Digital Commons Network^™

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, …

Avasimibe Abolishes The Efficacy Of Fluvastatin For The Prevention Of Cancer In A Spontaneous Mouse Model Of Breast Cancer, Anjana Bhardwaj, Alexander Koh, Rhea Bhala, Janvi Sandhu, Zhenlin Ju, Leslie Faye Cando, Jing Wang, Isabelle Bedrosian

Faculty, Staff and Student Publications

The cholesterol biosynthesis pathway is upregulated during breast cancer development and progression. Inhibition of the aberrantly upregulated cholesterol pathway by statins reduces breast tumor incidence and burden by 50% in SV40 C3(1) TAg mice, a mouse model of triple negative breast cancer. We hypothesized that fluvastatin's preventive efficacy could be further enhanced by co-targeting the statin-induced restorative feedback pathways that tightly control the cholesterol pathway and are involved in resistance to statins. Acyl-coenzyme A: cholesterol acyltransferase (

Zero & Infinity Two Divergent Concepts Converging Into Nothing, Aiden Hills

Osmosis Magazine

The concepts of zero and infinity have perplexed mathematicians, philosophers, and scientists since the very beginning of civilization. These abstract ideas challenged existing paradigms in arithmetic and geometry, paving the way for groundbreaking advances in fields ranging from quantum mechanics to cosmology. Let us examine the resistance and eventual acceptance of zero and infinity, highlighting their indispensable roles in modern science and technology.

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.

Rat Ultrasonic Vocalizations And Their Implication In Limiting Anthropomorphizing In Animal Research, Isabel Dilandro

Osmosis Magazine

Emotions in humans are very difficult to measure in a scientifically responsible manner.They are fickle, difficult to define, and even more difficult still to attach numerical value to as a subjective, malleable thing. If affective science, also known as the study of emotion, is difficult to fully grasp with participants that can talk back to us, effectively providing verbal insight to the inner workings of their cognition and self-reporting their thoughts and feelings for interpretation, then what are researchers meant to do when it comes time to measure the same responses in subjects that cannot provide them with any of …

“How Neonicotinoids In Pesticides Impact Bee Behavior And Ecological Interactions”, Jack Dupuy

Osmosis Magazine

Animal pollination, primarily facilitated by bees, represents a crucial ecosystem service, benefiting nearly 90 percent of flowering plants and contributing to the prosperity of 75 percent of the world's most prevalent crops.

Osmosis Magazine - Fall 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.

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 …

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 …

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 …

Antibacterial Activity Of Endophytic Actinobacteria Isolated From Ziziphus Mauritiana Against Multidrug-Resistant Strains, Hafifatunil Khairani, Jepri Agung Priyanto, Muhammad Eka Prastya, Dwi Retnowati

Makara Journal of Science

Increasing resistance to existing antibiotics has led to a need for new alternative sources. Among the possibilities that need to be explored is the endophytic actinobacteria associated with Ziziphus mauritiana. The present study aimed to evaluate the antibacterial activity of endophytic actinobacteria isolated from Z. mauritiana against five multidrug-resistant bacterial strains. Thirty actinobacteria isolates were obtained from the roots, stem, and leaves of the plant using the serial dilution technique. Using a double-layer agar test, we found that colonies from five of the 30 isolates (16%) exhibited antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and the M18 strain of Bacillus …

Creating Sustainable School And Home Gardens: Using Drones To Enhance Garden Projects, Douglas Weber, Rita Hagevik, Kathy Cabe Trundle

All Current Publications

This fact sheet explores using drones to enhance garden projects at home and in schools. It covers the benefits of drones, such as monitoring garden health, planning layouts, and assessing plant conditions through advanced imaging technologies. Additionally, it outlines essential factors to consider when selecting a drone, including cost, battery life, camera quality, and local regulations. Tips for safe operation and effective usage are also provided, as well as fun facts about drones.

A Phase I/Ii Trial Of Avelumab Combinations With Ivuxolimab, Utomilumab, And Radiation Therapy In Patients With Advanced Gastrointestinal Malignancies, Jibran Ahmed, Anne Knisely, Carlos Torrado, Bettzy Stephen, Yali Yang, Juhee Song, Anas Alshawa, Abdulrazzak Zarifa, Anuja Jhingran, Eugene J Koay, Van Karlyle Morris, Milind Javle, Robert A Wolff, Funda Meric-Bernstam, Shubham Pant, Jordi Rodon, Aung Naing

Faculty, Staff and Student Publications

Background: Checkpoint agonists utomilumab (4-1BB agonist) and ivuxolimab (OX40 agonist) enhance Teffector cell function. Preclinical studies suggest that combining these drugs with avelumab (anti-PD-L1 antibody) can potentially synergize this effect. In addition, tissue abscopal effects of radiation therapy may improve antigen presentation, complementing PD-L1 blockade. We conducted a single institution, open-label, multi-arm, non-randomized, phase 1/2 clinical trial of avelumab in combination with ivuxolimab, with or without utomilumab, and radiation therapy in patients with advanced solid tumors. Herein, we present a subgroup analysis in patients with gastrointestinal (GI) tumors (pancreatic, colon, gastric, and hepatocellular).

