Digital Commons Network^™

The Expression Profile Of The Rank/Rankl/Opg Pathway In Breast Cancer Stem Cells Isolated From Breast Cancer Cell Lines, Mohamed M. Kamal, Hassnaa H. Elgohary, Sherine Maher Rizk, Nadine H. Maurice

Pharmacy

The RANK/RANKL/OPG signaling pathway plays a crucial role in breast cancer progression and metastasis. However, its expression patterns and potential implications in breast cancer stem cells remain poorly understood. This study aimed to characterize the expression profile of this pathway in breast cancer stem cells isolated from two distinct breast cancer cell lines: MDA‐MB‐231 and MCF‐7. Mammospheres (MS), representing breast cancer stem cells, were generated using agar‐coated 6 well tissue culture plates in suitable mammospheres culture conditions. Flow cytometric analysis showed enrichment of the CD44+/ CD24− subpopulations in the mammospheres cultures, with MDA‐MB‐231 exhibiting a higher percentage compared to MCF‐7. …

General Biology 2 Laboratory Manual: In Person Edition, Dmitry Y. Brogun, Azure N. Faucette, Farshad Tamari, Kristin Polizzotto

Open Educational Resources

The completed project is an in-person teaching version of the General Biology II OER (Open Educational Resource) lab manual. This lab manual was initially written by the four of us during the pandemic when all courses were online, but it is now has been adapted for in-person lab activities. We also ensured it aligns with UDL (Universal Design for Learning) and accessibility principles. This adaptation aims to make the lab manual suitable for traditional classroom settings while incorporating diverse teaching practices to accommodate diverse learners.

Commodity Thermoplastic Elastomer-Enabled Templated Synthesis Of Large-Pore Ordered Mesoporous Materials, Anthony Griffin, Parker Frame, Yizhi Xiang, Zhe Qiang

Faculty Publications

Fabrication of ordered mesoporous materials (OMMs) has predominantly relied on templating-based methods. However, these methods are constrained by several limitations, especially the limited pore sizes attainable with commercially available surfactants used as structure-directing agents. To unlock the full potential of the OMMs, it is essential to develop synthetic strategies that facilitate the production of large-pore OMMs using scalable processes and cost-effective precursors. This work demonstrates the use of thermoplastic elastomer (TPE)-derived carbon replicas for synthesizing ordered mesoporous silica (OMS) and metal oxides (OMMOs) via precursor infiltration and template removal. The nanostructural evolution of the resulting inorganic materials was systematically investigated. …

Influence Of Inselbergs On Bat Diversity In Afrotropical Ecosystems, Amanda Lee Grunwald

Dissertations and Theses

Humans are altering biological communities on local to global scales, driving profound changes in biodiversity and ecosystem functioning. However, significant gaps and biases in biodiversity data hinder our understanding of ecosystem interactions, making it challenging to develop effective, data-driven policies to protect remaining biodiversity. Bats, the second most species-rich groups of mammals, have a global distribution, and perform a broad array of vital ecosystem functions. Their diversity peaks in the tropics, where they often constitute more than 50% of mammal species diversity. The Afrotropics host substantial bat diversity, yet have historically been perceived as having lower species richness compared to …

Impact Of Changes In Gestational Diabetes Mellitus Diagnostic Criteria During The Covid-19 Pandemic, Jessica Neville, Kelly Foley, Seán Lacey, Antoinette Tuthill, Oratile Kgosidialwa, Mairead O’Riordan, Fiona O’Halloran, Seán J. Costelloe

Department of Biological Sciences Publications

Background/Aims

During the COVID-19 pandemic, the Health Service Executive (HSE) and Royal College of Obstetricians and Gynaecologists (RCOG) recommended fasting and random plasma glucose (FPG/RPG) alongside glycated haemoglobin (HbA1c) to replace the oral glucose tolerance test (OGTT) for diagnosing Gestational Diabetes Mellitus (GDM).

Methods

The study compared testing patterns and diagnostic rates for GDM before and after implementing the RCOG guidelines (01/05/2020) in pregnancies beginning 01/11/2018 to 31/03/2021. Trends were inspected using Cochrane-Armitage tests. Differences between General Practice (GP) and Secondary Care (SCare) were assessed by chi-square analysis. A significance level of p <  0.05 was used for all analyses. Information on maternal and pregnancy characteristics was accessed where available.

