Digital Commons Network^™

Mapping The Tar Vrna Interaction With Hiv-1 Integrase, Jian Sun, Rahul Yadav, Tolga Catmakas, Luke Fisher, Nicholas C. Fitzkee, Jacques J. Kessl

Faculty Publications

A series of critical interactions within the viral core between viral RNA (vRNA) and HIV-1 Integrase (IN) has previously been reported. In these studies, contact points between vRNA and IN were identified using RNA-seq and MS-based protein foot-printing approaches. Several IN amino acids located in its C-terminal domain (CTD) were found to be essential for vRNA binding, and their alanine substitution severely impacted the correct morphogenesis of the mature viral core. Here, we have used the TAR element to extend these studies by performing a comprehensive mapping of the interaction by deploying RNA crosslinking and NMR methodologies. Together, these approaches …

One Assay To Rule Them All: Development Of A Global Environmental Dna Tool To Support Range-Wide Surveys Of An Imperiled Sawfish And Its Application In The Eastern Tropical Pacific, Juan C. Cubillos-M, Annmarie Fearing, Demian D. Chapman, Peter M. Kyne, P. Joana Dias, Cindy Gonzalez, Ryan N. Lehman, Yaliana Chichaco, Bryan L. Huerta-Beltrán, Kayla L. Mcculloch, Sarah M. Toepfer, John K. Carlson, Nicole M. Phillips

Faculty Publications

Environmental DNA (eDNA) has emerged as a powerful tool to support the conservation of threatened species. The sawfishes are one of the most imperiled vertebrate groups, with all five species classified as Critically Endangered on the IUCN Red List of Threatened Species. Owing to their toothy rostra, sawfishes are easily entangled in a wide range of fishing gear, with mortalities in fisheries and loss of habitat driving global declines. The Largetooth Sawfish, Pristis pristis, historically had a circumtropical range, but has experienced severe declines in geographic range and abundance. Viable populations are thought to be confined to northern Australia, but …

Blue Carbon Stocks, Accumulation Rates And Knowledge Gaps In Africa, Janine B. Adams, Pattrick, Pere Masqué, Dennis Adotey, Elsheikh Bashir Ali, Abdelgadir Bashir Mohamed Awatif, Mohamed Fathi Ben Hamouda, Moncef Benmansour, Joseph F. Charles, Jerome Harlay, Lucienne Human, Linet Kiteresi Imbayi, Rashid Omari Ismail, Anesu Machite, Nezha Mejjad, Athi N. Mfikili, Ndanu Mumo, Maurice Ndeye, Wilfried Essowè Panassa, Issa Sakho, Suleiman Suleiman, Vanessa Hatje

Research outputs 2022 to 2026

Blue carbon ecosystems (BCEs), including mangroves, salt marshes, and seagrasses, play a critical role in climate mitigation due to their high carbon sequestration capacity. Despite Africa's extensive and diverse coastal ecosystems, continent-wide assessments of blue carbon stocks and accumulation rates remain scarce. Here, we synthesized blue carbon data from 87 publications (January 1993 - March 2026) to evaluate the current state of knowledge and regional variability. Our analysis reveals marked regional heterogeneity in sediment organic carbon (SOC) stocks across Africa, reflecting both ecological variability and methodological differences among studies. Normalised to a sediment depth of 1 m, median SOC stocks …

Geographic Range And Body Size Influence Abundance Patterns In Reef Fishes, M. F. Maxwell, D. R. Barneche, R. Divieso, S. R. Floeter, O. J. Luiz, A. L. Luza, M. R. Pie, A. C. Siqueira, M. G. Bender

Research outputs 2022 to 2026

Aim: Understanding how body size and geographic range size influence species abundance is central to macroecology. Here, we characterized these relationships for reef fishes, the world's most diverse vertebrate group, across global and regional scales. Location: Global tropical and subtropical reefs. Time Period: Current. Major Taxa Studied: Reef-associated fishes. Methods: We compiled a comprehensive dataset on abundance, body size and geographic range size for 828 reef fish species. Abundance was measured as density (ind/m²) using transect-based observational data. To analyse global-scale patterns, we applied Bayesian quantile regressions and Bayesian phylogenetic regressions to account for phylogenetic relatedness. We also …

