Organisms Commons^™

Corporate ‘Capture Strategies’ Impacting Human And Ecosystem Health, Alex T. Ford, Marlene Ågerstrand, Michael G. Bertram, Miriam L. Diamond, Rainer Lohmann, Andreas Schäffer, Martin Scheringer, Gabriel Sigmund, Anna Soehl, Maria Clara V.M. Starling, Noriyuki Suzuki, Marta Venier, Penny Vlahos

Graduate School of Oceanography Faculty Publications

The concept of regulatory capture has been extensively studied in academic literature, primarily within the social sciences. This phenomenon has been increasingly discussed in the environmental sciences as the impacts of regulatory capture on human and ecosystem health have become increasingly apparent. Regulatory capture is just one tactic employed by vested interests in the strategy of delaying, weakening, or abolishing policies designed to protect the public interest. Here, we define capture strategies as ‘the act of influencing individuals, organizations, or governments to prioritize corporate interests over those of human and ecosystem health’. Similar to the evolution of terms like whitewashing …

The Role Of Horizontal Gene Transfer In Antibiotic Resistance Amidst Prevalent Community And Healthcare-Associated Mrsa Rates, Gabrielle Nascimento

Honors College Theses

In recent decades, cases of community-acquired MRSA (CA-MRSA) and healthcare-associated MRSA (HA-MRSA) have been on the rise. The ability of antibiotic resistance to transfer between microorganisms greatly expands its threat to the effective treatment and containment of bacterial infections. The mecA gene is found on a mobile cassette within the Staphylococcal cell and encodes for PBP2a, an alternate version of penicillin-binding protein (PBP) with less binding affinity for β-lactam antibiotics, increasing resistance to the effects of antibiotics. The goal of this research is to investigate the horizontal transfer of the mecA gene between various Staphylococcus species as well as to …

Investigating Regulation And The Regulome Of The Nucleic Acid Binding Protein Spovg Within Borrelia Burgdorferi, Timothy C. Saylor

Theses and Dissertations--Medical Sciences

Prior studies indicated Borrelia burgdorferi SpoVG protein was regulated, SpoVG binds specifically to a number of nucleic acids, and SpoVG binds to the non-variable section of the major virulence factor vlsE. Although a direct transcriptional activator or inhibitor was not elucidated, it is shown that SpoVG is regulated based on cell culture density independent of the growth rate of B. burgdorferi, indicating that SpoVG regulation is outside the scope of the alternative sigma factor RpoS. Using a dCas9 CRISPRi construct to target SpoVG resulted in protein expression trending towards upregulation of the BosR-RpoS regulon, and a marked decrease …

Gene Expression In Relation To Bone Fractures In Throughbred Racehorses, Anna M. Rauber-Ramos

Theses and Dissertations--Veterinary Science

Evidence that fractures in Thoroughbred racehorses are outcomes of chronic bone microdamage has led to extensive research into identifying horses at increased risk of fracture. This includes the use of biomarkers and messenger RNA (mRNA) as a measure of bone turnover. Previous research has found expression differences in horses with fractures compared to controls. Utilizing pre-race whole blood samples collected over an 18-month period from Thoroughbred racehorses in Southern California, RNA-sequencing was conducted on horses with bone fractures and race-matched controls to identify differences in gene expression. Focusing on third metacarpal (MC3) and proximal sesamoid bone (PSB) fractures, differentially expressed …

The Role Of Floodplain Complexity In Wood Turtle Habitat Use, Laura S. Deming

Antioch University Dissertations & Theses

Wood turtles occupy cold, low-gradient riverine habitat throughout the northeastern United State and southeastern Canada. Stream alterations, such as dams, channel straightening, and floodplain development have diminished the natural hydrologic and sedimentation regimes that result in complex channel and floodplain geomorphology. Studies throughout the species’ range have quantified many aspects of their habitat, but none have quantified components of geomorphology of wood turtle sites. The goal of this study was to explore the role of stream channel and floodplain geomorphology in wood turtle habitat use, with specific objectives to (1) quantify components of stream channel and floodplain geomorphic complexity, (2) …

Dengue Virus Modulates Critical Cell Cycle Regulatory Proteins In Human Megakaryocyte Cells, Swarnendu Basak, Shovan Dutta, Supreet Khanal, Girish Neelakanta, Hameeda Sultana