Results

Data indicated a significant reduction in …

Inter-Simple Sequence Repeats Application On The Identification Of Genetic Variation Of A New Indonesian Melon Cultivar “Melona”, Tantri Ajeng Salma Salsabila, Adib Fakhruddin Yusuf, Wiko Arif Wibowo, Prima Sekti Kusnanda, Budi Setiadi Daryono

Makara Journal of Science

The field of identification of molecular markers has seen significant advancements, with the Inter-Simple Sequence Repeat (ISSR) emerging as a prominent tool for characterizing genetic variation within species. This study focuses on the new Indonesian melon cultivar “Melona,” developed through selective breeding of commercial melons. This study aimed to assess the utility of ISSR markers in evaluating the genetic variation and stability of the “Melona” cultivar. Comparisons were made with established cultivars—‘Inthanon,” “Rich Sweetness,” “Chamoe,” and “Hikapel”—using five ISSR primers: UBC 807, UBC 808, UBC 810, UBC 812, and UBC 826. A total of 70 DNA fragments with a high …

Do Cheaters Prosper? Effect Of Externally Supplied Momentum During Resistance Training On Measures Of Upper Body Muscle Hypertrophy, Francesca Augustin, Jeff Nippard, Alec Pinero, Alysson Enes, Adam Mohan, Max Sapuppo, Max Coleman, Milo Wolf, Patroklos Androulakis Korakakis, Paul Swinton, Brad Schoenfeld

International Journal of Exercise Science

International Journal of Exercise Science 18(3): 329-342, 2025. Exercise technique, defined as the controlled execution of bodily movements to ensure an exercise effectively targets specific muscle groups while minimizing the risk of injury, is a resistance training (RT) variable frequently highlighted as critical to successful RT program outcomes, with proper technique suggested to play a role in maximizing muscle development. This study examined the effects of externally applied momentum on RT-induced muscular adaptations in the upper extremities. Thirty young adults were recruited to participate in a within-participant design, with one limb randomly allocated to perform biceps curls and triceps pushdowns …

Energy-Aware Clustering Using Intelligent Scheme For Heterogeneous Wireless Sensor Networks, Enaam A. Al-Hussain, Ghaida A. Al-Suhail

Karbala International Journal of Modern Science

Heterogeneous Wireless Sensor Networks (WSNs) involve nodes with varying capabilities, such as different energy levels, sensing ranges, and computational abilities, which enable them to execute different tasks professionally. Clustering techniques play a crucial role in improving energy efficiency and reliability in WSNs. The evolution of cluster based WSNs from homogeneous into heterogeneous techniques allowed the deployment of smart devices capable of performing complex operations in in diverse environments. However, the heterogeneity of nodes necessitates more sophisticated and adaptive algorithms to fully exploit these capabilities. This paper proposes a new protocol, referred to as IT2F-HLEACH, which integrates Interval Type-2 Fuzzy Logic …

Comprehensive Review On The Application Of Bio-Immunoinformatics In The Development Of Highly Ef-Fective New Candidate Vaccines Against Tuberculosis, Ahyar Ahmad, Andriansjah Rukmana, Miski A. Khairinisa, Dian A. E. Pitaloka, Rosana Agus, Rusdina B. Ladju, Tarwadi Ahmad, Astutiati Nurhasanah, Carina C. D. Joe, Muhammad N. Massi, Harningsih Karim, Irda Handayani, Siti Roszilawati Binti Ramli

Karbala International Journal of Modern Science

Tuberculosis (TB) remains a significant public health challenge worldwide. Currently, Bacillus Calmette-Guerin (BCG) is the only vaccine available for TB prophylaxis. However, the efficacy of the BCG vaccine against adult pulmonary TB is considered inconsistent. This condition encourages researchers to look for more effective options, such as subunit vaccines. This condition requires the development of a more effective subunit vaccine to protect active TB in productive and adult ages. There is an urgent need for more effective vaccines, as the Bacillus Calmette-Guérin (BCG) vaccine currently available has inconsistent efficacy and is only partially effective in adults. Bio-immunoinformatics, an interdisciplinary field …

Transcriptional Profiles Reveal Physiological Mechanisms For Compensation During A Simulated Marine Heatwave In Yellowtail Kingfish (Seriola Lalandi), Sharon E. Hook, Ryan J. Farr, Jenny Su, Alistair J. Hobday, Catherine Wingate, Lindsey Woolley, Luke Pilmer

