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  • Publication
    Gastrointestinal Delivery of an mRNA Vaccine Using Immunostimulatory Polymeric Nanoparticles.
    (US Department of Health and Human Services, 2023-08-17) Traverso, Giovanni
    mRNA vaccines can be translated into protein antigens, in vivo, to effectively induce humoral and cellular immunity against these proteins. While current mRNA vaccines have generated potent immune responses, the need for ultracold storage conditions (- 80 °C) and healthcare professionals to administer the vaccine through the parenteral route has somewhat limited their distribution in rural areas and developing countries. Overcoming these challenges stands to transform future deployment of mRNA vaccines. In this study, we developed an mRNA vaccine that can trigger a systemic immune response through administration via the gastrointestinal (GI) tract and is stable at 4 °C. A library of cationic branched poly(β-amino ester) (PBAE) polymers was synthesized and characterized, from which a polymer with high intracellular mRNA delivery efficiency and immune stimulation capacity was down-selected. mRNA vaccines made with the lead polymer-elicited cellular and humoral immunity in mice. Furthermore, lyophilization conditions of the formulation were optimized to enable storage under refrigeration. Our results suggest that PBAE nanoparticles are potent mRNA delivery platforms that can elicit B cell and T cell activation, including antigen-specific cellular and humoral responses. This system can serve as an easily administrable, potent oral mRNA vaccine.
  • Publication
    Potent 3CLpro inhibitors effective against SARS-CoV-2 and MERS-CoV in animal models by therapeutic treatment
    (mBio, 2024-12-21) Chang, Kyeong-Ok; Perlman, Stanley; Groutas, William C; Lovell, Scott; Johnson, David K; Meyerholz, David K; Nguyen, Harry Nhat; Dampalla, Chamandi S; Kim, Yunjeong; Li, Pengfei
    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV) are zoonotic betacoronaviruses that continue to have a significant impact on public health. Timely development and introduction of vaccines and antivirals against SARS-CoV-2 into the clinic have substantially mitigated the burden of COVID-19. However, a limited or lacking therapeutic arsenal for SARS-CoV-2 and MERS-CoV infections, respectively, calls for an expanded and diversified portfolio of antivirals against these coronavirus infections. In this report, we examined the efficacy of two potent 3CLpro inhibitors, and , in fatal animal models of SARS-CoV-2 and MERS-CoV to demonstrate their broad-spectrum activity against both viral infections. These compounds significantly increased the survival of mice in both models when treatment started 1 day post infection compared to no treatment which led to 100% fatality. Especially, the treatment with compound resulted in 80% and 90% survival in SARS-CoV-2 and MERS-CoV-infected mice, respectively. Amelioration of lung viral load and histopathological changes in treated mice correlated well with improved survival in both infection models. Furthermore, compound exhibited significant antiviral activities in K18-hACE2 mice infected with SARS-CoV-2 Omicron subvariant XBB.1.16. The results suggest that these are promising candidates for further development as broad-spectrum direct-acting antivirals against highly virulent human coronaviruses.IMPORTANCEHuman coronaviruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV) continue to have a significant impact on public health. A limited or lacking therapeutic arsenal for SARS-CoV-2 and MERS-CoV infections calls for an expanded and diversified portfolio of antivirals against these coronavirus infections. We have previously reported a series of small-molecule 3C-like protease (3CLpro) inhibitors against human coronaviruses. In this report, we demonstrated the efficacy of 3CLpro inhibitors for their broad-spectrum activity against both SARS-CoV-2 and MERS-CoV infections using the fatal animal models. The results suggest that these are promising candidates for further development as broad-spectrum direct-acting antivirals against highly virulent human coronaviruses.
  • Publication
    Transition metal-free decarboxylative olefination of carboxylic acid salts
    (Chemical Science, 2024-05-15) Tunge, Jon A
    The cost-effective and efficient synthesis of alkenes is highly significant due to their extensive applications in both synthetic and polymer industries. A transition metal-free approach has been devised for the chemoselective olefination of carboxylic acid salts. This modular approach provides direct access to valuable electron-deficient styrenes in moderate to good yields. Detailed mechanistic studies suggest anionic decarboxylation is followed by halogen ion transfer. This halogen transfer leads to an umpolung of reactant electronics, allowing for a rate-limiting rebound elimination.
