@article{dewey_jones_lucas_hall_sultana_abello_budhathoki-uprety_2023, title={Carbon Nanotubes for Optical Detection of Quaternary Ammonium Compounds in Complex Media}, volume={6}, ISSN={2574-0970 2574-0970}, url={http://dx.doi.org/10.1021/acsanm.3c02219}, DOI={10.1021/acsanm.3c02219}, abstractNote={Quaternary ammonium compounds (QACs) are widely used in disinfectants, cleaners, preservatives, cosmetics, and agriculture. Recently, QACs have been detected in the human bloodstream, breast milk, and neonatal mouse brain, which shows that these compounds can cross biological barriers. In vivo studies showed that chronic low-level exposure to QACs causes developmental, reproductive, and immune dysfunctions, whereas in vitro studies indicate that QACs can affect reproductive systems, disrupt cholesterol biosynthesis, increase inflammatory cytokines, and decrease mitochondrial functions. Effects of QACs on health are gradually emerging, amid increased use of QAC disinfectants during the COVID-19 pandemic. Analysis of biological fluids including blood, urine, sweat, and saliva can provide vital information in determining the biological effects of analytes. Biofluid analysis is convenient yet crucial because of non-invasive/or minimally invasive procedures that can be performed outside hospital settings. Interest in optical detection methods for biofluid analysis has been growing due to recent advances in detection technologies and availability of tunable materials to aid the technologies. Detection in the near-infrared (NIR) spectral range is advantageous over the visible range mainly due to minimal autofluorescence, light-scattering, and absorption from native biological molecules in the NIR range. Photoluminescent single-walled carbon nanotubes (SWCNTs) are promising candidates for the development of NIR optical probes and sensors due to their non-photobleaching NIR fluorescence, tunable surface chemistry, and high sensitivity. Herein, we report optical detection of QACs in protein-rich media and a model biofluid. We functionalized photoluminescent SWCNTs with bile salt derivatives that enabled the detection of QACs in artificial sweat and serum-protein-enriched media. The QAC detection was significant at nanomolar concentrations, which is within the threshold that can affect various physiological processes. Thus, nanotube-based optical detection could be well suited for the analysis of QACs in biological fluids.}, number={17}, journal={ACS Applied Nano Materials}, publisher={American Chemical Society (ACS)}, author={Dewey, Hannah M. and Jones, Jaron and Lucas, Sydney and Hall, Shelby and Sultana, Nigar and Abello, Sofia Mariapaz and Budhathoki-Uprety, Januka}, year={2023}, month={Aug}, pages={15530–15539} }
 @inproceedings{sultana_dewey_budhathoki-uprety_2023, title={Development of Optical Nanosensors for pH Measurements in Model Biofluids}, volume={243}, ISSN={2151-2043}, url={http://dx.doi.org/10.1149/ma2023-0191166mtgabs}, DOI={10.1149/MA2023-0191166mtgabs}, abstractNote={Changes in pH in biofluids such as urine, sweat, and blood can reveal pathophysiological conditions like tumor metastasis, microbial infection, acidosis, cystic fibrosis, wound healing, etc. Thus, monitoring pH could provide insights on those patho-physiological changes. Among others, sweat analysis provides convenient and non-invasive way to track personal health. Sweat pH changes can reveal information about atopic dermatitis, fungus infections, and cystic fibrosis. Thus, sweat pH measurements could aid in accurately identifying certain health issues. Although solution pH can be measured by various methods including electrochemical, colorimetric and fluorescence measurements, optical pH measurements have gained popularity in recent decades due to versatile material choices and new imaging technologies. Semiconducting single-walled carbon nanotubes (SWCNTs) are emerging molecular optical probes and sensors due to their outstanding photophysical properties, which include photo-stable near-infrared (nIR) fluorescence and sensitive molecular recognition. Here, we report that SWCNT-based sensors can reliably detect pH changes in a model biofluid - artificial sweat. The sensor exhibited significant responses within biologically relevant pH ranges within minutes through changes in the nIR fluorescence. The nanotubes' optical response to pH changes provides new opportunities to develop optical pH sensors for healthcare, bioengineering, environmental sciences, and chemistry.}, number={9}, booktitle={ECS Meeting Abstracts}, publisher={The Electrochemical Society}, author={Sultana, Nigar and Dewey, Hannah and Budhathoki-Uprety, Januka}, year={2023}, month={Aug}, pages={1166–1166} }
 @article{budhathoki-uprety_2023, title={Greener Dyeing}, volume={87}, ISSN={["2047-6329"]}, DOI={10.1002/cind.10081}, abstractNote={Chemistry & IndustryVolume 87, Issue 3 p. 22-25 Sustainability Greener Dyeing First published: 21 March 2023 https://doi.org/10.1002/cind.10081AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Volume87, Issue3March 2023Pages 22-25 RelatedInformation}, number={3}, journal={CHEMISTRY & INDUSTRY}, author={Budhathoki-Uprety, Januka}, year={2023}, month={Mar}, pages={22–25} }