Fisheries Research Articles

Background

Changing ocean temperatures are already causing declines in populations of marine organisms. Predicting the capacity of organisms to adjust to the pressures posed by climate change is a topic of much current research effort, particularly for species we farm or harvest. To explore one measure of phenotypic plasticity, the physiological compensations in response to heat stress as might be experienced in a marine heatwave, we exposed Yellowtail Kingfish (Seriola lalandi) to sublethal heat stress, and used the transcriptome in gill and muscle, benchmarked against heat shock proteins and oxidative stress indicators, to characterise the acute heat stress …

Structural Basis For Intrinsic Strand Displacement Activity Of Mitochondrial Dna Polymerase, Ashok Nayak, Viktoriia Sokolova, Sirelin Sillamaa, Karl Herbine, Juhan Sedman, Dmitry Temiakov

Department of Biochemistry and Molecular Biology Faculty Papers

Members of the Pol A family of DNA polymerases, found across all domains of life, utilize various strategies for DNA strand separation during replication. In higher eukaryotes, mitochondrial DNA polymerase γ relies on the replicative helicase TWINKLE, whereas the yeast ortholog, Mip1, can unwind DNA independently. Using Mip1 as a model, we present a series of high-resolution cryo-EM structures that capture the process of DNA strand displacement. Our data reveal previously unidentified structural elements that facilitate the unwinding of the downstream DNA duplex. Yeast cells harboring Mip1 variants defective in strand displacement exhibit impaired oxidative phosphorylation and loss of mtDNA, …

Why Can’T We Keep Making Antibiotics?, Kien Bui

Osmosis Magazine

Globally, the annual number of deaths due to antibiotic resistance infections is estimated to be 700,000, which can climb significantly with new viral diseases. The acquisition of antibiotic resistance in bacteria is a process related to the use of antibiotics to cure bacterial diseases. As bacteria replicate, mutations occur randomly, and there is a certain probability that this mutation introduces an antibiotic resistant gene. Upon exposure to antibiotics, all bacteria are cleared out, except for the ones that are antibiotic resistant. In other words, antibiotics significantly increase the gene frequency of the antibiotic resistant gene, allowing these bacteria to grow …

Exercise As A Drug: The Pharmacological Benefits Of Muscular Endurance Training For Type Ii Diabetes, Zack Ruighaver

Osmosis Magazine

In the United States, between 34 and 36 million people suffer from type II diabetes. That’s a little more than 1 in 10 Americans. Although type II diabetes typically develops in people 45 or older, cases are appearing more frequently in younger populations. But what if I told you that there was a drug that could help reverse this trend? No, I’m not talking about metformin or Ozempic. I’m talking about exercise – more specifically, muscular endurance training.

Letter From The Editor, Andrew Watts

Osmosis Magazine

Dear Reader,

Thank you for opening Osmosis Magazine. We are excited to bring you more accessible, intriguing stories in science and technology spanning the disciplines of biology, chemistry, psychology, and mathematics as well as faculty interviews.

Our goal as a magazine is to share the joy of science with the UR community in an accessible and entertaining fashion. We hope that you enjoy reading this Fall edition of Osmosis Magazine.

Finally, this is the last edition where I will serve as Editor in Chief. It has been a pleasure to work on this project with so many talented writers and …

Osmosis Magazine - Fall 2024

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.

Fostering Belief And Belonging: Catalysts For Success In Stem, Andrew Watts

Osmosis Magazine

As an aspiring scientist, have you ever found yourself consumed by the suffocating pressure to be perfect? Does the weight of failure loom ominously over your endeavors, threatening to derail your aspirations? And in the quiet moments of introspection, do whispers of self-doubt emerge, casting shadows of uncertainty over your path forward in STEM? I know I certainly have.

An Investigation Of Idaho Phragmites, Paxton Mills

Osmosis Magazine

In fall 2022, the Idaho State Department of Agriculture reached out to the lab of Dr. Carrie Wu, Associate Professor of Biology at the University of Richmond, for assistance in determining the genetic lineage of a suspected invasive stand of Phragmites australis, a wetland reed which has proved to be particularly troublesome throughout its introduced range. Like most invasive species, Phragmites wreaks havoc by outcompeting native plants, which disrupts normal ecosystem operations.