  • Publication
    Effects of Proline on Internal Friction in Simulated Folding Dynamics of Several Alanine-Based α-Helical Peptides
    (ACS, 2024-04-12) Szoszkiewicz, Robert
    We have studied in silico the effect of proline, a model cosolvent, on local and global friction coefficients in (un)folding of several typical alanine-based α-helical peptides. Local friction is related to dwell times of a single, ensemble-averaged hydrogen bond (HB) within each peptide. Global friction is related to energy dissipated in a series of configurational changes of each peptide experienced by increasing the number of HBs during folding. Both of these approaches are important in relation to future atomic force microscopic-based measurements of internal friction via force-clamp single-molecule force spectroscopy. Molecular dynamics (MD) simulations for six peptides, namely, ALA5, ALA8, ALA15, ALA21, (AAQAA), and HN-GN(AAQAA)G-COONH, have been conducted at 2 and 5 M proline solutions in water. Using previously obtained MD data for these peptides in pure water as well as upgraded theoretical models, we obtained variations of local and global internal friction coefficients as a function of solution viscosity. The results showed the substantial role of proline in stabilizing the folded state and slowing the overall folding dynamics. Consequently, larger friction coefficients were obtained at larger viscosities. The local and global internal friction, i.e., respective, friction coefficients approximated to zero viscosity, was also obtained. The evolution of friction coefficients with viscosity was weakly dependent on the number of concurrent folding pathways but was rather dominated by a stabilizing effect of proline on the folded states. Obtained values of local and global internal friction showed qualitatively similar results and a clear dependency on the structure of the studied peptide.
  • Publication
    Characterization of Volatile and Particulate Emissions from Desktop 3D Printers
    (MDPI, 2023-12-06) Morrin, Aoife
    The rapid expansion of 3D printing technologies has led to increased utilization in various industries and has also become pervasive in the home environment. Although the benefits are well acknowledged, concerns have arisen regarding potential health and safety hazards associated with emissions of volatile organic compounds (VOCs) and particulates during the 3D printing process. The home environment is particularly hazardous given the lack of health and safety awareness of the typical home user. This study aims to assess the safety aspects of 3D printing of PLA and ABS filaments by investigating emissions of VOCs and particulates, characterizing their chemical and physical profiles, and evaluating potential health risks. Gas chromatography-mass spectrometry (GC-MS) was employed to profile VOC emissions, while a particle analyzer (WIBS) was used to quantify and characterize particulate emissions. Our research highlights that 3D printing processes release a wide range of VOCs, including straight and branched alkanes, benzenes, and aldehydes. Emission profiles depend on filament type but also, importantly, the brand of filament. The size, shape, and fluorescent characteristics of particle emissions were characterized for PLA-based printing emissions and found to vary depending on the filament employed. This is the first 3D printing study employing WIBS for particulate characterization, and distinct sizes and shape profiles that differ from other ambient WIBS studies were observed. The findings emphasize the importance of implementing safety measures in all 3D printing environments, including the home, such as improved ventilation, thermoplastic material, and brand selection. Additionally, our research highlights the need for further regulatory guidelines to ensure the safe use of 3D printing technologies, particularly in the home setting.
  • Publication
    Cobalt-catalyzed decarboxylative difluoroalkylation of nitrophenylacetic acid salts
    (Chemical Science, 2023-11-16) Tunge, Jon A.; Smith, Ian; Joseph, Ebbin
    The selective installation of fluorine-containing groups into biologically relevant molecules has been used as a common strategy for the development of pharmaceutically active molecules. However, the selective incorporation of gem-difluoromethylene groups next to sterically demanding secondary and tertiary alkyl groups remains a challenge. Herein, we report the first cobalt-catalyzed regioselective difluoroalkylation of carboxylic acid salts. The reaction allows for the facile construction of various difluoroalkylated products in good yields tolerating a wide range of functionalities on either reaction partner. The potential of the method is illustrated by the late-stage functionalization of molecules of biological relevance. Mechanistic studies support the in situ formation of a cobalt(i) species and the intermediacy of difluoroalkyl radicals, thus suggesting a Co(i)/Co(ii)/Co(iii) catalytic cycle.