 @inproceedings{budhathoki-uprety_dewey_sultana_2023, title={Nanoscale Probes for Optical Detection of Emerging Contaminants and Biological Indicators}, volume={MA2023-01}, ISSN={2151-2043}, url={http://dx.doi.org/10.1149/MA2023-0191130mtgabs}, DOI={10.1149/MA2023-0191130mtgabs}, abstractNote={Photoluminescent single-walled carbon nanotubes exhibit outstanding potential in developing molecular probes for optical detection systems. Surface coatings on nanotubes could facilitate effective molecular interactions enabling targeted nanoscale probes, sensors, and imaging agents. This talk will be focused on the development and applications of carbon nanotube-based sensors for optical detection of emerging contaminants and biological indicators including pH, a measure of acidity and alkalinity of a sample. pH changes in tissues and biofluids could indicate patho-physiological conditions such as tumor growth, microbial infection, acidosis, cystic fibrosis, wound healing, etc. Thus, the optical pH sensor could find applications in disease detection, diagnosis, and improve clinical outcome. This talk will also discuss optical detection of chemical disinfectants using carbon nanotubes. COVID-19 pandemics has led into wide uses of various disinfectant chemicals to mitigate virus burden. Recent findings show that certain disinfectants can cross various biological barriers and accumulate within human body. Molecular tools that enable detection of such compounds within native biological environment are useful to understand complete biological fate of such chemicals to mitigate potential impact on health.}, number={9}, booktitle={ECS Meeting Abstracts}, publisher={The Electrochemical Society}, author={Budhathoki-Uprety, Januka and Dewey, Hannah and Sultana, Nigar}, year={2023}, month={Aug}, pages={1130–1130} }
 @inproceedings{dewey_sultana_budhathoki-uprety_2023, title={Optical Nanosensors for the Detection of Quaternary Ammonium Compounds}, volume={MA2023-01}, ISSN={2151-2043}, url={http://dx.doi.org/10.1149/MA2023-0191132mtgabs}, DOI={10.1149/MA2023-0191132mtgabs}, abstractNote={Quaternary ammonium compounds (QACs) are common active ingredients in chemical disinfectants, household cleaners, cosmetics, pesticides, etc. Recently QACs have been detected in human blood and breast milk during the COVID-19 pandemic. Humans can be exposed to QACs through dermal adsorption during application, hand-to-mouth ingestion of disinfectant residues, and inhalation of indoor air upon treatment with disinfectant spray. Exposure to these chemicals can cause respiratory illness such as asthma and chronic obstructive pulmonary disease, increase inflammatory cytokines, decrease mitochondrial function, and disrupt cholesterol biosynthesis. However, the complete biological fate of QACs is currently unknown. Therefore, a real-time continuous monitoring system in complex biological environments is crucial to learn the long-term effects of QACs on human health.
 Photoluminescent single-walled carbon nanotubes (SWCNTs) are great candidates for developing optical probes to monitor biological systems due to their outstanding photophysical properties in the tissue-transparent near-infrared spectral region, high sensitivity, and high stability. Furthermore, nanotube-based sensors exhibit a great potential for an implantable, real-time, wireless optical detection technology. Herein, we developed a carbon nanotube-based optical sensor for the detection of QACs in complex solution. Our findings from this research could provide a basis for engineering an optical detection technology to gain insight on the long-term effects of QACs to human health.}, number={9}, booktitle={ECS Meeting Abstracts}, publisher={The Electrochemical Society}, author={Dewey, Hannah and Sultana, Nigar and Budhathoki-Uprety, Januka}, year={2023}, month={Aug}, pages={1132–1132} }
 @misc{dewey_jones_keating_budhathoki-uprety_2022, title={Increased Use of Disinfectants During the COVID-19 Pandemic and Its Potential Impacts on Health and Safety}, volume={29}, ISSN={["1878-0504"]}, url={https://doi.org/10.1021/acs.chas.1c00026}, DOI={10.1021/acs.chas.1c00026}, abstractNote={The COVID-19 pandemic has called for the increased use of disinfectants worldwide in public facilities, transportation, hospitals, nursing homes, wastewater treatment facilities, and even common households to mitigate virus burden. Active ingredients in common disinfectants recommended for use against COVID-19 viruses include chemicals such as quaternary ammonium compounds (QACs), hydrogen peroxide, bleach (sodium hypochlorite), and alcohols. These disinfecting chemicals differ in their structures, properties, modes of action, environmental behaviors, and effects on human health upon exposure. Humans can be exposed to disinfecting chemicals mainly through dermal absorption, inhalation, and ingestion. The total exposure and relative contribution of each exposure route vary considerably among the disinfectants. QACs have been linked to occupational illnesses