Biological Sciences Faculty Publications

Suppression of human megakaryocytes by dengue virus (DENV) infection significantly reduces the platelet count that eventually leads to thrombocytopenia, severe dengue and death. To understand DENV interactions with megakaryocytes, we investigated the cell cycle in leukemic human megakaryocytic in vitro cell line (MEG-01 cells). Megakaryocytes are known for complex endomitotic cell cycle leading to their polyploidy state. Our study shows that DENV uses these polyploid cells for its replication. Understanding the modulation of DENV-mediated cell cycle regulation in megakaryocytes is therefore highly important. We show that DENV2 (serotype 2) infection significantly modulates cell cycle signaling. Our protein profile microarray data …

Mxene-Based Materials For Enhanced Water Quality: Advances In Remediation Strategies, Ali Mohammad Amani, Milad Abbasi, Atena Najdian, Farzaneh Mohamadpour, Seyed Reza Kasaee, Hesam Kamyab, Shreeshivadasan Chelliapan, Mostafa Shafiee, Lobat Tayebi, Ahmad Vaez, Atefeh Najafian, Ehsan Vafa, Sareh Mosleh-Shirazi

Electrical & Computer Engineering Faculty Publications

Two-dimensional MXenes are promising candidates for water treatment because of their large surface area (e.g., exceeding 1000 m²/g for certain structures), high electrical conductivity (e.g., >1000 S/m), hydrophilicity, and chemical stability. Their strong sorption selectivity and effective reduction capacity, exemplified by heavy metal adsorption efficiencies exceeding 95 % in several studies, coupled with facile surface modification, make them suitable for removing diverse contaminants. Applications include the removal of heavy metals (e.g., achieving >90 % removal of Pb(II)), dye removal (e.g., demonstrating >80 % removal of methylene blue), and radioactive waste elimination. Furthermore, 3D MXene architecture exhibit enhanced performance in antibacterial …

Man With An Itchy Back, Katherine Schaffer, Nevin Adamski, Brittany Ambrose, Kathleen Anderson

Department of Emergency Medicine Faculty Publications

[First paragraph] A 61-year old man with no significant past medical history presented with painful bug bites on his lower back 1 day after a 1.5-week-long visit to Africa. He noticed bug bites on his lower back 3 days ago; since then, they have increased in size and become more painful. He was prescribed doxycycline at urgent care earlier that morning and had taken 1 dose. He is taking prophylactic medications for malaria and has had no fever at home. Vital signs, exquisitely tender papular lesions with a central punctum and surrounding erythema in the bilateral paralumbar regions.

Bacterial Two-Hybrid Systems Evolved: Innovations For Protein-Protein Interaction Research, Rebecca M. Richardson, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Bacterial two-hybrid (B2H) systems offer a versatile platform for detecting protein-protein interactions (PPIs) in vivo. Originally developed to study bacterial transcriptional regulators, these systems have evolved to support a wide range of applications, including interaction mapping, domain analysis, and high-throughput screening. This review surveys the development and expansion of B2H systems across diverse biological contexts. We highlight technical considerations, platform-specific innovations, and recent adaptations that extend the utility of B2H systems in both prokaryotic and eukaryotic protein interaction research environments. By comparing different B2H variants and discussing their integration with complementary approaches, we provide a framework for leveraging these …

Nucleotide-Derived Bacterial Alarmones Attenuate The Induction Of Type-I Interferon Responses In A Murine Macrophage Reporter Cell Line, Ryan P. Kilduff, Erin B. Purcell, Lisa M. Shollenberger

Chemistry & Biochemistry Faculty Publications

The stringent response is a well-studied phenomenon in many bacterial systems and regulates resource-consuming activities such as transcription, translation, and replication. The stringent response is a well-conserved signaling framework, as are the nucleotide-derived signaling mediators, collectively referred to as (p)ppGpp or as alarmones. There is a wealth of research evaluating nucleotide-derived alarmone signaling in bacterial models, however, their potential to modulate innate immune signaling has not yet been evaluated. Several common pathogen-synthesized molecules, such as lipopolysaccharide (LPS) and cyclic-di-AMP (c-di-AMP), act as pathogen-associated molecular patterns (PAMPs), which are common patterns that alert the innate immune system of bacterial infection. The …

Environmentally Friendly Chelation For Enhanced Algal Biomass Deashing, Agyare Asante, George Daramola, Ryan W. Davis, Sandeep Kumar