  • Publication
    Oxidative Status of Ultra-Processed Foods in the Western Diet
    (MDPI, 2023-11-22) Medina-Meza, Ilce Gabriela
    Ultra-processed foods (UPFs) have gained substantial attention in the scientific community due to their surging consumption and potential health repercussions. In addition to their well-established poor nutritional profile, UPFs have been implicated in containing various dietary oxidized sterols (DOxSs). These DOxSs are associated with a spectrum of chronic diseases, including cardiometabolic conditions, cancer, diabetes, Parkinson's, and Alzheimer's disease. In this study, we present a comprehensive database documenting the presence of DOxSs and other dietary metabolites in >60 UPFs commonly consumed as part of the Western diet. Significant differences were found in DOxS and phytosterol content between ready-to-eat (RTE) and fast foods (FFs). Biomarker analysis revealed that DOxS accumulation, particularly 25-OH and triol, can potentially discriminate between RTEs and FFs. This work underscores the potential utility of dietary biomarkers in early disease detection and prevention. However, an essential next step is conducting exposure assessments to better comprehend the levels of DOxS exposure and their association with chronic diseases.
  • Publication
    A structure-dynamics relationship enables prediction of the water hydrogen bond exchange activation energy from experimental data
    (Chemical Science, 2024-02-07) Thompson, Ward H
    It has long been understood that the structural features of water are determined by hydrogen bonding (H-bonding) and that the exchange of, or "jumps" between, H-bond partners underlies many of the dynamical processes in water. Despite the importance of H-bond exchanges there is, as yet, no direct method for experimentally measuring the timescale of the process or its associated activation energy. Here, we identify and exploit relationships between water's structural and dynamical properties that provide an indirect route for determining the H-bond exchange activation energy from experimental data. Specifically, we show that the enthalpy and entropy determining the radial distribution function in liquid water are linearly correlated with the activation energies for H-bond jumps, OH reorientation, and diffusion. Using temperature-dependent measurements of the radial distribution function from the literature, we demonstrate how these correlations allow us to infer the value of the jump activation energy, , from experimental results. This analysis gives = 3.43 kcal mol, which is in good agreement with that predicted by the TIP4P/2005 water model. We also illustrate other approaches for estimating this activation energy consistent with these estimates.
  • Publication
    Electric field-enhanced backscatter interferometry detection for capillary electrophoresis
    (Nature Research, 2024-01-24) Dunn, Robert C
    Backscatter interferometry (BSI) is a refractive index (RI) detection method that is easily integrated with capillary electrophoresis (CE) and is capable of detecting species ranging from inorganic ions to proteins without additional labels or contrast agents. The BSI signal changes linearly with the square of the separation voltage which has been used to quantify sample injection, but has not been explored as a potential signal enhancement mechanism in CE. Here we develop a mathematical model that predicts a signal enhancement at high field strengths, where the BSI signal is dominated by the voltage dependent mechanism. This is confirmed in both simulation and experiment, which show that the analyte peak area grows linearly with separation voltage at high field strengths. This effect can be exploited by adjusting the background electrolyte (BGE) to increase the conductivity difference between the BGE and analyte zones, which is shown to improve BSI performance. We also show that this approach has utility in small bore capillaries where larger separation fields can be applied before excess Joule heating degrades the separation. Unlike other optical detection methods that generally degrade as the optical pathlength is reduced, the BSI signal-to-noise can improve in small bore capillaries as the larger separation fields enhance the signal.
  • Publication
    Monoclonal antibody and protein therapeutic formulations for subcutaneous delivery: high-concentration, low-volume vs. low-concentration, high-volume
    (mABs, 2023-11-27) Boisvert, D; Lou, H.; Hageman, M.; Kundu, A.; Desai, M.
