Physical Sciences and Mathematics Commons^™

Transcriptional Dynamics During Rhodococcus Erythropolis Infection With Phage Wc1, Dana Willner, Sudip Paudel, Andrew D. Halleran, Grace E. Solini, Veronica Gray, Margaret Saha

Arts & Sciences Articles

Background

Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process.

Results

By five …

Non-Native Rhizophora Mangle As Sinks For Coastal Contamination On Moloka’I, Hawai’I, Geoffrey Szafranski, Elise F. Granek, Michelle L. Hladik, Mia Hackett

Environmental Science and Management Faculty Publications and Presentations

Coastal mangrove forests provide a suite of environmental services, including sequestration of anthropogenic contamination. Yet, research lags on the environmental fate and potential human health risks of mangrove-sequestered contaminants in the context of mangrove removal for development and range shifts due to climate change. To address this, we conducted a study on Moloka'i, Hawai'i, comparing microplastic and pesticide contamination in coastal compartments both at areas modified by non-native red mangroves (Rhizophora mangle) and unmodified, open coastline. Sediment, porewater, and mangrove plant tissues were collected to quantify microplastic and pesticide concentrations across ecosystem type. Average microplastics were similar between …

Monarch Science Observer, Volume 18, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Spring 2024, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

Agricultural Groundcover Update February 2024, Justin Laycock

Natural resources published reports

• About 92% of the grainbelt had adequate (more than 50%) vegetative groundcover to prevent wind erosion in February 2024.

• Nearly 8% of the grainbelt (1,193,400 ha) had less than 50% groundcover, which is inadequate to prevent wind erosion.

• The northern grainbelt had the highest risk of wind erosion and 16.5% of this farmland had inadequate groundcover.

• Less than 0.7% of the grainbelt had a high to very high risk of wind erosion because groundcover was less than 30%.

Ecological Monitoring Program At Vims Esl: Annual Report 2023, Paige G. Ross, Richard A. Snyder

Reports

An Ecological Monitoring Program (EMP) has been established at the Virginia Institute of Marine Science Eastern Shore Laboratory (VIMS ESL) for the coastal environment near the Wachapreague lab. The goals of the initiative are to 1) provide status and trends information to scientists who study and regulators who manage Virginia’s marine resources, 2) provide a scientific context for short-term research and grant proposals 3) provide pedagogical enrichment for educators to use in their classes, and 4) build capacity in staff expertise and training of interns and students at VIMS ESL.

The program formalizes and standardizes data collection for a long-term …

Ecology And Conservation Of Diamondback Terrapins In Virginia, Cypress Ambrose

Undergraduate Honors Theses

The diamondback terrapin (Malaclemys terrapin) is the only turtle species native to North America with specific morphological and physiological adaptations to estuarine environments. Along with many other pressures contributing to population declines, terrapins frequently become trapped and drown as bycatch in crab pots used in the commercial and recreational blue crab (Callinectes sapidus) fishery. A wealth of evidence supports the use of inexpensive bycatch reduction devices (BRDs) that can be attached to the entrances of these traps, which leads to a marked decrease in terrapin bycatch while not reducing crab catch dramatically. Virginia is the only …

Mean Flow And Dispersion In The Western Mediterranean Sea From Drifter Observations, Helga Huntley, James Turbett, A.D. Kirwan, Jr., Pierre-Marie Poulain

Faculty Scholarship for the College of Science & Mathematics

Currents in the ocean distribute water masses and everything floating in them. To understand how fast the water (and its flotsam) travels and how effectively it mixes, we need to study the flow statistics. There are two types of measurements of ocean currents: Eulerian measurements that look at how the ocean velocities change at a stationary point on the Earth; and Lagrangian measurements that follow a water mass. Dispersion and mixing is generally best captured by Lagrangian measurements. At the submesoscale (~10-1 – 10 km), the observational tool of choice are drifters, or floating buoys, tethered to a drogue that …

An Investigation On The Intricacies Of Epigenetic Modulations In The Pathogenesis Of Human Papillomavirus-Associated Cervical Cancer: A Comprehensive Meta-Narrative Synthesis, Jade Carolina Cabello, Marcella Victoria Ras, Katelyn Thy Nhung Tran, Athit Voytas

Research Methods Poster Session 2024

Abstract

Objective: To conduct a meta-analysis of the available and relevant literature on E1/E2 genes and their affect on the epigenetics of Human Papillomavirus caused uterine cervical cancer.

