This aim of this study is to access the antioxidant mechanisms of benzoic acid, ellagic acid, gallic acid, and quercetin, four notable polyphenols abundant in superfoods such as berries (e.g., blackberries, cranberries, raspberries) and/or nuts (e.g., chestnuts and walnuts). The polyphenols are thought to play roles in combating oxidative stress, a process that is implicated in aging, cancer and a myriad of other diseases ranging from cardiovascular to neurological disorders. Two primary reactive oxygen species (ROS) that cause oxidative stress in living organisms are hydroxyl radicals and singlet oxygen, short-lived chemicals that aggressively oxidize DNA, proteins, lipids, and carbohydrates thus triggering cell death, most often through necrosis or apoptosis. In our approach, we utilize agarose gel electrophoresis plasmid DNA nicking assays in combination with ROS-specific fluorometric probes to rank the abilities of the four polyphenols to neutralize chemically and/or photochemically generated hydroxyl radicals and singlet oxygen in aqueous solutions (pH 7.0, 37 C). Our findings are intended to access the potentials of benzoic acid, ellagic acid, gallic acid, and quercetin from superfoods and dietary supplements to mitigate oxidative stress in living organisms and to highlight the broader applications of these antioxidants in therapeutic, dietary, and integrated biological studies.

Bacteriophage therapy has been around for more than 80 years and aids in healthcare advancements. Due to the specificity of phages, they have evolved to target a certain bacterial strain or species. CRISPR-cas immune system is a defense mechanism against invading nucleic acid, such DNA from invading bacteriophage. It has been proposed that as a system CRISPR-cas is favored when cells have abundant energy. Alternative to CRISPR-cas, bacteria can be selected and lose receptors that bacteriophages use to attach to the cell surface. However, modifications in these receptors can reduce bacteria fitness. To our knowledge no work has looked at the environmental osmolarity as a factor which would impact CRISPR-cas immune system fitness. Environmental osmolarity plays a large role in how nucleic acids are able to get across membranes. This project’s focus is to view how resistance to the phage (DMS3-vir) in PA14 differs in different environmental conditions. We propose, as salt concentration outside the cell become similar to inside, phage DNA will enter the at a slower rate due to the difference in water potential. Giving the CRISPR system more time to evaluate the incoming DNA. On the contrary, at low salt concentrations, the phage DNA should be entering the bacterial at a faster rate due to the same process of moving from low salt concentration on the outside to high salt concentration on the inside.

The response to the global COVID-19 pandemic by public health entities and the vaccine industry was unprecedented and highly successful. The primary focus of the first-generation vaccines was on the use of the SARS-CoV-2 spike (S) protein as the primary vaccine immunogen with the goal of inducing high levels of neutralizing antibodies. However, multiple limitations associated with this approach are now evident due to the emergence of variants of concerns, VOCs, with notable mutations in the Spike protein sequence. Consequently, vaccine efficacy was disrupted due to the diminished neutralizing capacity of vaccine-induced antibodies and hence vaccine protection against reinfection. Evaluation of immune responses in COVID-19 convalescent patients demonstrated numerous viral proteins to be highly immunogenic including S and N proteins, suggesting their primary role as immunodominant antigens for humoral and cellular immunity. Therefore, the inclusion of multiple SARS-CoV-2 antigens has the potential to broaden immunity and mitigate the impact of variants on vaccine efficacy. In response, GeoVax developed a clinical vaccine candidate GEO-CM04S1, a modified vaccinia Ankara vector (MVA) co-expressing spike and nucleocapsid antigens based on the Wuhan-Hu-1 reference strain. Here, we report GEO-CM04S1 vaccine efficacy against the ancestral Wuhan strain B.1 and the Omicron subvariant XBB.1.5 in K18-hACE-2 mouse model. We demonstrate that intramuscular vaccination of hACE2 mice with GEO-CM04S1 protects against weight loss, upper and lower respiratory tract infection, lung injury and viral neuroinvasion following intranasal challenge with B.1 and XBB.1.5. We also report the efficacy of MVA-vectored vaccines expressing only S or N protein termed MVA-S and MVA-N, respectively. In MVA-S-vaccinated mice, full protective efficacy against B.1 was observed; however, the vaccine had diminished protection against XBB.1.5 variant. Minimal protection against B.1 was observed in MVA-N-immunized mice. These results demonstrate the efficacy of GEO-CM04S1 that confers full cross-protective immunity against SARS-CoV-2 and its emerging VOCs.

