Microbiology Commons^™

Dual Targeting Of Orphan Nuclear Receptors Nr4a1 And Nr4a2 For Nonhormonal Endometriosis Therapy, Wai Ning Tiffany Tsui, Yuri Park, Srijana Upadhyay, Da Mi Kim, Lei Zhang, Gus Wright, Amanuel Hailemariam, Arafat Rahman Oany, Sang Jun Han, Stephen Safe

Faculty, Staff and Students Publications

Previous studies show that orphan nuclear receptor 4A1 (NR4A1) regulates endometriotic cell growth, survival, estrogen receptor β (ERβ), mechanistic target of rapamycin signaling and fibrosis. NR4A2 is also expressed in epithelial and stromal derived endometriotic cells, and in this study the effects of 1,1-bis(3'-indolyl)-(3,5-disubstitutedphenyl)methane (DIM-3,5) dual NR4A1/nuclear receptor 4A2 (NR4A2) ligands and knockdown of NR4A1 and NR4A2 were investigated. The dual NR4A1/2 DIM-3,5 analogs inhibited previously identified proendometriotic pathways and gene products, and they also inhibited TWIST1 and multiple markers associated with epithelial-to-mesenchymal transition (EMT). The results show that both NR4A1 and NR4A2 regulate the same pathways, including endometriotic cell …

Phosphorylation Of Ryr1 At Ser2902 Decreases Ca2+ Leak In Skeletal Muscle And Susceptibility To Malignant Hyperthermia And Heat Stroke, Rachel Sue Zhen Yee, Chang Seok Lee, Ting Chang, Sung Yun Jung, Omar Yousif, Courtney Cavazos, John Colyer, Filip Van Petegem, George G Rodney, Susan L Hamilton

Faculty, Staff and Students Publications

The ryanodine receptor 1 (RYR1) is the sarcoplasmic reticulum (SR) Ca2+ release channel required for both skeletal muscle contraction and Ca2+ leak. Mutations in RYR1 cause malignant hyperthermia susceptibility (MHS) and enhanced sensitivity to heat stroke (ESHS), which can result in death due to excessive skeletal muscle thermogenesis upon exposure to volatile anesthetics or heat. Here, we investigated the molecular and physiological functions of phosphorylation of RYR1 at Ser2902 by the kinase SPEG (striated muscle preferentially expressed protein). Muscle from SPEG-deficient mice expressing RYR1 with a Ser2902 →Asp2902 (S2902D) point mutation to mimic phosphorylation by SPEG showed decreased SR Ca2+ …

Strain-Specific Variability In Viral Kinetics, Cytokine Response, And Cellular Damage In Air-Liquid Cultures Of Human Nasal Organoids After Infection With Sars-Cov-2, Gina M Aloisio, Trevor J Mcbride, Letisha Aideyan, Emily M Schultz, Ashley M Murray, Anubama Rajan, Erin G Nicholson, David Henke, Laura Ferlic-Stark, Amal Kambal, Hannah L Johnson, Elina A Mosa, Fabio Stossi, Sarah E Blutt, Pedro A Piedra, Vasanthi Avadhanula

Faculty, Staff and Students Publications

SARS-CoV-2 variants have demonstrated distinct epidemiological patterns and clinical presentations throughout the COVID-19 pandemic. Understanding variant-specific differences at the respiratory epithelium is crucial for understanding their pathogenesis. Here, we utilized human nasal organoid air-liquid interface (HNO-ALI) cell cultures to compare the viral replication kinetics, innate immune response, and epithelial damage of six different strains of SARS-CoV-2 (B.1.2, WA, Alpha, Beta, Delta, and Omicron). All variants replicated efficiently in HNO-ALIs, but with distinct replication kinetic patterns. The Delta variant exhibited delayed replication kinetics, achieving a steady state at 6 days post-infection compared to 3 days for other variants. Cytokine analysis revealed …

