bleeding and management of transfusion and to suggest key quality metrics for cardiac surgical bleeding. The panel reviewed relevant literature from the previous 10 years and used a modified RAND Delphi methodology to achieve consensus.

Results: The panel developed 30 consensus statements in 8 categories, including prioritizing control of bleeding, prechest closure checklists, and the need for additional quality indicators beyond reexploration rate, such as time …

Virus-Specific T-Cell Therapy For The Management Of Viral Infections In The Immunocompromised, Kiriakos Koukoulias, Penelope Georgia Papayanni, Ann Marie Leen, Spyridoula Vasileiou

Faculty, Staff and Students Publications

Background: Immunocompromised individuals are at major risk for severe infectious complications. This is particularly relevant in the context of allogeneic hematopoietic stem cell transplantation (allo-HCT) - a treatment modality that has proven curative for a range of malignant and nonmalignant hematological diseases. However, transplant-associated immune suppression leaves patients susceptible to infectious complications from viruses such as cytomegalovirus (CMV), adenovirus (AdV), Epstein-Barr virus (EBV), and BK virus (BKV). While pharmacological agents are available to prevent and/or treat some of these viruses, they can be associated with significant toxicities and are often ineffective. To circumvent these issues, several groups have explored the …

The Role Of Biofilm Matrix On The Growth, Survival, And Diagnosis In Enterobacteriaceae, Kavi Bharathi R

Theses and Dissertations

Bacteria in nature live together encased in a matrix creating community ecosystems called biofilms, this structured space protects them from hostile environments. This study aimed to understand the role of the biofilm matrix in the growth and survival of Enterobacteriaceae. Our hypothesis proposes that subgroups of individuals within a biofilm can specialize in the production of different matrix components.

Matrix expression is metabolically costly, despite its unicellular simplicity, microbes can coordinate complex behaviour like sharing of matrix between producers and non-producers as an adept evolutionary strategy. Their resilience to stress during biofilm formation was studied to assess their abilities to …

Immuno-Bioinformatics Study Of Secondary Metabolites From Watercress Nasturtium Officinale As Immunostimulant In Whiteleg Shrimp Litopenaeus Vannamei By Targeting Peroxinectin And Scavenger Receptor Class B, Qurrota A’Yunin, Muhaimin Rifa’I, Maftuch Maftuch, Yoga Dwi Jatmiko, Muhammad Hermawan Widyananda, Triyanto Triyanto, Muhammad Tegar Handrianto

Karbala International Journal of Modern Science

The viral disease affects the whiteleg shrimp (Litopenaeus vannamei) and causes losses. Immunostimulants are recognized as a more environmentally friendly approach to disease management and antimicrobial properties of aquatic organisms. Watercress (Nasturtium officinale) is an aquatic plant species that contains antioxidant properties that can protect the organism from disease and boost the immune system. Shrimp rely heavily on innate immunity to combat infectious agents due to their absence of adaptive immunity. Peroxinectin and scavenger receptor class B (SRB) play essential roles in the shrimp defense system. This research employs a bioinformatic to assess the immunostimulatory potential …

Review Of New Treatment Options For Toxoplasmosis, Kiley Roman

D.U.Quark

Toxoplasmosis is an infectious disease caused by the parasite, Toxoplasma Gondii. The parasite is often carried in cats and contaminated food and water. Toxoplasmosis is not serious most of the time but can be harmful to immunocompromised people, pregnant women, and their fetuses or babies. Treatments are commonly given to the immunocompromised. However, there are problems with the current treatments, in which they only treat active parasites and cannot remove the cysts created by disease progression. Due to the treatments’ inability to remove cysts, an infected person may not fully recover from the infection. This review evaluated the new …

Geographic Disparities Impacting Oral Vaccine Performance: Observations And Future Directions, Rachel M Burke, Sasirekha Ramani, Julia Lynch, Laura V Cooper, Haeun Cho, Ananda S Bandyopadhyay, Carl D Kirkwood, A Duncan Steele, Gagandeep Kang

Faculty, Staff and Students Publications

Oral vaccines have several advantages compared with parenteral administration: they can be relatively cheap to produce in high quantities, easier to administer, and induce intestinal mucosal immunity that can protect against infection. These characteristics have led to successful use of oral vaccines against rotavirus, polio, and cholera. Unfortunately, oral vaccines for all three diseases have demonstrated lower performance in the highest-burden settings where they are most needed. Rotavirus vaccines are estimated to have >85% effectiveness against hospitalization in children < 12 months in countries with low child mortality, but only ~65% effectiveness in countries with high child mortality. Similarly, oral polio vaccines have lower immunogenicity in developing country settings compared with high-resource settings. Data are more limited for oral cholera vaccines, but suggest lower titers among children compared with adults, and, for some vaccines, lower efficacy in endemic settings compared with non-endemic settings. These disparities are likely multifactorial, and available evidence suggests a role for maternal factors (e.g. transplacental antibodies, breastmilk), host factors (e.g. genetic polymorphisms-with the best evidence for rotavirus-or previous infection), and environmental factors (e.g. gut microbiome, co-infections). Overall, these data highlight the rather ambiguous and often contradictory nature of evidence on factors affecting oral vaccine response, cautioning against broad extrapolation of outcomes based on one population or one vaccine type. Meaningful impact on performance of oral vaccines will likely only be possible with a suite of interventions, given the complex and multifactorial nature of the problem, and the degree to which contributing factors are intertwined.

Antimicrobial Effect Of Herbs Extracted With Ethanol Compared To Ampicillin, Brianna Neilan, Laura Rowe

Posters-at-the-Capitol

Antibiotics are commonly used to treat bacterial infections within the medical field, however there are growing concerns of antibiotic resistance. Before the introduction of antibiotics herbs were commonly used to treat infections, and herbal medicine is still used in many communities and cultures. Bacteria’s increasing resistance to traditional antibiotics has caused herbal medicines to become a significant research topic recently. Methods of herbal medicine preparation include preparing teas using hot water, and tinctures that soak herbs in alcohol for several weeks. Previous research has shown significant antimicrobial effects of some herbs when soaked in water and other liquids. The aim …