Background/Significance: Human Papillomavirus is strongly linked to cervical cancer, and cervical cancer is the fourth most common type of cancer in women. 99.7% of patients with cervical cancer have a “high risk HPV genotype” which factors greatly into the causation if their diagnosis. The HPV vaccine that came out in 2006 has greatly decreased cervical cancer in the population as well as increased the preventative chances of highly susceptible individuals.

Methods: To …

Climate Change-Associated Declines In Water Clarity Impair Feeding By Common Loons, Walter H. Piper, Max R. Glines, Kevin C. Rose

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Climate change has myriad impacts on ecosystems, but the mechanisms by which it affects individual species can be difficult to pinpoint. One strategy to discover such mechanisms is to identify a specific ecological factor related to survival or reproduction and determine how that factor is affected by climate. Here we used Landsat imagery to calculate water clarity for 127 lakes in northern Wisconsin from 1995 to 2021 and thus investigate the effect of clarity on the body condition of an aquatic visual predator, the common loon (Gavia immer). In addition, we examined rainfall and temperature as potential predictors …

Simultaneous Extraction And Quantitative Analysis Of S-Methyl-L-Cysteine Sulfoxide, Sulforaphane And Glucosinolates In Cruciferous Vegetables By Liquid Chromatography Mass Spectrometry, Armaghan Shafaei, Caroline R. Hill, Jonathan M. Hodgson, Lauren C. Blekkenhorst, Mary C. Boyce

Research outputs 2022 to 2026

Sulfur containing compounds including glucosinolates (GLS), sulforaphane (SFN) and S-methyl-L-cysteine sulfoxide (SMCSO) have been proposed to be partly responsible for the beneficial health effects of cruciferous vegetables. As such, greater understanding of their measurements within foods is important to estimate intake in humans and to inform dietary intervention studies. Herein is described a simple and sensitive method for simultaneous analysis of 20 GLS, SFN and SMCSO by liquid chromatography mass spectrometry. Analytes were effectively retained and resolved on an Xbridge C18 column. Detection can be achieved using high resolution or unit resolution mass spectrometry; the latter making the method more …

Desalination As A Source Of Freshwater, Jacob Pensky

Best Integrated Writing

Jacob Pensky's article deals with technology we use to make saltwater drinkable. Drought-stricken coastal communities need desalination plants, especially as Earth's climate warms, but they are expensive and energy-intensive. This article describes ways to reduce the environmental and monetary costs.

Use Of Unoccupied Aerial Vehicle (Drones) Based Remote Sensing To Model Platform Topography And Identify Human-Made Earthen Barriers In Salt Marshes, Joshua J. Ward

Masters Theses

Elevation is a foundational driver of salt marsh morphology. Elevation governs inundation and hydrological patterns, vegetation distribution, and soil health. Anthropogenic impacts at grand scales (e.g., rising sea levels) and local scales (e.g., infrastructure) have altered the elevation of the salt marsh surface, changing the topography and morphology of these ecosystems. This study establishes and assesses means to document and analyze these impacts using Unoccupied Aerial Vehicle (UAV) based remote sensing to model platform topography. This thesis’s first and primary study presents and compares methods of producing high-resolution digital terrain models (DTMs) with UAV-based Digital Aerial Photogrammetry (DAP) and Light …

Synthesis, Molecular Characteristics, And Antibacterial Assessment Of Marine Hydroid Aqueous Extract-Based Silver Bio-Nanoparticles, Fredryk Mandey, Aulia Rhamdani Arfan, Rugaiyah Andi Arfah

Makara Journal of Science

This investigation aims to synthesize, analyze the molecularity, and test the ability of bacterial inhibition capability of silver nanoparticles that have been synthesized by simply mixing silver nitrate and aqueous extracts of marine natural products with and without the addition of amylum as a stabilizing agent. This research, with and without the addition of amylum as a stabilizing agent, obtained 39.0 and 55.2 mg of solids of round-shaped morphology silver nanoparticles with diameters of 87.9 and 103.0 nm., respectively. In addition, the antibacterial testing assay against Staphylococcus aureus and Escherichia coli showed some considerably good results. S. aureus with the …

Multi-Scale Simulations Of Dynamic Protein Structures And Interactions, Yumeng Zhang