    Biologic drugs are used to treat a variety of cancers and chronic diseases. While most of these treatments are administered intravenously by trained healthcare professionals, a noticeable trend has emerged favoring subcutaneous (SC) administration. SC administration of biologics poses several challenges. Biologic drugs often require higher doses for optimal efficacy, surpassing the low volume capacity of traditional SC delivery methods like autoinjectors. Consequently, high concentrations of active ingredients are needed, creating time-consuming formulation obstacles. Alternatives to traditional SC delivery systems are therefore needed to support higher-volume biologic formulations and to reduce development time and other risks associated with high-concentration biologic formulations. Here, we outline key considerations for SC biologic drug formulations and delivery and explore a paradigm shift: the flexibility afforded by low-to-moderate-concentration drugs in high-volume formulations as an alternative to the traditionally difficult approach of high-concentration, low-volume SC formulation delivery.
  • Publication
    Combining the Benefits of Biotin–Streptavidin Aptamer Immobilization with the Versatility of Ni-NTA Regeneration Strategies for SPR
    (MDPI, 2024-04-27) Hanson, Eliza K.; Whelan, Rebecca J.
    The high affinity of the biotin–streptavidin interaction has made this non-covalent coupling an indispensable strategy for the immobilization and enrichment of biomolecular affinity reagents. However, the irreversible nature of the biotin–streptavidin bond renders surfaces functionalized using this strategy permanently modified and not amenable to regeneration strategies that could increase assay reusability and throughput. To increase the utility of biotinylated targets, we here introduce a method for reversibly immobilizing biotinylated thrombin-binding aptamers onto a Ni-nitrilotriacetic acid (Ni-NTA) sensor chip using 6xHis-tagged streptavidin as a regenerable capture ligand. This approach enabled the reproducible immobilization of aptamers and measurements of aptamer–protein interaction in a surface plasmon resonance assay. The immobilized aptamer surface was stable during five experiments over two days, despite the reversible attachment of 6xHis-streptavidin to the Ni-NTA surface. In addition, we demonstrate the reproducibility of this immobilization method and the affinity assays performed using it. Finally, we verify the specificity of the biotin tag–streptavidin interaction and assess the efficiency of a straightforward method to regenerate and reuse the surface. The method described here will allow researchers to leverage the versatility and stability of the biotin–streptavidin interaction while increasing throughput and improving assay efficiency.
  • Publication
    Potent small molecule inhibitors against the 3C protease of foot-and-mouth disease virus
    (American Society for Microbiology, 2024-03-11) Kim, Yunjeong; Pool, Emma; Kim, Eunji; Dampalla, Chamandi S.; Nguyen, Harry Nhat; Johnson, David K.; Lovell, Scott; Groutas, William C.; Chang, Kyeong-Ok
    Foot-and-mouth disease (FMD) is one of the most devastating diseases of livestock which can cause significant economic losses, especially when introduced to FMD-free countries. FMD virus (FMDV) belongs to the family Picornaviridae and is antigenically heterogeneous with seven established serotypes. The prevailing preventive and control strategies are limited to restriction of animal movement and elimination of infected or exposed animals, which can be potentially combined with vaccination. However, FMD vaccination has limitations including delayed protection and lack of cross-protection against different serotypes. Recently, antiviral drug use for FMD outbreaks has increasingly been recognized as a potential tool to augment the existing early response strategies, but limited research has been reported on potential antiviral compounds for FMDV. FMDV 3C protease (3Cpro) cleaves the viral-encoded polyprotein into mature and functional proteins during viral replication. The essential role of viral 3Cpro in viral replication and the high conservation of 3Cpro among different FMDV serotypes make it an excellent target for antiviral drug development. We have previously reported multiple series of inhibitors against picornavirus 3Cpro or 3C-like proteases (3CLpros) encoded by coronaviruses or caliciviruses. In this study, we conducted structure-activity relationship studies for our in-house focused compound library containing 3Cpro or 3CLpro inhibitors against FMDV 3Cpro using enzyme and cell-based assays. Herein, we report the discovery of aldehyde and α-ketoamide inhibitors of FMDV 3Cpro with high potency. These data inform future preclinical studies that are related to the advancement of these compounds further along the drug development pathway. IMPORTANCE Food-and-mouth disease (FMD) virus (FMDV) causes devastating disease in cloven-hoofed animals with a significant economic impact. Emergency response to FMD outbreaks to limit FMD spread is critical, and the use of antivirals may overcome the limitations of existing control measures by providing immediate protection for susceptible animals. FMDV encodes 3C protease (3Cpro), which is essential for virus replication and an attractive target for antiviral drug discovery. Here, we report a structure-activity relationship study on multiple series of protease inhibitors and identified potent inhibitors of FMDV 3Cpro. Our results suggest that these compounds have the potential for further development as FMD antivirals.