Civil & Environmental Engineering Faculty Publications

High ash content in algal biomass limits its suitability for biofuel production by reducing combustion efficiency and increasing fouling. This study presents a green deashing strategy using nitrilotriacetic acid (NTA) and deionized (DI) water to purify Scenedesmus algae, which was selected for its high ash removal potential. The optimized sequential treatment (DI, NTA chelation, and DI+NTA treatment at 90–130 °C) achieved up to 83.07% ash removal, reducing ash content from 15.2% to 3.8%. Elevated temperatures enhanced the removal of calcium, magnesium, and potassium, while heavy metals like lead and copper were reduced below detection limits. CHN analysis confirmed minimal …

Synthesis And Evaluation Of Anti-Hiv Activity Of Fatty Acyl Conjugates Of Tenofovir Alefanamide, Muhammad Sajid, Naglaa Salem El-Sayed, Louise A. Ouattara, Amita Verma, Gustavo F. Doncel, Keykavous Parang, M. Iqbal Choudhary, Hina Siddiqui

CONRAD Publications

The activity of nucleoside and nucleotide analogs as antiviral agents requires phosphorylation by intracellular enzymes. Phosphate-substituted analogs have low bioavailability due to the presence of ionizable negatively-charged groups. To circumvent this limitation, several prodrug approaches have been proposed and developed. Herein, we hypothesized that the conjugation of anti-HIV fatty acids with the nucleotide tenofovir alafenamide (TAF) (1) could improve the anti-HIV activity of the nucleotide. Several fatty acyl amide conjugates of TAF were synthesized and evaluated in comparative studies with TAF. The synthesized compounds were evaluated as racemic mixtures for anti-HIV activity in vitro in a single-round HIV-1 infection assay …

The Importance Of Solution Studies For The Structural Characterization Of The Enterovirus 5' Cloverleaf, Morgan G. Daniels, Meagan E. Werner, Xiaobing Zuo, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Enteroviruses initiate genomic replication via a highly conserved mechanism that is controlled by an RNA platform, also known as the 5' cloverleaf (5'CL). Here, we present a biophysical analysis of the 5'CL conformation of three enterovirus serotypes under various ionic conditions, utilizing CD spectroscopy, size-exclusion chromatography, and small-angle X-ray scattering. In general, a tendency toward a smaller monomeric hydrodynamic radius in the presence of salts was observed, but the exact structural signature of each 5'CL varied depending upon the serotype. Rhinovirus B14 (RVB14) exhibited at least two monomeric conformations and a low propensity for dimerization, while poliovirus 1 (PV1) showed …

An E. Coli Two-Hybrid System To Investigate Human Protein-Protein Interactions, Rebecca M. Richardson, Sarah M. Ho, Lane Tong, Morgan G. Daniels, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Abstract

The LexA-E. coli two-hybrid (LexA-E2H) system was initially developed to study interactions between microbial proteins in an Escherichia coli (E. coli) environment. We here demonstrate its utility for studying mammalian protein interactions. Specifically, this study uses LexA-E2H to provide the first direct and quantitative validation of Glucose Regulated Protein 78 (GRP78) binding to the cleaved-Prostate Apoptosis Response 4 (cl-Par-4) tumor suppressor. Furthermore, the results establish that this interaction does not require phosphorylation of either protein. MacConkey agar was used for initial detection of the interaction through colorimetric colony screening, distinguishing pale white-pink colonies (+ interaction) from …

Copula-Based Bayesian Model For Detecting Differential Gene Expression, Prasansha Liyanaarachchi, N. Rao Chaganty

Mathematics & Statistics Faculty Publications

Deoxyribonucleic acid, more commonly known as DNA, is a fundamental genetic material in all living organisms, containing thousands of genes, but only a subset exhibit differential expression and play a crucial role in diseases. Microarray technology has revolutionized the study of gene expression, with two primary types available for expression analysis: spotted cDNA arrays and oligonucleotide arrays. This research focuses on the statistical analysis of data from spotted cDNA microarrays. Numerous models have been developed to identify differentially expressed genes based on the red and green fluorescence intensities measured using these arrays. We propose a novel approach using a Gaussian …

Contact Pathway Factors As Potential Modifiers Of Bleeding Related To Factor Xi Deficiency, Ivy R. Han, Leah Rosenfeldt, Courtney Young, Bal Krishan Phd, Rachel Cantrell Phd, Cassie Sprague, Mousa Kharnaf, William Abplanalp, Joseph Palumbo Md

Williams Honors College, Honors Research Projects

Factor XI (FXI) deficiency, also known as Hemophilia C, is characterized by mild to moderate bleeding symptoms. However, the factors that modify bleeding severity in FXI deficiency are not fully understood. In this study, we investigated whether components of the contact activation pathway can act as modifiers of bleeding in the context of FXI deficiency. Using a tail vein transection (TVT) model in rats, we assessed bleeding in four experimental groups: wild-type Sprague-Dawley rats, Prekallikrein knockout (PKK^-/-) rats, rats treated with a FXI-inhibiting antibody, and PKK-/- rats treated with the FXI antibody.