The Effects Of Plastic Mulch And Irrigation On Hemp Chemistry And Leaf Endophytes, Allison Rietman, Connor Morozumi, Robert C. Pearce, Natalie Christian

Journal of Agricultural Hemp Research

As an emerging crop, cultivation techniques for industrial hemp (Cannabis sativa L.) are still being developed and optimized. For example, irrigation and plastic mulching are some management practices that have been touted for their benefits in improving crop quality. Both techniques ensure ample water availability, which has often been attributed to improving hemp cannabinoid and terpene composition. In this study, we examined how supplemental irrigation implemented in a plastic mulch system influenced the cannabinoid and terpene profiles of one cultivar of CBD hemp, Lifter. We grew industrial hemp in field with plastic mulch and applied regular irrigation to one group …

Preliminary Microbial Community Analysis Of Non-Native And Native Plants In The Depauw Nature Park Quarry Bottom, Madeleine Cruz, Dana Dudle

Annual Student Research Poster Session

The DePauw Nature Park Quarry Bottom is a former limestone quarry that was mined for decades and then lay dormant. Through the years, it has developed from being uninhabited to being populated by a diversity of organisms at every scale of life. All organisms in the Quarry Bottom must withstand the changing conditions of the quarry, including the proliferation of invasive plants that are well-adapted to stress. In particular, two invasive wetland grasses, Phragmites and Typha have observed competitive interactions, increased spatial distributions, and possible influence on native species. We have studied these species at our scale of life, but …

Role Of Growth Factors In The Pathogenesis Of Systemic-Sclerosis-Associated Fibrosis, Fabian A. Mendoza, Sonsoles Piera-Velazquez, Sergio A. Jimenez

Jefferson Institute of Molecular Medicine Papers and Presentations

Systemic Sclerosis (SSc) is a systemic autoimmune disease of unknown etiology characterized by a severe fibroproliferative vasculopathy and frequently progressive cutaneous and internal organ fibrosis. The small-vessel vasculopathy and the tissue fibrotic alterations are responsible for the most serious clinical and pathological manifestations of the disease and for its high mortality. Despite the high severity and frequent mortality, there are currently no optimal therapeutic approaches for SSc, and its complex pathogenesis has not been fully elucidated. Numerous studies have suggested that growth factors and related regulatory macromolecules released from inflammatory and other cells present in the affected tissues play a …

Exploring The Diversity And Biology Of Unique Giant Broad Host Range Bacteriophages In Natural Environments, Tannaz Mohammadi

Theses and Dissertations

Microbial interactions within the rhizosphere play a crucial role in shaping bacterial community diversity and function. To explore these dynamics, we isolated 21 bacterial strains from soil and plant root samples collected near Rocky Branch Creek on the University of South Carolina campus. Our findings revealed that a significant proportion of these bacteria are lysogenic for CbK-like phages belonging to the Dolichocephalovirinae subfamily. Additionally, we isolated free bacteriophages directly from the same soil samples and found them to be closely related to those harbored within lysogenic bacteria. Surprisingly, despite predictions of a narrow host range, most of these phages, both …

Exploring The Transformative Effects Of Calorie Restriction On The Lacrimal Gland In Adult Mice, Olivier Mauduit, Prashant Kumar, Kaitlin K Scholand, Emre Aksan, Laura Schaefer, Anmar Abu-Romman, Vanessa Delcroix, Zhiyuan Yu, Aude I Sindikubwabo, Ron Korstanje, Helen P Makarenkova, Cintia S De Paiva

Faculty, Staff and Students Publications

Advanced age is one of the most recognizable risk factors for dry eye. Dry eye disease affects millions worldwide and can result from age-related lacrimal gland dysfunction, which correlates with a decline in lacrimal gland secretory cell function and chronic inflammation. This study investigated the potential of calorie restriction to maintain lacrimal gland and ocular surface health. Adult female C57BL/6 J mice were subjected to a 40% calorie restriction for 4 months, starting at 6-7 months and continuing until 10-11 months. These mice were compared to controls fed ad libitum. Bulk RNA sequencing of lacrimal glands, conjunctiva, and cornea subjected …