  • Publication
    Changing the Paradigm in Prognostic Breast Cancer Testing Based on Extracellular Vesicles
    (US Department of Health and Human Services, 2023-06-22) Witek, Malgorzata A.; Soper, Steven A.; Godwin, Andrew K.
    Women with early-stage breast cancer have several options for genomic tests including Oncotype DX®, MammaPrint®, and Prosigna® that can estimate risk of distant recurrence and help determine whether they will benefit from adjuvant chemotherapy, but these tests depend on access to tumor tissue samples [1-3]. Our recently published work on “Assessing Breast Cancer Molecular Subtypes Using Extracellular Vesicles’ mRNA” was driven by a desire to develop a liquid-based biopsy approach to estimate the risk of distant recurrence for breast cancer patients receiving endocrine therapy [4]. The clinical relevance in therapeutic stratifications of different molecular subtypes of breast cancer has been demonstrated [5]. Molecular subtyping in breast cancer looks beyond the common prognostic clinical-pathological parameters (e.g., age, tumor size, presence of node metastases and histological grade) and receptor status (i.e., progesterone, estrogen, and HER2) to make sure breast cancer patients receive proper treatment. One such test is the Prosigna® Breast Cancer Prognostic Gene Signature Assay (formerly called the PAM50 test). Prosigna® is used to estimate the risk of distant recurrence for postmenopausal women within 10 years of diagnosis of early-stage, hormone-receptor-positive disease with up to three positive lymph nodes after 5 years of hormonal therapy. Our study focused on molecular profiling and subtyping of breast cancer patients using a minimally invasive approach. We focused our attention specifically on Extracellular Vesicles (EVs) and their molecular cargo (i.e., exo-mRNA) that can be secured from a simple blood draw. The premise of our research was that EVs carry RNA cargo believed to be associated with the cell-of-origin and thus, have the potential to serve as a liquid biopsy marker for supplying molecular information to identify characteristics of the disease (i.e., precision medicine). EVs were affinity selected by targeting epithelial and mesenchymal surface markers and the harvested exo-mRNA cargo was analyzed using the PAM50® gene panel on the Nanostring nCounter. We also developed a new analysis algorithm (exo- PAM50), which aided in the examination of the exo-mRNA data. Our initial results were very encouraging and suggested that the quantitation of PAM50-based exo-mRNA transcripts collected from both epithelial and mesenchymal EVs could generate profiles with high concordance to tumor tissue-based testing. Additional studies are required to further validate our exo-mRNA-based PAM50 assay and potentially other clinical approved prognostic tests in breast cancer patients; however, in our work we have demonstrated the feasibility of using novel methods to efficiently isolate exo-biomarkers and their analysis with the validated technologies or clinical lab-developed tests. Liquid biopsy assays will be important in the future as they can be used in the stratification and subtyping of other epithelial cancers. For example, molecular subtypes have been identified for other epithelial malignancies such as pancreatic, colorectal, prostate, bladder, and sub-classification of triple-negative breast cancers [6-10]. Extracellular Vesicles (EVs) have the potential to function as a minimally invasive liquid biopsy marker for delivering molecular information to assist treatment decisions (i.e., precision medicine) since they carry RNA cargo that is thought to be connected with the cell-of-origin. We describe the high-volume production-capable affinity isolation of EV subpopulations using monoclonal antibodies mounted to the surface of a microfluidic chip made of plastic. The efficacy of the EV-Microfluidic Affinity Purification (EV-MAP) chip was established in a proof-of-concept application to give molecular subtyping data for breast cancer patients by isolating EVs derived from two-orthogonal cell types.