Sporadic Appetites: Unearthing The Fungal Diets Of Two Mycophagous Mammals Across An Australian Climate Gradient, Rebecca J. Quah, Saul J. Cowen, Robert A. Davis, Harriet R. Mills, Anna J.M. Hopkins

Research outputs 2022 to 2026

Translocating threatened ecosystem engineers may offer the dual benefit of contributing to species conservation and ecosystem restoration. Boodies (burrowing bettong; Bettongia lesueur) and woylies (brush-tailed bettong; Bettongia ogilbyi) are threatened mycophagous marsupials known for their crucial role in ecosystem health through fungal dispersal and bioturbation. As part of restoration efforts across Australia, these bettong species are frequently targeted for translocations, where a better understanding of their fungal dietary requirements is essential for ensuring their resource requirements are met and in predicting their ecological contributions to recipient ecosystems. Here, we used DNA metabarcoding to study the fungal diets of boodies and …

Viruses Causing Panleukopenia In Domestic Cats: A Review Of Feline And Canine Parvoviruses, Simon Colby

University Honors Theses

Parvoviruses remain among the most important viral pathogens in domestic cats today. Despite this, there is much confusion around which parvoviruses can infect cats, and what extent of disease they can cause. One of the two parvoviruses infecting cats, canine parvovirus type-2 (CPV-2), likely evolved from the other parvovirus infecting cats, feline parvovirus (FPV). These viruses differ at only a few places in their genomes, and share the method of cell entry via the transferrin receptor. The disease caused by FPV has been well characterized in cats, but disease caused by CPV-2 is more obscure. Additionally, current testing methods for …

Exploring The Durability Of Marine Picocyanobacterial Microcolonies, Erik Swanson

University Honors Theses

Picocyanobacteria of the genus Synechococcus are widespread aquatic photoautotrophs that play essential roles in primary production and carbon cycling. Some Synechococcus strains form multicellular microcolonies, but the mechanisms of cell-to-cell attachments and structural durability of these microcolonies remain poorly understood. This research investigated the physical durability of microcolonies in two marine Synechococcus strains (CC9605 and CC9311) using physical disruption treatments. Cultures were subjected to vortexing and sonication treatments, and populations of single cells and microcolonies were quantified using flow cytometry based on differences in measures of size. Results indicated that strain CC9605 showed no significant treatment effect, whereas CC9311 displayed …

Developing A High-Resolution Off-Axis Common-Mode Digital Holographic Microscope, Lucy Cook

University Honors Theses

Off-axis digital holographic microscopy (DHM) is a powerful tool for 3D, non-invasive live-cell tracking without moving parts. However, traditional setups face an inherent dilemma: split-path interferometers offer high spatial resolution but poor temporal stability, while more stable common-mode configurations are historically limited to lower numerical aperture (NA) regimes. This thesis bridges that gap by scaling a common-mode DHM architecture into a high-resolution benchtop instrument featuring NA = 0.65 objectives, paired with a high-power 520 nm laser source to combat transmission losses and sustain imaging frame rates across an expanded optical footprint. We map the multi-variable design space required to satisfy …

Shallow-Marine Crinoid Genera May Have Been More Resilient Across Permian Extinction Events In Terms Of Richness Than Deep-Marine Crinoid Genera, Amelia C. Kolstad

University Honors Theses

Throughout the Phanerozoic, one of the most successful phyla of marine invertebrates has been Echinodermata. Echinodermata was particularly successful throughout the Paleozoic, with class Crinoidea making up a majority of occurrences. The proportion of echinoderm occurrences that are crinoids declined massively at the end of the Permian and continued to decrease into modern day, never fully recovering. One of the factors thought to have been so important for crinoid success in the Paleozoic and their decreasing success throughout geologic time has been their propensity for success in shallow-marine environments, though crinoids also exist within deep-marine environments. This study seeks to …

Routine Transfusion Of Rh(D)-Positive Rbcs To Rh(D)-Negative Patients Designated As Do Not Resuscitate Conserves Rh(D)-Negative Red Blood Cell Inventory, Julie Katz Karp, Jovanna Everetts, Juliana Guarente, Angelica Vivero, Tiffany Bohr, Mary Harach

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Background: A minority of blood donors are Rh(D)-negative, and Rh(D)-negative red blood cell (RBC) products are often overutilized. As such, Rh(D)-negative RBCs may be difficult to maintain in blood bank inventory.