Nrf2 Hyperactivation As A Driver Of Radiotherapy Resistance And Suppressed Antitumor Immunity In Head And Neck Squamous Cell Carcinoma, Rutulkumar Patel, Kalil Saab, Lixia Luo, Yan Ma, Rashid Abdullah Osman, Nerissa T Williams, Jeffrey Everitt, Maciej J Zelazowski, Patricia Castro, William K Decker, William H Hudson, Jeffrey N Myers, Vlad C Sandulache, Mitchell J Frederick, Yvonne M Mowery, David G Kirsch

Faculty, Staff and Students Publications

Purpose: Alterations in the KEAP1/NFE2L2 (NRF2)/CUL3 pathway occur in ∼20% of human head and neck squamous cell carcinomas (HNSCC) and are associated with resistance to standard-of-care therapy. However, this pathway's role in radiotherapy resistance in HNSCC has not been well studied.

Experimental design: We generated genetically engineered mouse models and developed primary murine cancer cell lines harboring mutations commonly observed in human HNSCC, including inducible activation of PIK3CA and deletion of Trp53, with or without Keap1 loss. Primary tumors were initiated via 4-hydroxytamoxifen injection ± the tobacco carcinogen benzo[a]pyrene (BAP) into the oral buccal mucosa. Tumors were analyzed by Western …

Author Correction: Clonal Dynamics And Somatic Evolution Of Haematopoiesis In Mouse, Chiraag D Kapadia, Nicholas Williams, Kevin J Dawson, Caroline Watson, Matthew J Yousefzadeh, Duy Le, Kudzai Nyamondo, Sreeya Kodavali, Alex Cagan, Sarah Waldvogel, Xiaoyan Zhang, Josephine De La Fuente, Daniel Leongamornlert, Emily Mitchell, Marcus A Florez, Krzysztof Sosnowski, Rogelio Aguilar, Alejandra Martell, Anna Guzman, David Harrison, Laura J Niedernhofer, Katherine Y King, Peter J Campbell, Jamie Blundell, Margaret A Goodell, Jyoti Nangalia

Faculty, Staff and Students Publications

No abstract provided.

Plasma Proteome Correlations With Liver Stiffness In Pediatric Cholestasis Implicate Epithelial To Mesenchymal Transition, Benjamin L Shneider, Rupa S Kanchi, Sandra L Grimm, Sridevi Devaraj, Juliet Emamaullee, Jeremy Schraw, Philip J Lupo, Jorge A Bezerra, Kathleen M Loomes, John C Magee, Ronald J Sokol, Kasper S Wang, Alyssa Kriegmeier, Evelyn Hsu, Jean P Molleston, Philip Rosenthal, Rohit Kohli, Saul J Karpen, Simon P Horslen, M Kyle Jensen, Arianna Barbetta, Cristian Coarfa

Faculty, Staff and Students Publications

Background: Pediatric cholestatic liver diseases can be characterized by rapidly progressive fibrosis. A multicenter cross-sectional analysis of vibration-controlled elastography in biliary atresia (BA), alpha-1 antitrypsin deficiency (A1AT), and Alagille syndrome (ALGS) was leveraged to interrogate the plasma proteome relative to liver stiffness measurements (LSM).

Methods: Slow off-rate modified aptamer scanning profiling of >7000 proteins in plasma from 187 children with BA (n=93), A1AT (n=31), ALGS (n=46), and healthy pediatric controls (n=17) was performed, and correlations with LSM were undertaken.