  • Publication
    The Anti-Cancer Activity of the Naturally Occurring Dipeptide Carnosine: Potential for Breast Cancer
    (MDPI, 2023-11-08) Maugeri, Salvatore; Sibbitts, Jay; Privitera, Anna; Cardaci, Vincenzo; Pietro, Lucia Di; Leggio, Loredana; Iraci, Nunzio; Lunte, Susan M.; Caruso, Giuseppe
    Carnosine is an endogenous dipeptide composed of β-alanine and L-histidine, possessing a multimodal pharmacodynamic profile that includes anti-inflammatory and anti-oxidant activities. Carnosine has also shown its ability to modulate cell proliferation, cell cycle arrest, apoptosis, and even glycolytic energy metabolism, all processes playing a key role in the context of cancer. Cancer is one of the most dreaded diseases of the 20th and 21st centuries. Among the different types of cancer, breast cancer represents the most common non-skin cancer among women, accounting for an estimated 15% of all cancer-related deaths in women. The main aim of the present review was to provide an overview of studies on the anti-cancer activity of carnosine, and in particular its activity against breast cancer. We also highlighted the possible advantages and limitations involved in the use of this dipeptide. The first part of the review entailed a brief description of carnosine’s biological activities and the pathophysiology of cancer, with a focus on breast cancer. The second part of the review described the anti-tumoral activity of carnosine, for which numerous studies have been carried out, especially at the preclinical level, showing promising results. However, only a few studies have investigated the therapeutic potential of this dipeptide for breast cancer prevention or treatment. In this context, carnosine has shown to be able to decrease the size of cancer cells and their viability. It also reduces the levels of vascular endothelial growth factor (VEGF), cyclin D1, NAD+, and ATP, as well as cytochrome c oxidase activity in vitro. When tested in mice with induced breast cancer, carnosine proved to be non-toxic to healthy cells and exhibited chemopreventive activity by reducing tumor growth. Some evidence has also been reported at the clinical level. A randomized phase III prospective placebo-controlled trial showed the ability of Zn–carnosine to prevent dysphagia in breast cancer patients undergoing adjuvant radiotherapy. Despite this evidence, more preclinical and clinical studies are needed to better understand carnosine’s anti-tumoral activity, especially in the context of breast cancer.
  • Publication
    Protection against Aβ-induced neuronal damage by KU-32: PDHK1 inhibition as important target
    (Frontiers Media, 2023-11-14) Pal, Ranu; Hui, Dongwei; Menchen, Heather; Zhao, Huiping; Mozziconacci, Olivier; Wilkins, Heather; Blagg, Brian S. J.; Schöneich, Christian; Swerdlow, Russell H.; Michaelis, Mary L.; Michaelis, Elias K.
    A feature of most neurodegenerative diseases is the presence of “mis-folded proteins” that form aggregates, suggesting suboptimal activity of neuronal molecular chaperones. Heat shock protein 90 (Hsp90) is the master regulator of cell responses to “proteotoxic” stresses. Some Hsp90 modulators activate cascades leading to upregulation of additional chaperones. Novobiocin is a modulator at the C-terminal ATP-binding site of Hsp90. Of several novobiocin analogs synthesized and tested for protection against amyloid beta (Aβ)-induced neuronal death, “KU-32” was the most potent in protecting primary neurons, but did not increase expression of other chaperones believed to help clear misfolded proteins. However, KU-32 reversed Aβ-induced superoxide formation, activated Complex I of the electron transfer chain in mitochondria, and blocked the Aβ-induced inhibition of Complex I in neuroblastoma cells. A mechanism for these effects of KU-32 on mitochondrial metabolism appeared to be the inhibition of pyruvate dehydrogenase kinase (PDHK), both in isolated brain mitochondria and in SH-SY5Y cells. PDHK inhibition by the classic enzyme inhibitor, dichloroacetate, led to neuroprotection from Aβ25-35-induced cell injury similarly to KU-32. Inhibition of PDHK in neurons would lead to activation of the PDH complex, increased acetyl-CoA generation, stimulation of the tricarboxylic acid cycle and Complex I in the electron transfer chain, and enhanced oxidative phosphorylation. A focus of future studies may be on the potential value of PDHK as a target in AD therapy.