Study design and methods: We changed our blood bank laboratory policy to approve non-alloimmunized Rh(D)-negative patients to receive Rh(D)-positive RBCs for routine transfusion under defined criteria. Those criteria included Rh(D)-negative males (all ages) and females (aged >50 years) who were designated as do not resuscitate (DNR), either with or without intubation, in the electronic medical record.

Results: From August 15, 2024 through August 15, 2025, a total of 204 …

Intervention Levers For Stunting Reduction In Indonesia: Evidence From The 2023 Indonesian Health Survey Data, Iwan Ariawan, Hafizah Jusril, Zahra Izza Afifa, Azka Fitri, Elmarizha Sekar Utami, Mikail Hasan, Dwi Puspasari

Kesmas

Stunting remains the largest public health challenge among macro-nutrition problems in Indonesia, affecting almost a quarter of children under five in 2023. The prevalence is considered high according to the World Health Organization standard. This study analyzed 15 aggregated provincial variables from the 2023 Indonesian Health Survey using Structural Equation Modeling (SEM), focusing on determinants of stunting among children under two to identify primary intervention levers. Findings indicated that intervention urgency should focus on the first 1,000 days, particularly the steep increase in stunting prevalence observed in the 12–24-month age range. While the highest prevalence is in Eastern provinces (e.g., …

Transcranial Ac Modulation Of Cerebellar Nuclear Activity In Awake Animals, Nuran Kavakli

Dissertations

Entrainment of cerebellar nuclear (CN) cells via cerebellar transcranial alternating current stimulation (ctACS) has been reported in animals under ketamine/xylazine anesthesia. Our main objective was to demonstrate modulation of CN activity in unanesthetized, freely moving animals using ctACS. Multi-channel carbon-fiber electrodes were implanted into the interpositus nucleus for recording multi-unit (MU) activity, and thin-film electrodes were implanted subcutaneously over the posterior cerebellum for stimulation. A frequency-domain-based metric was developed to quantify modulation from MU signals. The results demonstrated modulation in a wide range of frequencies (4 Hz-300 Hz) as in anesthetized animals. In contrast, the amplitude of the peak in …

Pickleweed In The Disappearing Marsh: Population Genetics & Metal Accumulation In Salicornia Depressa, Alice Kaisla

Graduate Doctoral Dissertations

Salicornia is a genus of succulent halophytes found in salt marshes around the world. Salicornia species have a remarkably high tolerance for heavy metal pollution and have been shown to accumulate high concentrations of heavy metals in their tissue under experimental conditions. As a result, they are both a useful system for studying evolution in polluted coastlines and a potential candidate for use in phytoremediation. My research focuses on Salicornia depressa, known as pickleweed, a species commonly found in marshes along the heavily urbanized and industrialized New England coast. I investigate genetic diversity and population structure in S. depressa populations …

Adapting Population Genetics, Practice, And Policy For Plant Conservation In A Changing World, Cooper M. Kimball-Rhines

Graduate Doctoral Dissertations

Biodiversity conservation is an inherently interdisciplinary goal that requires effective collaboration among academics, ecosystem managers, policymakers, and other stakeholders. Codesigning research with these groups ensures experiments are useful and improves adoption of policy and practice recommendations while advancing our understanding of basic science. This dissertation explores the power of codesigned research in shaping plant conservation strategies using stakeholder engagement, causal inference, demographic modeling, and multi-omic sequencing techniques. In chapter 1 I discuss the history of New England ecosystems and the need for research-driven changes to plant conservation policy and practice in the face of global change. In chapter 2, I …