Results: There was an abundance of LSM correlated proteins (BA n=2720, A1AT n=694, ALGS n=5968). Interestingly, a distinct plasma proteome was …

Examining The Relationship Between Dysphagia, Eating-Related Symptoms, And Diet Quality Among Oropharyngeal Cancer Patients During Critical Stages Of Cancer Survivorship: The U-Dine Study, Beatrice Manduchi, Vlad C Sandulache, Ji Yun Tark, Shreela Sharma, Ruosha Li, Emily Roller, Andrew Bevelhimer, Katherine A Hutcheson, Marcia C De Oliveira Otto

Faculty, Staff and Students Publications

Background: Diet quality is a modifiable factor impacting treatment outcomes in oropharyngeal cancer (OPC), yet the effect of dysphagia and self-reported eating-related symptoms remains unclear. This study examined their associations with diet quality in OPC patients.

Methods: A cross-sectional analysis was conducted with two parallel cohorts from MD Anderson Cancer Center and Michael E. DeBakey Veterans Affairs Medical Center as part of the Uncovering the Long-Term Impact of OPC and Dysphagia on Dietary Quality and Nutrition Among Cancer Survivors (U-DINE) Study. Participants at varying survivorship stages (prediagnosis, 3-6 and 18+ months posttreatment) were assessed for dysphagia (DIGEST scale) and six …

Decorin Evokes A Pro-Lysosomal Pathway In Lymphatic Endothelial Cells, Gabriel J. Pascal, Dipon K. Mondal, Sadie Kim, Christopher Xie, Devanarayanan Siva Sankar, Jörn Dengjel, Renato V. Iozzo

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

The lymphatic system is critical to the body's immune and circulatory system, and lymphangiogenesis, the development of new lymphatic vessels from pre-existing ones, is a significant process capitalized upon by cancer during tumorigenesis. Decorin is a small leucine-rich proteoglycan which we have previously shown to be anti-tumorigenic and a suppressor of lymphangiogenesis. We have also shown that decorin exercises its anticancer properties through its ability to evoke autophagy. Through a comprehensive and unbiased proteomic analysis, we explored the implications of decorin exposure on protein expression within mouse lymphatic endothelial cells. We discovered that decorin enriches several protein pathways, notably proteasomal …

Observational Activation Of Anterior Cingulate Cortical Neurons Coordinates Hippocampal Replay In Social Learning, Xiang Mou, Daoyun Ji

Faculty, Staff and Students Publications

Social learning enables a subject to make decisions by observing the actions of another. How neural circuits acquire relevant information during observation to guide subsequent behavior is unknown. Utilizing an observational spatial working memory task, we show that neurons in the rat anterior cingulate cortex (ACC) associated with spatial trajectories during self-running in a maze are reactivated when observing another rat running the same maze. The observation-induced ACC activities are reduced in error trials and are correlated with activities of hippocampal place cells representing the same trajectories. The ACC activities during observation also predict subsequent hippocampal place cell activities during …

A Novel Self-Inhaled Nicotine Exposure System In Murine Models Reveals Age-Dependent Metabolic Effects Of Nicotine, Xu Xu, Hailan Liu, Meng Yu, Qingzhuo Liu, Yongxiang Li, Yue Deng, Yuxue Yang, Jingjing Cheng, Yutian Liu, Mengjie Wang, Xing Fang, Longlong Tu, Olivia Z Ginnard, Kristine M Mcdermott, Darah Threat, Fuhui Wang, Meixin Sun, Xinming Liu, Jiamin Qiu, Xi Wu, Jinjing Jian, Tong Zhou, Megan E Burt, Sanika V Jossy, Junying Han, Chunmei Wang, Yongjie Yang, Yong Xu, Yuhan Shi

Faculty, Staff and Students Publications

Background: Nicotine is known to influence metabolism and body weight, yet existing murine models of nicotine exposure often fail to replicate human smoking behaviors accurately. To address this gap, we designed a cost-effective, self-administered nicotine inhalation system that allows mice to voluntarily inhale nicotine vapor generated from e-liquid.