  • Publication
    Strategies for Mitigating Commercial Sensor Chip Variability with Experimental Design Controls
    (MDPI, 2023-07-26) Hanson, Eliza K.; Wang, Chien-Wei; Minkoff, Lisa; Whelan, Rebecca J.
    Surface plasmon resonance (SPR) is a popular real-time technique for the measurement of binding affinity and kinetics, and bench-top instruments combine affordability and ease of use with other benefits of the technique. Biomolecular ligands labeled with the 6xHis tag can be immobilized onto sensing surfaces presenting the Ni2+-nitrilotriacetic acid (NTA) functional group. While Ni-NTA immobilization offers many advantages, including the ability to regenerate and reuse the sensors, its use can lead to signal variability between experimental replicates. We report here a study of factors contributing to this variability using the Nicoya OpenSPR as a model system and suggest ways to control for those factors, increasing the reproducibility and rigor of the data. Our model ligand/analyte pairs were two ovarian cancer biomarker proteins (MUC16 and HE4) and their corresponding monoclonal antibodies. We observed a broad range of non-specific binding across multiple NTA chips. Experiments run on the same chips had more consistent results in ligand immobilization and analyte binding than experiments run on different chips. Further assessment showed that different chips demonstrated different maximum immobilizations for the same concentration of injected protein. We also show a variety of relationships between ligand immobilization level and analyte response, which we attribute to steric crowding at high ligand concentrations. Using this calibration to inform experimental design, researchers can choose protein concentrations for immobilization corresponding to the linear range of analyte response. We are the first to demonstrate calibration and normalization as a strategy to increase reproducibility and data quality of these chips. Our study assesses a variety of factors affecting chip variability, addressing a gap in knowledge about commercially available sensor chips. Controlling for these factors in the process of experimental design will minimize variability in analyte signal when using these important sensing platforms.
  • Publication
    Distinguishing academic science writing from humans or ChatGPT with over 99% accuracy using off-the-shelf machine learning tools
    (Elsevier, 2023-06-21) Desaire, Heather; Chua, Aleesa E.; Isom, Madeline; Jarosova, Romana; Hua, David
    ChatGPT has enabled access to artificial intelligence (AI)-generated writing for the masses, initiating a culture shift in the way people work, learn, and write. The need to discriminate human writing from AI is now both critical and urgent. Addressing this need, we report a method for discriminating text generated by ChatGPT from (human) academic scientists, relying on prevalent and accessible supervised classification methods. The approach uses new features for discriminating (these) humans from AI; as examples, scientists write long paragraphs and have a penchant for equivocal language, frequently using words like “but,” “however,” and “although.” With a set of 20 features, we built a model that assigns the author, as human or AI, at over 99% accuracy. This strategy could be further adapted and developed by others with basic skills in supervised classification, enabling access to many highly accurate and targeted models for detecting AI usage in academic writing and beyond.
  • Publication
    Distinguishing academic science writing from humans or ChatGPT with over 99% accuracy using off-the-shelf machine learning tools
    (Elsevier, 2023-06-07) Desaire, Heather; Chua, Aleesa E.; Isom, Madeline; Jarosova, Romana; Hua, David
    ChatGPT has enabled access to artificial intelligence (AI)-generated writing for the masses, initiating a culture shift in the way people work, learn, and write. The need to discriminate human writing from AI is now both critical and urgent. Addressing this need, we report a method for discriminating text generated by ChatGPT from (human) academic scientists, relying on prevalent and accessible supervised classification methods. The approach uses new features for discriminating (these) humans from AI; as examples, scientists write long paragraphs and have a penchant for equivocal language, frequently using words like “but,” “however,” and “although.” With a set of 20 features, we built a model that assigns the author, as human or AI, at over 99% accuracy. This strategy could be further adapted and developed by others with basic skills in supervised classification, enabling access to many highly accurate and targeted models for detecting AI usage in academic writing and beyond.