Under anesthesia, each rat underwent a …

Forecasting Covid-19 Cases, Hospital Admissions, And Deaths Based On Wastewater Sars-Cov-2 Surveillance Using Gaussian Copula Time Series Marginal Regression Model, Hueiwang Anna Jeng, Norou Diawara, Cynthia Jackson, Rekha Singh, Kyle Curtis, Raul Gonzalez, David Jurgens, Sasanka Adikari

Epidemiology, Biostatistics, & Environmental Health Faculty Publications

Modeling efforts are needed to predict trends in COVID-19 cases and related health outcomes, aiding in the development of management strategies and adaptation measures. This study was conducted to assess whether the SARS-CoV-2 viral load in wastewater could serve as a predictor for forecasting COVID-19 cases, hospitalizations, and deaths using copula-based time series modeling. SARS-CoV-2 RNA load in wastewater in Chesapeake, VA, was measured using the RT-qPCR method. A Gaussian copula time series (CTS) marginal regression model, incorporating an autoregressive moving average model and Gaussian copula function, was used as a forecasting model. Wastewater SARS-CoV-2 viral loads were correlated with …

Interobserver Variability Regarding Adequacy Of Oropharyngeal Exposure For Transoral Robotic Surgery May Necessitate Staging Endoscopy: Evaluating Tors Exposure, Colleen Schinderle, Kevin J. Carlson, Reem Sharaf Alddin, Jeffery J. Houlton, Matthew J. Bak, Daniel W. Karakla, Jonathan R. Mark

Department of Otolaryngology (ENT) Faculty Publications

[First paragraph] Transoral robotic surgery (TORS) for the treatment of oropharyngeal cancer has become centered at tertiary referral centers. To avoid treatment delays or multiple anesthetics, the need for repeat operative endoscopy may be questioned when the diagnosis has been made at an outside institution. However, inadequate visualization of relevant anatomy can preclude TORS candidacy and may lead to procedure abortion or conversion to an open technique.²,³ To evaluate this dilemma, we explored the ability to assess oropharyngeal exposure for TORS candidacy via operative endoscopic photo-documentation.

Diffuse Unilateral Leg Swelling, Bruce M. Lo, Kylie Butler, Navjot Kaur, Kirsten Pennell

Department of Emergency Medicine Faculty Publications

[Patient Presentation] A 46-year-old woman with a history of hypertension presented with 14 days of right leg pain. The pain began after straining her leg while lifting heavy boxes at work, with diffuse leg swelling noted 3 days later. She reported subjective fever but no other complaints. Patient denies any illicit drug use. Initial vital signs included a temperature of 100.1 °F, heart rate of 122 beats per minute, and blood pressure of 158/91 mm Hg. Physical examination revealed a diffusely swollen and tender right leg (Fig 1). Computed tomography (CT) of the right leg identified a 19 X 7 …

The Effect Of Temperature And Salinity On Margalefidinium Polykrikoides Group Iii Va, Usa Strain Growth, Eduardo Pérez-Vega, Margaret R. Mulholland, Katherine E. Crider, Kimberly E. Powell, P. Dreux Chappell, Alexander Bochdansky

OES Faculty Publications

Margalefidinium polykrikoides is a cosmopolitan dinoflagellate that blooms in coastal waters. Despite genomic evidence that it belongs to Group III and so closely related to isolates from Puerto Rico, Malaysia, North America, and Central America, M. polykrikoides blooms in the Chesapeake Bay at warmer temperatures and lower salinities than in coastal ecosystems occupied by its closest relatives. In this study, the effect of temperature and salinity on the growth rate and total cell yield of an M. polykrikoides VA culture isolate were examined and compared with environmental observations made during M. polykrikoides blooms in the Chesapeake Bay. M. polykrikoides group …