Results: Using this system, we investigated the metabolic effects of nicotine exposure in adult and adolescent mice. Adult mice exposed to nicotine vapor for 10 days exhibited significant weight loss, which was rapidly regained upon cessation, paralleling human smoking patterns. In contrast, adolescent mice did not lose weight during nicotine exposure but …

Effect Of Red And Blue Light On Lipid, Protein, Carbohydrate, And Pigment Contents Of Navicula Sp., Sofyan Maulana, Aulia Setyo Nurul Hida, Ismia Wulandari, Siti Mudrikah, Dedy Kurnianto, Khusnul Qonita Maghfiroh, Ria Amelia, Tia Erfianti, Renata Adaranyssa Egistha Putri, Irika Devi Anggraini, Septhian Marno, Eko Agus Agus Suyono

Makara Journal of Science

Light quality critically modulates the physiology of diatoms, influencing photosynthetic efficiency and metabolite synthesis. This study examines how monochromatic red (620–750 nm) or blue (450–495 nm) light affects the biochemical profiles and pigment production in Navicula sp. versus white light (control). Cultures were grown in sterile f/2 medium, and biomass was tracked via OD₆₈₀. Biochemical analyses included lipids (Bligh and Dyer method), carbohydrates (phenol-sulfuric acid assay), proteins (Bradford assay), and pigments (spectrophotometric quantification). The growth dynamics were modeled using logistic and Gompertz equations. No significant differences in OD-based growth rates, carbohydrates, proteins, or lipids content were observed with …

Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy

Makara Journal of Science

Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …

Characteristics And Potential Indigenous Bacteria Isolated From Shallot Farming In Brebes Regency As Diazinon Pesticide Remediation Agents, Wahyu Purbalisa, Dian Hendrayanti, Wahida Annisa Yusuf

Makara Journal of Science

Diazinon is an organophosphate pesticide that is widely used by shallot farmers in Brebes Regency. Due to its toxicity, diazinon residue in agricultural lands as well as plants’ cultivation is harmful to humans and the environment. Using indigenous soil bacteria as a remediation agent is an alternative solution to overcome diazinon contamination. Firstly, this study aimed to characterize isolates from diazinon-contaminated shallot farming. The second objective was to test the diazinon tolerance of the isolates in various diazinon concentrations. Isolation was carried out using nutrient agar (NA) media containing diazinon concentrations of 5, 25, 50, and 100 ppm. The characterization …

Artificial Intelligence In Head And Neck Cancer: Towards Precision Medicine, Jacob Hagen, Logan Hornung, William Barham, Supratik Mukhopadhyay, Adam Bess, Kevin Contrera, Devraj Basu, Vlad Sandulache, Guillaume Spielmann, Sagar Kansara

Faculty, Staff and Students Publications

Over the past 20 years, the capabilities of artificial intelligence (AI) have gained significant interest. While AI has been implemented to various degrees in several disciplines, its unique applications in head and neck cancer (HNC) remain underdeveloped. This narrative review examines the existing body of literature regarding the use of AI in HNC. Studies to date have demonstrated AI’s utility across multiple phases of the HNC treatment continuum. Despite its promise, integrating AI into clinical practice faces several challenges, including concerns about system integrity, generalizability, privacy, and bias. In this review, we address these challenges and offer insights into future …

Clinical Applications Of Probiotics: A Comprehensive Review Of Benefits And Challenges, Riyam Wissam Hassan

Maaen Journal for Medical Sciences

Probiotics are beneficial microorganisms that help balance microbes in intestines and promote growth beneficial bacteria, they vary between bacteria, yeasts, and fungi and they are helpful to human health when taken in adequate and suitable amounts. In addition to maintaining intestinal health and help with digestion and absorption, also inhibiting development and preventing spread of harmful microorganisms. It exists in different forms, in the intestines and in the foods, products fermented, and in the pharmaceutical supplements. Because human health depends largely on the interaction between humans and these microorganisms known as probiotics, it has found that these organisms have vital …