  • Publication
    Breaking Barriers: Diversity and Equity in Chemistry
    (University of Kansas, 2023-07) Sun, Shuai; Kaiser, John; Meier, Alex
    The field of chemistry has long been associated with the pursuit of objective facts and the uncovering of the building blocks of our universe. However, this view can often exclude the important role that diversity, equity, and inclusion (DEI) play in the advancement of scientific knowledge. By highlighting the contributions of minority chemists and integrating DEI principles into chemistry education, we can promote a more inclusive environment and foster greater understanding of the complex connections between chemistry and society. In the first section, we provide a biography of each chemist, discussing their personal and professional lives and how their minority identity has interacted with their careers. The second section summarizes their research and accomplishments in the field of chemistry, emphasizing the importance of their work and the implications it has had on the broader scientific community. Finally, the third section explores how their research is related to the topics and contents taught in general chemistry, creating a connection between the material students learn in the classroom and the real-world applications of chemistry. In recent years, there has been a growing recognition of the need to incorporate DEI into STEM education, and chemistry is no exception. Despite this, there remains a scarcity of learning materials that directly introduce diversity and equality in chemistry education. As a result, students may view chemistry as an isolated discipline that is removed from the broader community. This book aims to challenge that perception by introducing readers to minority chemists, their research, and the ways in which their work is related to topics taught in general chemistry courses. By exploring the lives and research of chemists who come from diverse backgrounds, we hope to showcase the importance of diverse perspectives in the advancement of the field and inspire a new generation of scientists who embrace and promote DEI in their own work. Each chapter of this book is divided into three main sections, highlighting the personal and professional lives of these extraordinary individuals and demonstrating the impact their work has had on the field.
  • Publication
    Assessing Breast Cancer Molecular Subtypes Using Extracellular Vesicles’ mRNA
    (American Chemical Society, 2023) Hu, Mengjia; Brown, Virginia; Jackson, Joshua M.; Wijerathne, Harshani; Pathak, Harsh; Koestler, Devin C.; Nissen, Emily; Hupert, Mateusz L.; Muller, Rolf; Godwin, Andrew K.; Witek, Malgorzata A.; Soper, Steven A.
    Extracellular vesicles (EVs) carry RNA cargo that is believed to be associated with the cell-of-origin and thus have the potential to serve as a minimally invasive liquid biopsy marker for supplying molecular information to guide treatment decisions (i.e., precision medicine). We report the affinity isolation of EV subpopulations with monoclonal antibodies attached to the surface of a microfluidic chip that is made from a plastic to allow for high-scale production. The EV microfluidic affinity purification (EV-MAP) chip was used for the isolation of EVs sourced from two-orthogonal cell types and was demonstrated for its utility in a proof-of-concept application to provide molecular subtyping information for breast cancer patients. The orthogonal selection process better recapitulated the epithelial tumor microenvironment by isolating two subpopulations of EVs: EVEpCAM (epithelial cell adhesion molecule, epithelial origin) and EVFAPα (fibroblast activation protein α, mesenchymal origin). The EV-MAP provided recovery >80% with a specificity of 99 ± 1% based on exosomal mRNA (exo-mRNA) and real time–droplet digital polymerase chain reaction results. When selected from the plasma of healthy donors and breast cancer patients, EVs did not differ in size or total RNA mass for both markers. On average, 0.5 mL of plasma from breast cancer patients yielded ∼2.25 ng of total RNA for both EVEpCAM and EVFAPα, while in the case of cancer-free individuals, it yielded 0.8 and 1.25 ng of total RNA from EVEpCAM and EVFAPα, respectively. To assess the potential of these two EV subpopulations to provide molecular information for prognostication, we performed the PAM50 test (Prosigna) on exo-mRNA harvested from each EV subpopulation. Results suggested that EVEpCAM and EVFAPα exo-mRNA profiling using subsets of the PAM50 genes and a novel algorithm (i.e., exo-PAM50) generated 100% concordance with the tumor tissue.