Many natural and engineered networks involve units coupled through multiple layers of interaction. For instance, neurons interact via excitatory, inhibitory, and electrical synapses whose co-action often leads to synergistic effects. Understanding how network topology governs synchronization in multilayer networks remains a fundamental challenge, largely due to limitations in current stability analysis methods. To address this gap, we introduce a connection graph approach that provides analytical predictions, revealing surprising roles of multilayer links in shaping synchronization dynamics in networks of saddle-focus oscillators.

Here we report the effects of net charge on DNA photocleavage by a series of six negative, neutral, and positive near-infrared (NIR) donor-π-acceptor chromophores (D-π-A) each containing an indole donor group attached to a chloroacrylic acid acceptor vs. an analogous positively charged cyanine dye in which the chloroacrylic acid moiety is replaced by a second indole group. UV-visible spectrophotometry was utilized to investigate dye stability and DNA interactions. Competitive DNA binding experiments with pentamidine and methyl green suggest that the neutrally and positively charged dyes may interact with both the minor and major grooves of B-form DNA. Additionally, using radical specific fluorescent probes and chemical additives in microplate experiments, we show that the irradiation of the neutrally and positively charged dyes with a 750 nm LED medical lamp sensitizes the production of DNA damaging Type II singlet oxygen and/or Type I hydroxyl radicals that cleave plasmid DNA in good to high yields (pH 7.0, 10 °C). NIR phototoxicity data of the dyes in E. coli cultured cells will be discussed. Our goal is to develop indole-based chromophores as NIR photosensitizing agents (PS) in photodynamic therapy (PDT).

Understanding marine molluscan extinctions across Plio-Pleistocene units in Georgia and north-central Florida is key to understanding community changes in the Western Atlantic. Previous research focused on assemblages from the Carolinas and south Florida, but a biogeographic gap in data exists for Georgia and north-central Florida. This study aims to examine changes across the Plio-Pleistocene at this biogeographic gap. Samples from four localities representing different formations span coverage in studying these extinction episodes over the last few million years. Six samples of the Plio-Pleistocene Nashua Formation were retrieved from spoil piles at different sites within a quarry at East Coast Aggregates (ECA) in Hastings, FL. Multiple in situ samples of the Nashua Formation from lower and upper sections of the quarry wall were processed from Buck Hammock Materials (BH) near Deer Park, FL. Additional Pleistocene samples from GA and FL were made available through the Florida Museum of Natural History. Laboratory methods involve sieving samples and picking, sorting, identifying shells including separating whole from fragmented specimens. Analytical methods include examination of diversity, abundance, ecology, and drilling predation across samples. Preliminary results reveal differences in the diversity of faunas between lower and upper BH samples, and in comparison to rich ECA assemblages. Next steps include research contributing new data from understudied formations in GA and FL to see how paleocommunities change in younger units. This work can help us understand ecosystems' natural variability with implications for addressing human impacts in modern habitats related to the sixth extinction.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains an ongoing threat to public health globally. The emergence of highly mutated variants displaying increased immune evasion and transmissibility have necessitated the need for updated vaccines, therapeutics, and diagnostic tools. The omicron subvariant JN.1 displays significant antigenic differences from previous omicron subvariants, owing to approximately 30 mutations within its spike protein. In June 2023, the FDA released recommendations for updated COVID-19 vaccines to be formulated against JN.1 instead of the previously dominant XBB.1.5 variant. Understanding viral infection in established models is crucial for expanding our knowledge of the basic virology of JN.1 and its subvariants, evaluating vaccine efficacy, and identifying key factors involved in host-virus interaction. In this study, Intranasal infection of K18-hACE2 mice with the SARS-CoV-2 Omicron subvariant JN.1 resulted in 100% survival. Weight loss and clinical disease indicators if present were mild and transient. Virus titers peaked in the lungs on day 3 before gradually declining on days 5, 6, and 7 after infection. JN.1 was found to productively infect nasal turbinate cells, with the highest viral RNA detected on day 5 post-infection. While low levels of viral RNA were detected in the brain tissue of infected mice, plaque assay revealed infectious virus was absent in all tissue homogenates. Our results indicate that intranasal infection with the SARS-CoV-2 Omicron subvariant JN.1 produces attenuated disease in K18-hACE2 mice, productive infection of respiratory tissues, and a marked decrease in neuroinvasion compared to previous variants.