Methods: The primary objectives of this study …

Advances In Extracellular Matrix-Associated Diagnostics And Therapeutics, Morten Karsdal, Thomas R Cox, Amelia L Parker, Nicholas Willumsen, Jannie Marie Bülow Sand, Gisli Jenkins, Henrik H Hansen, Anouk Oldenburger, Kerstin E Geillinger-Kaestle, Anna Thorsø Larsen, Darcey Black, Federica Genovese, Alexander Eckersley, Andrea Heinz, Alexander Nyström, Signe Holm Nielsen, Lucas Bennink, Lars Johannsson, Anne-Christine Bay-Jensen, Dana E Orange, Scott Friedman, Mads Røpke, Vincent Fiore, Detlef Schuppan, Florian Rieder, Benjamin Simona, Lee Borthwick, Mark Skarsfeldt, Haakan Wennbo, Paresh Thakker, Ruedi Stoffel, Graham W Clarke, Raghu Kalluri, Darren Ruane, Faiez Zannad, Joachim Høg Mortensen, Dovile Sinkeviciute, Fred Sundberg, Molly Coseno, Christian Thudium, Adam P Croft, Dinesh Khanna, Michael Cooreman, Andre Broermann, Diana Julie Leeming, Ali Mobasheri, Sylvie Ricard-Blum

Faculty, Staff and Student Publications

The extracellular matrix (ECM) is the common denominator of more than 50 chronic diseases. Some of these chronic pathologies lead to enhanced tissue formation and deposition, whereas others are associated with increased tissue degradation, and some exhibit a combination of both, leading to severe tissue alterations. To develop effective therapies for diseases affecting the lung, liver, kidney, skin, intestine, musculoskeletal system, heart, and solid tumors, we need to modulate the ECM's composition to restore its organization and function. Across diverse organ diseases, there are common denominators and distinguishing factors in this fibroinflammatory axis, which may be used to foster new …

A Role For The Actin Cytoskeleton And Plastin-3 In Osteoblast Mineralization And Mechanosensation, Samantha Meagan Chin

Arts & Sciences Graduate Student Theses and Dissertations

The great diversity in actin network architectures and dynamics is exploited by cells to drive fundamental biological processes including cell migration, intracellular trafficking, and cell division. One such system that relies on the actin cytoskeleton to fulfill its physiological function are osteoblasts, which are mesenchymal lineage bone cells that promote bone formation through depositing a collagen scaffold and subsequently promoting mineralization of this matrix. A number of factors are known to drive osteogenic differentiation of pre-osteoblast cells including extracellular matrix cues such as substrate stiffness, which are primarily detected via mechanosensitive machinery linked to the actin cytoskeleton. Disruptions to β-actin, …

Creating Sustainable School And Home Gardens: Organic Pest Management, Ruby Mohr, Kathy Cabe Trundle, Rita Hagevik

All Current Publications

This fact sheet on organic pest management outlines sustainable gardening practices that promote ecological balance and biodiversity. It defines organic pest management as a proactive method, using natural insecticides like sulfur and neem oil, along with unique pest control strategies such as beer traps and cinnamon repellents. Additionally, it highlights plants like mint and marigolds that repel harmful pests while attracting beneficial insects. By implementing these approaches, gardeners can protect crops sustainably, enhance soil health, and reduce reliance on synthetic pesticides, thus supporting a healthier food system.

External Jugular Vein Catheterization Technique For Continuous Blood Sampling In Gilts, Preechaphon Taechamaeteekul, Yosua Kristian Adi, Chutikan Srisang, Pirada Virankabutra, Natchanon Dumniem, Jinda Singlor, Padet Tummaruk

The Thai Journal of Veterinary Medicine

External jugular vein blood collection is common in gilts and sows, but continuous sampling for hormonal and pharmacokinetic research requires catheterization. The standard protocol has remained largely unchanged for nearly 40 years. This study aimed to develop a modified external jugular vein catheterization technique in gilts. Ten gilts (72.0 ± 3.4 kg) underwent surgery under general anesthesia after 12-hour fasting. Sedation was induced with intramuscular Xylazine (4.4 mg/kg) and Tiletamine–Zolazepam (2.2 mg/kg), followed by intravenous Thiopental sodium (10 mg/kg). Once anesthetized, gilts were placed in dorsal recumbency, and the external jugular fossa was prepared under sterile conditions. A 10 cm …