Doctoral Dissertations

Intrinsically disordered proteins (IDPs) are functional proteins that lack stable tertiary structures in the unbound state. They frequently remain dynamic even within specific complexes and assemblies. IDPs are major components of cellular regulatory networks and have been associated with cancers, diabetes, neurodegenerative diseases, and other human diseases. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for mechanistic understanding of IDPs in biology, diseases, and therapeutics. However, accurate simulation of the heterogeneous ensembles and dynamic interactions of IDPs is extremely challenging because of both the prohibitive computational cost and demanding force field …

High Resolution Mass Spectrometry As A Platform For The Analysis Of Polyoxometalates, Their Solution Phase Dynamics, And Their Biological Interactions., Daniel T. Favre

Doctoral Dissertations

Polyoxometalates (POMs) are a class of inorganic molecule of increasing interest to the inorganic, bioinorganic and catalytic communities among many others. While their prevalence in research has increased, tools and methodologies for the analysis of their fundamental characteristics still need further development. Decavanadate (V10) specifically has been postulated to have several unique properties that have not been confirmed independently. Mass spectrometry (MS) and its ability to determine the composition of solution phase species by both mass and charge is uniquely well suited to the analysis of POMs. In this work we utilized high-resolution mass spectrometry to characterize V10 in aqueous …

Methionyl-Trna Synthetase Synthetic And Proofreading Activities Are Determinants Of Antibiotic Persistence, Whitney N. Wood, Miguel Angel Rubio, Lorenzo Eugenio Leiva, Gregory J. Phillips, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bacterial antibiotic persistence is a phenomenon where bacteria are exposed to an antibiotic and the majority of the population dies while a small subset enters a low metabolic, persistent, state and are able to survive. Once the antibiotic is removed the persistent population can resuscitate and continue growing. Several different molecular mechanisms and pathways have been implicated in this phenomenon. A common mechanism that may underly bacterial antibiotic persistence is perturbations in protein synthesis. To investigate this mechanism, we characterized four distinct metG mutants for their ability to increase antibiotic persistence. Two metG mutants encode changes near the catalytic site …

In Silico Analysis Of C-Type Lectins As Co-Infection Receptors Of Dengue And Chikungunya Viruses In Aedes Aegypti, Munawir Sazali, R. C. Hidayat Soesilohadi, Nastiti Wijayanti, Tri Wibawa, Arif Nur Muhammad Ansori

Makara Journal of Science

Aedes aegypti is a primer vector of dengue virus (DENV) and chikungunya virus (CHIKV). The susceptibility of mosquitoes to DENV and CHIKV depends on their recognition receptor of pathogens. C-type lectins (CTLs) are an important mediator of virus infection in A. aegypti. This study aims to identify potential receptors and determine the binding affinity between ligand–receptor interaction, CTLs and virus envelopes (DENV-1, 2, 3, and 4 and CHIKV) interaction based on in silico analysis. Sample sequences were obtained from GenBank (NCBI), and 10 CTLs were acquired from VectorBase. Homology modeling based on a minimum standard of 20% was processed …

Mathematically Modeling How Trapping Regimes That Target Specific Crayfish Life Stages Impact Removal Efficacy, Rini Pattison

Seaver College Research And Scholarly Achievement Symposium

The red swamp crayfish, Procambarus clarkii, is an invasive species introduced into several streams within the Santa Monica Mountains (SMM) in Southern California. Crayfish predation decimates native aquatic species. Thus, the Mountains Restoration Trust (MRT) and Environmental Restoration Group have worked to remove crayfish through regular trapping in Malibu Creek.

To aid conservation efforts, former SURB students William Milligan and Dev Patel developed mathematical models of crayfish removal efficacy. Milligan created a differential equation model of how crayfish removal affects local newt populations. Patel expanded Milligan’s crayfish model by creating a discrete model of the crayfish life cycle that newly …

Coomassie Brilliant Blue Dye As A Method For Analyzing Fracture Markings In Bone, Abigail Hoffmeister, David Harutunyan, Matthew Aizawa, Everett Baker, Brandon Mendoza, Chase Freeman, Siran Iskanian

Seaver College Research And Scholarly Achievement Symposium

Coomassie Brilliant Blue Dye is a dye commonly used to stain proteins. Because of its ability to adhere to proteins, this research has focused on perfecting a method of dyeing a fractured flat bone in order to most accurately observe and analyze fracture markings within the trabecular layer. Stereoscopic microscopy was the chosen technique of analysis for this research because of its proven effectiveness in glass and ceramic fractography to observe varying depths. In order to most effectively apply stereoscopic microscopy to this research, the following variables were manipulated to maximize color contrast in the trabecular layer in order to …