Deep neural networks (DNNs) have been widely applied to solve complex real-world problems. However, selecting optimal network structures remains challenging. This study addresses this challenge by linking neuron selection in DNNs to knot placement in spline basis expansion models, introducing a difference penalty that automates knot selection and bypasses traditional neuron selection complexities. We name the method Deep P-Spline (DPS). Such method extends the model class considers in conventional DNNs modeling. It also forms a latent variable modeling method based on Expectation Conditional Maximization (ECM) algorithm for efficient network structure tuning. From a non-parametric regression perspective, DPS is proved to overcome the curse of dimensionality, enabling effective handling of high-dimensional inputs. The methodology is applied to computer experiments and image data analysis, where the underlying regression problems with many inputs are common. Numerical results validate the model effectiveness, highlighting its potential in advanced nonlinear regression tasks.

In medical diagnostic, especially when the gold standard test is costly or invasive, it is a common case that not all subjects with diagnostic test results ultimately have their true disease status verified. This generally leads to a verification biased evaluation of the ability of the diagnostic tests. To address this problem, Todd A. Alonzo and Margaret S. Pepe introduced four partially parametric point estimators of sensitivity, specificity and ROC under the missing-at-random (MAR) assumption. However, to the best of our knowledge, no verification bias correction interval estimation for continuous tests has been specifically developed yet. This paper aims to fill this gap. Inspired by bootstrap method and the method of variance estimates recovery (MOVER), we propose new bias-corrected interval estimations for the two-class Youden index, which is a well-accepted measure of accuracy for continuous tests, under the MAR assumption. Extensive Monte Carlo simulation studies are conducted to test and compare our approach. The results show that when 36% of the subjects have their true disease status missing, our proposed methods can achieve an expected 95% coverage probability with appropriate length. Real data study using Wisconsin Diagnostic Breast Cancer biomarker data also confirms our approaches' strong robustness across all scenarios, even when only 36% of patients have verified diagnoses and without any assumptions about the underlying disease model.

Plastic and petroleum hydrocarbon pollution have become ubiquitous in natural and man-made environments, alarming concerns about serious harm to humans and nature. Polyethylene terephthalate (PET) plastics and petroleum are used widely worldwide, and their pollution has become a global concern. Our previous studies demonstrated that a novel anaerobic bacterium Sporomusaceae strain BFN5 isolated from oil spill-impacted salt marsh sediment can degrade various plastics and aromatic hydrocarbons. This study investigated physiological and molecular mechanisms of anaerobic degradation of PET by strain BFN5 and aimed to elucidate the accelerating conditions for PET and aromatic hydrocarbon degradation. Strain BFN5 was anaerobically cultured with PET microplastic (< 5mm), naphthalene, benzene or toluene as a carbon source and nitrate as an electron acceptor. The plastic degradation rates were measured via weight loss studies. Post-incubation resulted in significant PET degradation (1.43%/month) in strain BFN5 cultures, with a calculated total degradation time of 9.24 years, compared to known abiotic degradation times of 16-48 years. Increased biofilm formation was indicative of more efficient PET degradation and was quantified. Topology of the biofilms on PET microplastics and PET surface morphology changes were analyzed via Confocal Laser Scanning Microscopy and Scanning Electron Microscopy. Genes involved in anaerobic PET and aromatic hydrocarbon degradation pathways were identified via genomic analysis. Transcript level analyses for putative plastic and aromatic degradation genes such as buk, ubiD, and ncrA are underway to unravel the metabolic pathways of strain BFN5. The ultimate aim of this study is to provide effective bioremediation solutions for plastic and petroleum wastes.