Restricted Feeding Of Goats During The Last Third Of Gestation And Trans-Generational Effects On Plasma Progesterone In Their Female Offspring, Andrew A. Ponter, Bérengère Laporte, Sabine Roussel, Winai Kaewlamun, Pascale Chavatte-Palmer, Christine Duvaux-Ponter

The Thai Journal of Veterinary Medicine

Feeding levels can vary in goat farms for several reasons. Underfeeding of gestating dairy goats can occur and may influence fetal follicle development and future reproductive performance in their offspring. The objective of this experiment was to study the effect of restricted feeding during the last third of gestation on some reproductive parameters in female offspring (F1). Two feeding groups were formed using 60 Alpine and Saanen dairy goats to produce the F1 female offspring. The control group (C, n = 30) was fed to requirements. The restricted group (R, n = 30) was given the same diet, but the …

Stepwise Regression Analysis To Assess Various Factors Affecting On Fresh Sperm Quality In Ouled Djellal Ram, Yamina Belkhiri, Souheyla Benbia, Farida Bouzebda-Afri, Zoubir Bouzebda, Ramzi Lamraoui

The Thai Journal of Veterinary Medicine

The aim of this study was to evaluate the effect of various factors on fresh semen quality in Ouled Djellal rams. Specifically, we examined the impact of semen collection method, season, ram age, testosterone levels, body weight , and testicular weight. Twelve mature Ouled Djellal rams were used in the trial. Six rams were trained for semen collection using an artificial vagina (AV), while semen from the other six rams was collected using an electroejaculator (EE) biweekly throughout the year. Stepwise regression analysis showed that 62.50% of the variation in sperm volume, 48.60% of the variation in mass motility, 62.70% …

Impact Of Acute Stress On Circadian Rhythm Regulation Of Locomotor Activity In Syrian Hamsters, Raquel A. Villarreal, Laura E. Garcia, Mario Gil

Research Symposium

Background: Disruptions of circadian rhythms, caused by factors such as environmental changes or stress, are linked to health conditions, including metabolic disorders, cardiovascular diseases, and mood disorders. Circadian rhythm disturbances are particularly relevant for understanding the etiology of conditions like insomnia, depression, and anxiety. The circadian rhythm, primarily regulated by the suprachiasmatic nuclei (SCN) in the hypothalamus, coordinates biological processes to align with daily environmental cycles. Acute stress, especially when experienced immediately upon waking, has been shown to disrupt these rhythms, impair sleep regulation, and exacerbate mood dysregulation. Given the significant clinical implications, understanding how stress impacts circadian rhythms is …

The Triassic Cuddle: A Tale Of Love And Extinction, Jack Dupuy

Osmosis Magazine

An injured amphibian crawls into a burrow to escape from harsh reality. Outside, the shrieks of dying animals pierce the silence over a hellish backdrop of flowing lava and dark, ominous clouds of volcanic ash. Still recovering from broken ribs and trying its best to survive the desolate conditions, the amphibian curls up next to the burrow's owner, a mammal-like reptile. Moments later, a flash flood traps and drowns the unlikely roommates, immortalizing their relationship for the next 250 million years.

An Ever-Growing Web: Spider Silk In Medicine, Andrew Watts

Osmosis Magazine

For decades, graduates from the University of Richmond have crafted a robust web of alumni spanning various regions and professions. Much like its graduates, Richmond’s famed spider mascot has been capitalizing on the strength of its own web and engineering solutions to the most pressing problems in a new and rather unexpected territory–medicine.

Spider silk has unique chemical and physical properties that allow it to be used in many different capacities.

Osmosis Magazine - Fall 2022

Osmosis Magazine

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

Balancing Nutrients For The Seen And Unseen: A Study Of The Nitrate Levels At The University Of Richmond, Courtney Simpson, Nathan Winiarski

Osmosis Magazine

The Westhampton Lake is one of the University of Richmond’s most beautiful features. Though, when studied, the lake is a more complex ecosystem than it appears. While students can easily identify birds, reptiles, and fish, we often fail to recognize the importance of microscopic organisms and their role in nutrient reduction.

The Octopus: An Alien On Earth, Jack Dupuy

Osmosis Magazine

Imagine scientists discover a new creature that can change colors at will and blend into any background. It can also shapeshift to imitate other species of animals. It even has arms that can smell and taste! Thankfully, this intelligent, alien creature cannot wreak havoc on earth’s soil, but it is not a figment of our wildest imagination. This creature lives in our oceans…

The Footprints Disrupting Pre-Historic American Archeology, Caterina Erdas

Osmosis Magazine

Bold claims that 60 ancient footprints in White Sands National Park in New Mexico are over 21,000 years ago, published broadly in 450 news outlets, are unconvincing to key archeologists of prehistoric America.