Deep Learning Can Be Used To Classify And Segment Plant Cell Types In Xylem Tissue, Reem Al Dabagh, Benjamin Shin, Sean Wu, Fabien Scalzo, Helen Holmlund, Jessica Lee, Chris Ghim, Samuel Fitzgerald, Marinna Grijalva

Seaver College Research And Scholarly Achievement Symposium

Studies of plant anatomical traits are essential for understanding plant physiological adaptations to stressful environments. For example, shrubs in the chaparral ecosystem of southern California have adapted various xylem anatomical traits that help them survive drought and freezing. Previous studies have shown that xylem conduits with a narrow diameter allows certain chaparral shrub species to survive temperatures as low as -12 C. Other studies have shown that increased cell wall thickness of fibers surrounding xylem vessels improves resistance to water stress-induced embolism formation. Historically, these studies on xylem anatomical traits have relied on hand measurements of cells in light micrographs, …

La1-Xsrxcoo3 Perovskite Nanomaterial: Synthesis, Characterization, And Its Biomedical Application, Adhira Tippur, Anyet Shohag, Luke Franco, Ahmed Touhami, Swati Mohan, Mohammed Uddin

Research Symposium

Early cancer detection is paramount for effective treatment and potential cures. This research explores the application of perovskite materials, specifically Sr2+-doped Lanthanum Cobaltite (La1-xSrxCoO3) nanomaterials, in cancer detection, with a focus on rats as an experimental model. The ferroelectric nature of these materials, synthesized through a combination of sol-gel and molten-salt processes, was examined at varying Sr2+ doping levels (1-20 wt%). Rigorous characterization, employing X-ray diffraction and scanning electron microscopy, confirmed the uniform morphology of nano cubes, laying the foundation for subsequent investigations. The magnetic properties of the perovskite nanoparticles were probed, suggesting their potential as a diagnostic tool for …

Silvopastoral Agroforestry In Upland And Lowland Uk Grassland: Tree Growth And Animal Performance, W R. Eason, R Lavender, R O. Clements, C Duller, E Gill, M Hislop

IGC Proceedings (1997-2023)

Trees, individually protected from herbivore damage using plastic shelters, were planted at two densities (100 and 400 stems/ha) into sheepgrazed pasture in upland and lowland UK grassland sites in 1988. Tree and animal performance were compared with conventional forestry (no sheep) and pasture (no tree) systems. Effects on tree growth and survival are highly species and site dependent although some treatment effects did emerge. Tree shelters encouraged rapid early height growth compared to forestry controls although in some cases tree form was also adversely affected. Generally tree performance within agroforestry treatments was better at the higher planting density. Eight years …

Use Of Annual Self-Reseeding Legumes In An Oak Forest In Central Italy, P Talamucci, G Argenti, A Pardini, S Piemontese, N Stagliano

IGC Proceedings (1997-2023)

A trial has been carried out for three years in an oak coppice geometrically thinned out of Mediterranean Central Italy, about the functioning of a pastoral system made by four different resources: native pasture, subterranean clover (Trifolium brachycalycinum Katzn. et Morley) in pure stand, strips thinned out and firebreaks improved with oversown subclover, all grazed by sheep. Subclover increased the forage yield and improved the palatabilty of the pasture and the regularity of grazing; the higher biomass intake by animals reduced the quantity of dried biomass in summer and contributed to keep low either fire hazards or flame diffusion …

The Effects Of Shelterbelts On Adjacent Pastures And Soils In A Temperate Climate, A G. Gillingham, M F. Hawke

IGC Proceedings (1997-2023)

Two trials were conducted to differentiate the direct (exposure) from the indirect (modified soil fertility due to nutrient transfer by grazing animals) effects of farm shelterbelts on associated pasture growth.Soil from close to “unmanaged”shelterbelts with dense shelter to ground level had relatively high potassium (K) levels and, in a glasshouse situation, provided more pasture growth than soil from further distances, or from adjacent to “managed” shelterbelts. Pasture grown in boxes of a common soil implanted at increasing distances from a shelterbelt also produced highest growth rates close to shelter. These results generally explain the pattern of resident pasture growth, except …

Temperate Pasture And Sheep Performance Under Radiata Pine And In Open Pasture, K M. Pollock, R J. Lucas, D B. Pownall, S E. Thomson

IGC Proceedings (1997-2023)

Forage production from years 4 to 6 of an agroforestry system at 400-600 trees per ha and pasture alone were compared for a temperate sub-humid environment. Forage production was best for lucerne pasture followed by phalaris/clover and cocksfoot/clover, and least for ryegrass/clover and the ryegrass only pastures. Total pasture production in the agroforest relative to the open pasture was from 10% more for phalaris to 20% less for lucerne. Sheep carrying capacity over all pastures was 14.6 sheep/ha in the open and 11.8 sheep/ha in the agroforest and varied by ±15% according to the pasture types.