Australian Bat Lyssavirus (ABLV) is a highly pathogenic virus belonging to the family Rhabdoviridae, similar to the classic Rabies virus (RABV), which causes fatal encephalitis in mammals. Each year, RABV is responsible for over 55,000 deaths, with approximately 3 billion people at risk of infection. Current vaccines and treatments have limited effectiveness against bat lyssaviruses like ABLV. In addition to requiring multiple doses, the high cost of Rabies Immune Globulin (RIG), which is often derived from human sources, makes these treatments inadequate for protecting at-risk populations. Therefore, there is a pressing need for affordable immunotherapeutics that maintain broad coverage. Lyssaviruses utilize their trimeric surface glycoprotein (G) for receptor binding and membrane fusion during viral entry, making it an attractive target for therapy. Previously identified neutralizing monoclonal antibodies can target domain III of the lyssavirus G protein. In this study, we enhance immune recognition of the conserved lyssavirus-G domain III by immunizing camelid mice (nanomice) and isolating a panel of nanobodies. The isolated nanobodies demonstrated strong competition with ABLV-neutralizing mAb RVC20 in Bio-layer interferometry assays, suggesting their potential for neutralization. Following further confirmation of their neutralizing ability through cell-fusion assays, selected nanobodies will be tandem fused and engineered into an IgG format to increase their potency and breadth of coverage. In summary, our work highlights the potential of nanobodies as an affordable, effective, and easily engineered alternative to traditional antibodies for combating ABLV infections, with the prospect of developing a pan-lyssavirus therapeutic.

In collaboration with the South River Watershed Alliance and with support of the Chattahoochee Riverkeeper, the study examines industrial stormwater permits in a dense concentration of industrial sites in the highly impacted South River Watershed of metro Atlanta, Georgia. South River rises from tributaries in downtown Atlanta and in East Point, Georgia, immediately north of the international airport. Contaminated sites and combined sewer overflows greatly impair the upper watershed. Focusing on an area of concentrated industrial activity, the study aims to establish a systematic methodology to determine the industrial facilities without required stormwater permits and to provide useful information to river advocates seeking to increase compliance and improve water quality. In selected industrial zones, Google Earth, United States Environmental Protection Agency (EPA) databases, and National Pollutant Discharge Elimination System (NPDES) permit lists are used to identify sites with Standard Industrial Classification (SIC) codes that require permits or exemptions to be filed with the Georgia Environmental Protection Division (EPD). Moreover, water and sediment samples will be collected in the South River above, between, and below each selected zone from six sampling points to assess for accessibility and safety. Building key informant interviews (KII) with experts and advocates from environmental non-governmental organizations, as well as an in-depth literature review on industrial stormwater compliance, the study contributes to the work of local community and regulatory organizations enhancing the water quality in the region and towards developing a replicable model of collaboration toward greater industrial stormwater management and compliance for similar watersheds.

Optoacoustic imaging is an emerging bioimaging technique that combines optical excitation and ultrasound detection to generate a signal. The signal is generated through the optoacoustic effect, and the signal generated can be tracked at multiple wavelengths by Multispectral optoacoustic tomography (MSOT). As sound waves are the detection method, they have lower light scattering in tissue compared to light, allowing for deeper tissue penetration and higher-resolution images. For optoacoustic imaging contrast agents, the two main criteria are optimal: strong absorbance and weak fluorescence. Current agents are designed for fluorescence imaging, resulting in poor signal intensity and spectral shape, making them not applicable for optoacoustic imaging. Squaraine dyes are a class of Near Infrared (NIR) region scaffolds that have shown promising biological applications. The drive to achieve NIR region optical properties is due to biomolecules having limited to no interference in this region. This allows for deeper penetration into the cell and a better signal-to-noise ratio. Current squaraine dyes primarily utilize the indolium heterocycles, which are designed for fluorescence imaging in the NIR region. In addition, indolium-based squaraine dye has an absorbance below 700 nm, which underutilizes the full NIR potential. When the perimidine heterocycle is introduced to squaraine dyes, the absorbance is redshifted to over 800 nm. Perimidine-based squaraine is designed to be an optoacoustic imaging contrast agent due to strong absorbance and weak fluorescence. Herein, we report the synthesis, optical properties, and initial optoacoustic imaging data for the new squaraine dyes. These perimidine-based squaraine dyes have shown high optoacoustic signal and unique spectral shape that range the NIR region.