Investigation Of Environmental Influences On Multiple Sclerosis: A Study For Egypt’S Health, Noha Ezzaldin Alziny Ali

Theses and Dissertations

Background: Multiple sclerosis (MS) is a complex, chronic neuroinflammatory disease influenced by both genetic and environmental factors. While global research has identified potential environmental influences, most evidence comes from Western populations, creating a significant knowledge gap for regions like Egypt, which has witnessed a dramatic rise in MS prevalence over recent decades. This study hypothesized that Egyptian MS patients exhibit a distinct biological signature in their blood, characterized by an imbalance in essential and toxic trace elements (the metallome) and alterations in stress-response biomarkers associated with neuroaxonal injury and cellular stress. Objective: This study aimed to comprehensively profile and compare …

Is Trimethylamine N-Oxide A Friend, Foe, Or Hormetic Agent In Patients With Parkinson’S Disease: A Focused Review Of One Microbial Metabolite, Abraham B. Alton

Student Works

This review synthesizes recent literature examining trimethylamine N-oxide (TMAO) synthesis and its potential role in Parkinson’s Disease (PD) pathology. An increase in TMAO plasma and CSF concentration is associated with PD progression and severity. TMAO biosynthesis is a two-step process. First, precursors including carnitine and choline are converted to trimethylamine (TMA) by gut microbes. Second, TMAO is oxidized to TMAO in the liver. Once absorbed into circulation TMAO crosses the blood brain barrier and may influence PD disease pathology by increasing neuroinflammation and astrocyte activation and damaging the cerebral lymphatic system. These mechanisms may contribute to the cognitive and motor …

Rocatinlimab As A Novel Treatment Strategy For Atopic Dermatitis, Haylee Whyde, Evan Blazek, Macy Davis, Parker George, Alex Lowery, Connor Dains, Brenna Hissong, David Koh

Pharmacy and Wellness Review

Atopic dermatitis is a common chronic inflammatory skin disease that affects millions of children and adults in the United States. Atopic dermatitis is characterized by recurrent pruritus, erythema, and relapsing symptoms that can significantly impair quality of life. The pathophysiology of atopic dermatitis involves epidermal barrier dysfunction, immune dysregulation, and genetic susceptibility. Atopic dermatitis guidelines follow a stepwise approach that begins with a severity assessment, trigger avoidance, and nonpharmacologic and pharmacologic treatments. First-line therapies include topical corticosteroids (TCSs), topical calcineurin inhibitors (TCIs), and emollients. Crisaborole and topical ruxolitinib are used for mild-to-moderate disease when prior therapy has been inadequate. Monoclonal …

Evaluating The Market Withdrawal Of Andexanet Alfa, Jordyn Linfield, Addisyn Cooper, Alexander Defranco, Emma Gerding, Jessica Kelley, Tyler Henney, Connor Dains, Brenna Hissong, Brittany Bates

Pharmacy and Wellness Review

The coagulation cascade comprises intrinsic, extrinsic, and common pathways that converge when thrombin converts fibrinogen (factor I) into fibrin, leading to fibrin mesh formation, stabilization of the platelet plug, and ultimately thrombus formation. Inhibition of the coagulation cascade can be achieved with a variety of anticoagulant medications, including direct oral anticoagulants (DOACs). The mechanism of action of DOACs is to inhibit either factor Xa or thrombin. Reversal of anticoagulation remains an important clinical consideration when managing patients on DOACs who experience serious bleeding events. Andexanet alfa is a recombinant, modified human factor Xa protein previously indicated for patients receiving rivaroxaban …

Patents And Technology Evolution: Altering Innovations And Innovators Via Patent Influences, Richard Gruner

Georgia Journal of Law & Technology

Technologies improve primarily through evolutionary change not rational optimization. New technologies emerge as attempts to solve practical problems, the technologies are tested in marketplaces to determine if they are superior in cost and function to alternatives, and those that fare well in the testing gain widespread adoption.  Widely adopted technologies, and their problems, form the basis for the next round of technology improvements and evolution.  Through these steps, evolutionary processes lacking rational direction can generate changing technologies matched to the desires and problems of present society.