Meet The Pollock Lab: Understanding Breast Cancer And Disease Development, Jeff Tsai

Osmosis Magazine

In October 2023, I was eagerly looking for my lab home, as most Gottwald students would refer to the process. I had the pleasure of talking with Dr. Julie Pollock about her significant research in breast cancer. A great part of the reason why I enjoy learning about proteins and their functions is because of my mother’s history of battling stage II breast cancer. During my time taking care of her and eventually taking a class at the University of Richmond studying gene regulation and protein functions, I gained a greater appreciation for the work that biochemists do in breaking …

Osmosis Magazine - Spring 2024

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.

Seafood Mislabeling: Molecular Strategies To Identify Fish Species And Rethinking Public Outreach In Taiwan And The U.S., Ping Yen (Jeff) Tsai

Osmosis Magazine

Swapping identical fish with substitutes has been a widespread issue across the globe. Despite the valiant efforts of policymakers, seafood misidentification continues to be pervasive among large and small vendors, from sushi venues to grocery stores in the United States.

The Origins Of Mathematics: Invented Or Discovered?, Andrew Watts

Osmosis Magazine

A divisive subject amongst students of all ages, Mathematics remains an integral part of each student’s educational journey. Why is that? you may wonder. The answer is that Mathematics lies at the center of the natural world.

Osmosis Magazine - Spring 2023

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.

Conservation Status Of Virginia Populations Of The Rare And Jeopardized Bridle Shiner, Notropis Bifrenatus, Wayne C. Starnes, Gabriela M. Hogue, Morgan E. Raley

Southeastern Fishes Council Proceedings

The Bridle Shiner, Notropis bifrenatus (Cope, 1867), Family Leuciscidae, is a small minnow species that ranges in Atlantic coastal river drainages of eastern North America from the St. Lawrence in Canada southward to the Santee River basin of South Carolina. Over several decades notable declines throughout its range have been observed and multiple natural resource agencies note it to be jeopardized with probable extirpations evident in a number of drainages. The Virginia Department of Game and Inland Fisheries recognized the need to assess the status of the Bridle Shiner within its historical range in Virginia. Here we report the results …

Hiv And Bacterial Lps Synergistically Activate Aim2 Inflammasome In Primary Human Oral Keratinocytes, Md Shafayat Jamil, Deepa Roy, Upal Roy, Hansapani Rodrigo, Nirakar Sahoo, Chun Xu

Research Symposium

Background: HIV infection profoundly disrupts the oral microbiome, increasing the presence of Gram-negative bacteria such as Porphyromonas gingivalis (P. gingivalis), which is detected in over 80% of cases. P. gingivalis secretes lipopolysaccharide (LPS), a potent immune stimulant that can damage primary human oral keratinocytes (HOK) even in antiretroviral therapy (cART) treated people with HIV (PWH). HOK cells respond to bacterial and viral stimuli by activating inflammasome complexes, including AIM2, a DNA-sensing inflammasome protein. While LPS alone is known to trigger canonical and non-canonical pathways, leading to inflammasome activation, our study investigates how HIV exposure synergizes with LPS to induce the …

Leveraging Large Language Models For Knowledge-Free Weak Supervision In Clinical Natural Language Processing, Enshuo Hsu, Kirk Roberts

Faculty, Staff and Student Publications

The performance of deep learning-based natural language processing systems is based on large amounts of labeled training data which, in the clinical domain, are not easily available or affordable. Weak supervision and in-context learning offer partial solutions to this issue, particularly using large language models (LLMs), but their performance still trails traditional supervised methods with moderate amounts of gold-standard data. In particular, inferencing with LLMs is computationally heavy. We propose an approach leveraging fine-tuning LLMs and weak supervision with virtually no domain knowledge that still achieves consistently dominant performance. Using a prompt-based approach, the LLM is used to generate weakly-labeled …

Assessment Of Fish Biodiversity Of The Cimandiri Watershed, West Java, Indonesia, Rudhy Gustiano, Haryono Haryono, Gema Wahyudewantoro, Krismono Krismono, Rusdianto Rusdianto, Firman M. Nur