Elevated concentration of inorganic contaminants in urban streams is a widespread issue that must be addressed to ensure sustainable and equitable development. Heavy metals (HMs) are one such contaminant, typically sourced from the poor management of industrial and domestic waste. Past studies have revealed that the mobility of HMs is constrained by the movement of nanoparticles known as colloids. Herein, we present an investigation of the concentration of HMs in the South River, a perennial urban stream located in East Point, Georgia. The headwaters of the river lie immediately downstream of a class 1 designated hazardous waste site, whose groundwater and soil are known to be contaminated with copper, lead, nickel, and zinc, among several other pollutants. Six sampling points were selected in collaboration with local community members to evaluate the spatial extent of HM contamination, beginning where the river first daylights 0.4 miles away from the hazardous site and adjacent to public housing property. Following their collection, the samples were fractionated into < 415 nm, < 260nm, and < 35nm size fractions using differential centrifugation and a final “dissolved” < 3kDa fraction using ultrafiltration. HM concentrations were quantified using an inductively coupled plasma-mass spectrophotometer. The colloid’s physiochemical characteristics in the different size fractions were assessed using scanning electron microscopy and energy-dispersive X-ray spectroscopy. Preliminary results show a uniform distribution of relative HM concentrations across the fractions, with decreased concentrations moving downstream. Knowledge of the preferential fraction and chemical characteristics of the colloids HMs are sorbed onto will help inform more effective remediation techniques.

Fluorescence imaging is a pivotal tool in modern biomedical research, offering non-invasive, real-time visualization of biological structures and processes with high resolution1. Among the various fluorophores, near-infrared (NIR) dyes are particularly valuable due to their deeper tissue penetration, reduced scattering, and minimal background autofluorescence2-4. In this study, we synthesized a class of squaraine fluorophores functionalized with primary and secondary amines, including amino acids, to investigate their optical and physicochemical properties. The incorporation of amino acids into the squaraine backbone not only enhances the biocompatibility of the dyes but also provides a specific targeting mechanism towards receptors that are overexpressed in tumor cells, enabling improved precision in tumor imaging5, 6. Additionally, the functionalization with amines and amino acids has been shown to improve the solubility of these dyes in aqueous environments, which is critical for their use in vivo. The modified squaraine NIR dyes will have improved optical properties for imaging applications.

Current HIV-1 treatments, primarily antiretroviral therapies, face significant challenges including resistance mutations and high costs, particularly in developing regions. Broadly neutralizing antibodies hold promise, but their potential is hindered by limitations in traditional approaches. While monotherapy often leads to viral resistance, the efficacy of antibody cocktails is challenged by their varying half-lives and pharmacokinetics. Similarly, multi-specific antibodies encounter manufacturing challenges related to heavy-light chain mispairing. Nanobodies, cloned from heavy chain-only antibodies of camelids, offer a unique advantage in combating HIV-1 infection due to their compact size and feasibility for engineering. Here, we immunized alpacas with recombinant HIV-1 envelope trimer proteins (Env) from clade A strain BG505 and clade C strain CH505 to induce heterologous antibody responses. Alpacas were immunized 15 times over a period of 300 days, during which we observed gradual increase of serum antibody titer against both BG505 and CH505 Env. Neutralization tests on the two strains revealed that a heterologous neutralization response developed in day 200 and day 300 serum samples, potentially targeting various vulnerable sites on HIV-1 Env. To isolate nanobody binders against those sites, nanobody phage libraries were constructed from the alpaca PBMCs 200 and 300 days post immunization, followed by phage screening using various probes. Dozens of CD4 binding site-directed nanobodies were identified, and we are currently isolating nanobodies targeting V1/V2 apex and V3-glycan sites. These nanobodies have the potential for the study of HIV-1 immune responses and development of novel bispecific/multi-specific antibodies, ultimately advancing vaccine design and treatment options for HIV-1 infections.