As they operate to advance diverse technologies, evolutionary processes governing technology change are subject …

Fate Of Nitrogen Applied To Grassland In Animal Wastes, M Sherwood

IGC Proceedings (1977-2023)

The experiment was designed to determine the effects of land spreading of animal manures on the nutrient content of surface runoff water and infiltrating soil water. This report deals only with nitrogen (N) and attempts to quantify the losses through runoff, leaching, and volatilization of ammonia (NH3) as well as N uptake in the grass over a 3-year period. Experimental plots sited on grassland, on two soil types (a moderately drained loam and an impermeable gley), were equipped to collect surface runoff water. Ceramic probes were installed in each plot at 15-, 30-, 60-, and 100-cm depths to extract in­filtrating …

Annual Losses Of Ammonia From A Grazed Pasture Fertilized With Urea, V R. Catchpoole, L A. Harper, R J.K Keyers

IGC Proceedings (1977-2023)

Nitrogen-balance studies have shown losses of applied nitrogen (N) from grazed pastures in southeastern Queensland. Losses as high as 80% have been observed from urea N broadcast at 376 kg N/ha/yr over 8 years on a Setaria sp1uu:elata cv. Nandi pasture. Management techniques aimed at reducing this loss and thereby increasing the efficiency of use of N by pastures cannot be devised until the pathways of loss are known. The objective of this research was to estimate the annual ammonia (NH3) loss by convective transport from a urea-fertilized pasture at Samford Pasture Research Station in southeastern Queensland. Urea was broadcast …

Nitrogen Losses From Urine-Affected Areas Of A New Zealand Pasture, Under Contrasting Seasonal Conditions, P R. Ball, D R. Keeney

IGC Proceedings (1977-2023)

Grazing ruminants aggregate large quantities of forage nitrogen (N) into urine patches. Pasture plots treated with urine N were studied to assess its fate under contrasting seasonal conditions: cool-moist (representing winter-spring); warm-moist (late spring-early summer), and warm-dry (late summer-autumn). A permanent ryegrass (Lolium perenne L.)-white clover (Trifolium repens L.) sward on free-draining alluvial soil was studied. 'freatments were replicated in randomized blocks. Urine N was applied at 30 or 60 g N/m2• Relevant measurements were then continued until treatment differences disappeared. Apparent N balances for urine treatments were compiled. Fixation by white clover was always greatly reduced in …

Effects Of Grazing Management On Seasonal Variation In Nitrogen Fixation, J L. Brock, J H. Hoglund, R H. Fletcher

IGC Proceedings (1977-2023)

Using the acetylene reduction assay, field studies in recent years have investigated the variation in N fixation in grazed systems, and some of the principles involved in the interaction with available soil N have been described. This experiment ex­tends this work to include the effect of grazing management on the factors influencing N fixation. Two self-contained sheep-grazed units, one a 10-paddock rotationally grazed system and the other set stocked, were estab­lished on a high-fertility ryegrass-white clover pasture, with a basic stocking rate of 22 sheep/ha. Over the 1975-1978 period, both units were monitored for pasture growth, N fixation, and associated …

Symbiotic Nitrogen Fixation Of Alfalfa, Birdsfoot Trefoil, And Red Clover, G H. Heichel, C P. Vance, D K. Barnes

IGC Proceedings (1977-2023)

Forage legumes such as alfalfa (Medicago sativa L.), birdsfoot trefoil (Lotus comiculatus L.), and red clover (Trifolium pratense L.), grown in crop rotations, can provide an inexpensive source of nitrogen (N) to succeeding crops. Few quantitative measurements of seasonal patterns of N fixation in managed communities of perennial forage legumes have been undertaken, chiefly because of the lack of satisfactory methods. Therefore, there is little knowledge of how N fixation varies with crop development, yielding ability, and weather patterns. Quantitative measurements of N fixation are important in choosing the appropriate legume for use in a crop rotation and for …

Photosynthate Supply And Nitrogen Fixation In Forage Legumes, P M. Murphy

IGC Proceedings (1977-2023)

Photosynthate supply is known to limit nitrogen fixation in legumes, and the resulting shortfall in energy supply necessary for maximum crop production may be aggravated by the energy-wasteful process of hydrogen (H2) evolution by the legume N2 fixing system. There is less information available on these aspects of the nitrogen-fixing process in forage legumes, such as white clover (Trifolium repens). The objectives of the present work were to determine how N2(C2H2) fixation and H2 production are in­fluenced by carbohydrate supply in forage legumes.