Grazing Management Of Tagasaste (Chamaecytisus Proliferus) For Sheep And Cattle Production In Southern Australia, N J. Edwards, G M. Allen, D M. Mcneill, C M. Oldham

IGC Proceedings (1997-2023)

Direct grazing of hedgerows of tagasaste (Chamaecytisus proliferus) by sheep or cattle appear to be very robust systems. Tagasaste persists under a continuous grazing regime with cattle such that plant regrowth maintained between 5 and 10 cm in length produces in excess of 215 kg of animal liveweight/ha/year. This level of production is also sustained within a rotational grazing regime. Under both grazing systems cattle production within a year is highly seasonal, with liveweight gains from young cattle peaking at 1.0-1.5 kg/head/day in winter and spring, but dropping to maintenance only by late summer-autumn. Sheep, like cattle, can …

Shrub Palatability To Rusa Deer (Cervus Timorensis Russa) In New Caledonia, C Corniaux, S Le Bel, J M. Sarrailh

IGC Proceedings (1997-2023)

The objective of this study was to determine a palatability scale of five shrub legumes to rusa deer during the dry season in New Caledonia. Acacia ampliceps and Samanea saman remain low in acceptability. Gliricidia sepium is more palatable but quite less than Leucaena leucocephala (native cultivar) and Calliandra calothyrsus (San Ramon). Therefore, since the regression of Leucaena leucocephala population, Calliandra calothyrsus could be very promising to replace it in the deer diet. On the other hand, Acacia ampliceps seems to be the most interesting shrub legume to plant in the west coast, where soil erosion, due to successive droughts …

Soil Nutrient Redistribution Pattern About The Tree In A Silvopastoral System, L C. Nwaigbo, H G. Miller, A R. Sibbald, G Hudson

IGC Proceedings (1997-2023)

The objective of this paper is to report the effect of animal-tree interactions on soil nutrient redistribution pattern in a grazed silvopastoral experiment site at Glensaugh, in NE Scotland. Scots pine (Pinus sylvestris L) tree species were planted in square lattice arrangements at 5 m x 5 m, spacing (400 stems/ha) on plots replicated over three blocks in Randomized Complete Block design on a predominantly rye grass (Lolium perenne L) pasture which was grazed by sheep yearly from April to October. Included in the design were grazed pasture plots without trees (Control). Soil samples were collected from around …

Trees For Shelter: The Implications In Agroforestry System, L C. Nwaigbo, A R. Sibbald, G Hudson

IGC Proceedings (1997-2023)

The objective of this study was to determine the horizontal and vertical variations in soil penetration resistance (PR) observed at tree-scale in silvopastoral plots that were grazed by sheep with and without trees. Sycamore trees (Acer pseudoplatanus L) were planted in the spring of 1988 at 10 m x 10 m spacing (100 stems/ha) at Glensaugh NE of Scotland on plots replicated over three blocks in Randomized Complete Block design on a predominantly rye grass (Lolium perenne L) pasture. Included in the design were pasture plots without trees (Control). The experiment is grazed by sheep yearly from April to …

A Silvopastoral System In The North Atlantic Zone Of Costa Rica: Combining Indigenous Timber Species With Dairy Pasture Swards, A Moulaert- Quiros, J P. Mueller, M Villarreal, R Piedra, L Villalobos

IGC Proceedings (1997-2023)

The objective of this study was to design, establish and monitor a silvo pastoral experiment on a dairy farm in the northern Atlantic region of Costa Rica. Indigenous timber species, Vochysia guatemalensis and Hyeronima alchorneoides were used together with or without the tropical pasture legume, Arachis pintoi in a split plot design with a 4 x 2 x 2 factorial arrangement. First year establishment was good for the tree component (2.3 to 10 % mortality) but poor for A. pintoi (4 to 5 % of sward). Poor legume establishment was attributed to lax grazing management and excess competition from existing …