Makara Journal of Science

Information on the fish biodiversity of the Cimandiri Watershed is incomplete, and human activities and anthropogen-ic impacts pose a significant threat to this biodiversity. The purpose of this study was to assess the biodiversity of fish in the Cimandiri Watershed. The results indicated that fish biodiversity in the area included 104 species belonging to 49 families. There were 26 species in the upstream area, 47 species in the middle area, and 61 species in the downstream area. Forty-three species were native to Indonesia, and 7 of the native fish were endemic to the area. There were 11 introduced species belonging …

Diversity And Distribution Of Macrofungi In The Mid-Hills Of Bagmati Province, Central Nepal, Hari Sharan Adhikari, Suman Shrestha, Manoj Gurung, Sushma Pandit, Sujan Balami

Makara Journal of Science

The current study was carried out at seven research sites in the mid-hills (900-2500m asl) across six districts in Bagmati province, central Nepal to analyze the variety and distribution of macrofungal communities. The survey was carried out in the wet seasons from August 2017 to September 2022, including frequent field visits to the selected forests. Vari-ous diversity indices were applied to ascertain the composition of the macrofungal communities in the study area. A total of 133 wild macrofungal species belonging to 80 genera, 50 families, and 19 orders were observed. The macro-fungal population in the Bagmati province was dominated by …

Development Of A Multi-Epitope Peptide Vaccine Against Monkeypox Virus: Immunoinformatics Analysis For South East Asian Hla Alleles, Nelson Chandra, Mochammad Aqilah Herdiansyah, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Arli Aditya Parikesit

Makara Journal of Science

The monkeypox virus (MPXV), a DNA virus causing zoonotic disease, poses major global public health challenges, with mortality rates between 3%–6%. Although smallpox vaccines provide partial cross-protection, there is a critical need for a dedicated, effective monkeypox (mpox) vaccine. This study aimed to design a multi-epitope peptide-based vaccine specifically adapted to the HLA allele profiles common in Southeast Asian populations, where MPXV cases are rising. Using immunoinformatics, we screened for and detected B and T cell epitopes from the MPXV cell surface antigen and IFN-alpha/beta receptor proteins. The vaccine design was validated through a rigorous evaluation of its antigenicity, immunogenicity, …

Cloning And Expression Of Scamp3 In Escherichia Coli Bl21(De3) With In Silico Sequence-Based Cancer Epitopes Prediction, Selly Setiati Rajagukguk, Sabar Pambudi, Astari Dwiranti, Doddy Irawan Setyo Utomo, Anom Bowolaksono

Makara Journal of Science

Secretory carrier membrane protein 3 (SCAMP3) is a crucial membrane protein involved in intracellular vesicle traffick-ing and exocytosis. The SCAMP3 expression has been observed in diverse cancer types, such as melanoma, glioma, hepatocellular and breast cancer. Increased SCAMP3 expression has been reported in certain cancer cells relative to that in normal cells, suggesting the potential role of SCAMP3 in cancer development or progression. In this study, we successfully cloned and expressed SCAMP3 in Escherichia coli strain BL21(DE3). SCAMP3 was amplified and insert-ed directionally into the prokaryotic expression vector pET21d(+). The transformation of recombinant plasmid into E. coli BL21(DE3) cells were …

Screening For Penicillin G Acylase (Pga)-Producing Bacteria And Gene Cloning Using Degenerate Oligonucleotide Primed-Pcr, Masdalifah Masdalifah, Sri Rezeki Wulandari, Gabriela Christy Sabbathini, Maria Ulfah, Dini Achnafani, Ahmad Wibisana, Feronika Heppy Sriherfyna, Is Helianti, Niknik Nurhayati

Makara Journal of Science

The growing concern over antibiotic resistance has driven global efforts to explore innovative solutions, including the use of Penicillin G acylase (PGA) to produce semisynthetic β-lactam antibiotics. This study screened four potential in-tracellular PGA-producing bacteria: Alcaligenes faecalis InaCC B444 (AfPGA), Kluyvera cryocrescens InaCC B850 (KcPGA), Providencia rettgeri InaCC B25 (Pr25PGA), and P. rettgeri InaCC B466 (Pr466PGA). Penicillin G Acylase encoding genes (pgas) were isolated from them using a Degenerate Oligonucleotide Primed-PCR (DOP-PCR) approach and sequenced. Microbiological assays confirmed all tested crude extracts to exhibit inhibitory effects. Penicillin G was used for evaluating hydrolytic activity and 6-Amino Penicillanic Acid (6-APA) coupled …