Plants were grown under controlled environmental conditions, and nodule energy supply was varied by adjusting …

Selection Of Rhizobium Strains For Enhanced Dinitrogen Fixation In Forage Legume Production, C Hagedorn, W E. Knight

IGC Proceedings (1977-2023)

A set of procedures for the selection of Rhizobium strains for enhanced dinitrogen fixation in forage legumes is presented. Although forage legumes are among the most efficient members of the Leguminosae regarding biological nitrogen fixation (BNF), they are generally neither productive nor persistent without effective nodulation by appropriate rhizobia. The following methods define a selection and evaluation process to obtain appropriate Rhizobium strains. These include (1) regional survey of the production area, (2) strain collection and soil analyses, (3) strain characterization, (4) strain selection and manipulation, and (5) field evaluation of strains. The initial procedure is to survey the region …

Interactions Between Grasses And Rhizosphere Nitrogen-Fixing Bacteria, M H. Gaskins, D H. Hubbell, S L. Albrecht

IGC Proceedings (1977-2023)

Sorghum and Digitaria cultivars grown in soil or nutrient solutions were inoculated with a strain of Azospirillum in short-term greenhouse experiments. Carbon compounds lost by roots in solution culture experiments were determined in order to estimate the quantity of energy substrates that might be obtained by rhizosphere organisms from growing plants. Other plants were treated with plant growth hormones, and responses were compared to those of plants treated with killed Azospirillum cells. The similarity of the responses suggests that growth-hormone production by the inoculant organism, rather than nitrogen (N) fixa­tion, is responsible for part or all of the increase in …

Simple Computer Simulation Models For Forage-Management Applications, G W. Fick, D Onstad

IGC Proceedings (1977-2023)

Dynamic computer simulation models of forage growth can be useful in interpreting physical and biological limitations on production and in designing management systems for testing in the field. The explanatory detail of such models makes them both more reliable and more expensive to use than simple empirical formulations. Simple simulation models reduce the expense. They can also serve as reference points for designing, evaluating, or selecting more complex versions and thus provide a more ra­tional basis for using models in grassland research and management. Our objectives were to develop and to test a simple dynamic simulation model of alfalfa (Medicago …

Energy Flow And Conversion Efficiency In Grazing Grassland, T Akiyama, S Takahashi, M Shiyomi, T Okubo

IGC Proceedings (1977-2023)

Measurable energy storage on grassland ecosystems was examined for 5 years at the Fujinita site under the same rotation pro­gram with two grazing intensities. Daily global solar radiation and photosynthetic active radiation were measured as the energy sources in the ecosystem. Primary production by pasture plants and amount grazed by cattle were estimated by the biomass dif­ferences inside and outside of protection cages. For the estimation of energy produced or stored by plants or cattle, calorific values were examined for dominant plant species at the Fujinita site. Seasonal changes in digestibility were investigated to ascertain the energy of herbage digested …

A System Approach To Swedish Ley Production, J F. Angus, A Kornher, B.W R. Torssell

IGC Proceedings (1977-2023)

A simulation model for estimating yield of leys from standard meteorological observations is described. It is based on an S-shaped growth curve also accounting for phasic development and regrowth depression. Effects of temperature, radiation, and soil moisture are accounted for by a growth index. Soil moisture is simulated with a standard water budget. The parameters in the model were estimated by comparing measured with calculated growth. The model then predicted final harvest with reasonable accuracy, but with underestimate of early season growth, presumably due to mobilization of car­bohydrate from storage organs. Observed ley yields from 49 Swedish parishes (1961-1978) were …