Abstract: Music classification is a fundamental task in the fields of music information retrieval and sound processing, with applications ranging from music recommendation systems to genre classification. Traditional deep learning approaches, particularly Convolutional Neural Networks (CNNs), have shown great success in classifying music data. However, these methods often require large datasets and computational resources due to their deep architectures. Quantum computing, a novel computational paradigm, offers potential speedup for certain types of machine learning problems. In this project, we propose to explore the use of Quantum Convolutional Neural Networks (QCNNs) to improve the efficiency and performance of music classification tasks. The QCNN will leverage quantum circuits to replicate the functionality of classical CNNs while taking advantage of quantum parallelism and probabilistic sampling. We will develop a quantum-enhanced CNN model that includes both quantum convolutional layers and classical post-processing. By applying quantum gates and measurements, we will demonstrate how the QCNN can extract meaningful features from music spectrograms, allowing for faster and more efficient music classification. The focus of this project will be on the classification of musical genres and mood, with a potential reduction in the computational complexity traditionally associated with deep CNNs.

Near-infrared (NIR) cyanine dyes are an interesting class of fluorophores due to their unique optical properties and tunable structure which can be manipulated to obtain fluorophores optimized for different applications. One of the sites of modifications is the central meso position which can be modified using the Smiles rearrangement to attach different heteroatoms to the conjugated system. A specific form of Smiles Rearrangement was used in this project that includes an electrophile integration which allowed the formation of a quaternary ammonium center, leading to the formation of highly positively charged fluorophores. Two sets of fluorophores were synthesized in the same scheme; the first one was obtained from the meso modification of heptamethine dyes using 2-(Methylamino)ethanol, and the other one was obtained by using the Smiles rearrangement on the meso-modified fluorophores. The first set showed metal sensing ability toward copper (II) ions and not to other metal cations. The second set, characterized by having a quaternary ammonium center, are highly positively charged and are promising candidates for bioimaging of the cartilage. Our lab has developed cartilage-specific fluorophores that showed excellent cartilage targeting but a very expensive synthetic pathway due to the use of thiocholine. Using the Smiles rearrangement will allow the formation of fluorophores of similar cartilage targeting ability, but in a much more economical synthesis. This optimization approach not only allowed the formation of two sets of fluorophores with different and beneficial applications but also opened the horizon for additional optimizations towards more biomedical applications.

Autophagy is the process of degradation of the intracellular components within lysosomes in mammals or vacuoles in yeast. Autophagy is activated by cellular stress, nutrient deprivation, or pathogen invasion, and is vital for cell survival during prolonged starvation. Lipophagy, which specifically targets lipid droplets (LDs) for degradation, is conserved in various organisms and proceeds via direct interaction of LDs with vacuoles in yeast. Recent studies have shown that LDs are tagged with ubiquitin under lipophagy-inducing conditions. The E3 ubiquitin ligase, Rsp5, plays a crucial role by transferring ubiquitin to substrates and is involved in lipid biosynthesis, stress responses, and regulates several ubiquitin-dependent autophagic pathways. On the other hand, the ubiquitin-binding protein, Ubx5, has been shown to selectively degrade the dysfunctional Cdc48 by selective autophagy in yeast. We investigated the involvement of Rsp5 and Ubx5 in nitrogen starvation-induced lipophagy using mutant variants of these proteins. First, we found that Rsp5 is essential for lipophagy in yeast under nitrogen starvation conditions, as evidenced by the impairment of lipophagy in the rsp5-1 ts-mutant and RSP5 overexpression strains. We also found that the deletion of UBX5 gene in Saccharomyces cerevisiae impairs lipophagy under nitrogen starvation conditions. Therefore, we propose a model where Rsp5 ubiquitinates LDs and Ubx5 recognizes the ubiquitinated LDs for their autophagic degradation in the vacuole.