such as asthma and an increased risk of chronic obstructive pulmonary disease (COPD), whereas excess use of bleach, hydrogen peroxide, or alcohol-based disinfectants can cause respiratory damage and has been linked to an increased risk of developing and controlling asthma. Recent studies showed that the presence of QACs in human blood has been associated with changes in health biomarkers such as an increase in inflammatory cytokines, decreased mitochondrial function, and disruption of cholesterol homeostasis in a dose-dependent manner. Therefore, repeated human exposure to disinfectants during the pandemic has raised questions on exposure-related long-term health risks and occupational safety. Furthermore, in lieu of a lack of adequate knowledge and public awareness, these chemicals have been frequently used on porous surfaces, including fabrics/textiles and consumer plastics and even for disinfecting cloth facemasks, on which disinfectant chemical residues may persist for longer duration, causing potential degradation of plastic materials, releasing additives, and shedding microplastics. In addition, the increased use of these disinfectant chemicals and the subsequent discharge into wastewater may cause adverse impacts on aquatic ecosystems, accumulation on vegetables, and contamination of the food chain via wastewater irrigation and sludge application. This article provides a well-rounded understanding of the most common disinfectants and reviews modes of action of those disinfectants, their interactions with aquatic and terrestrial environments, the exposure to humans, and potential impacts to human health and safety.}, number={1}, journal={ACS CHEMICAL HEALTH & SAFETY}, publisher={American Chemical Society (ACS)}, author={Dewey, Hannah M. and Jones, Jaron M. and Keating, Mike R. and Budhathoki-Uprety, Januka}, year={2022}, month={Jan}, pages={27–38} }
 @article{sultana_dewey_budhathoki-uprety_2022, title={Optical detection of pH changes in artificial sweat using near-infrared fluorescent nanomaterials}, volume={1}, ISSN={2635-0998}, url={http://dx.doi.org/10.1039/D2SD00110A}, DOI={10.1039/D2SD00110A}, abstractNote={Photoluminescent single-walled carbon nanotubes are versatile tools for the development of optical nanosensors. Carbon nanotubes were employed for the optical detection of pH within a biologically relevant range in a model biofluid.}, number={6}, journal={Sensors & Diagnostics}, publisher={Royal Society of Chemistry (RSC)}, author={Sultana, Nigar and Dewey, Hannah and Budhathoki-Uprety, Januka}, year={2022}, pages={1189–1197} }
 @article{lord_neve_keating_budhathoki-uprety_2022, title={Polycarbodiimide for Textile Dye Removal from Contaminated Water}, volume={7}, ISSN={["2637-6105"]}, url={https://doi.org/10.1021/acsapm.2c00959}, DOI={10.1021/acsapm.2c00959}, abstractNote={Water pollution has been a significant challenge for the environment and human health. Dyes in water resources cause severe water pollution and block sunlight penetration through water, which impairs photosynthesis of aquatic plants as well as causes a significant alteration in ecological conditions of aquatic life. Dye-contaminated water sources can pose serious public health concerns, including toxicity, mutagenicity, and carcinogenicity among other adverse health effects. Therefore, it is imperative to develop efficient methods to remove dye contaminants from water sources. Synthetic polymers, due to their versatile chemical structure, size, and shape, could provide a tunable platform to remove dyes from contaminated sources. Herein, we report a polymer-mediated removal of textile dyes from aqueous solutions. A nitrogen-rich polymer, polycarbodiimide, efficiently removed anionic dyes from a dye-contaminated acidic solution. Upon dye removal, the polymer was regenerated through modulation of the solution pH. Further investigations showed that the polymer’s ability to remove dyes was dependent on solution pH and the topological polar surface area of the dyes. Thus, the molecular mechanism for polymer–dye interactions could be attributed to a combined ionic and hydrophobic interaction. The effects of pH, ionic strength, dye concentration, and composition were also investigated. Removal of dyes from contaminated aqueous resources is important in reducing environmental pollutants and mitigating environmental and health impacts. The findings from this study provide insights into the development of polymeric materials to remove soluble dyes from contaminated water to foster environmental and water sustainability.}, journal={ACS APPLIED POLYMER MATERIALS}, author={Lord, Meghan Davis and Neve, Graham and Keating, Mike and Budhathoki-Uprety, Januka}, year={2022}, month={Jul} }
 @inproceedings{budhathoki-uprety_dewey_sultana_chen_jones_2021, title={Carbon Nanotubes Cloaked in Synthetic Polymers: Aqueous Dispersion, Characterization, and Applications}, volume={MA2021-01}, ISSN={2151-2043}, url={http://dx.doi.org/10.1149/MA2021-0110513mtgabs}, DOI={10.1149/MA2021-0110513mtgabs}, abstractNote={Surface chemistry plays a crucial role in interactions of carbon nanotubes in the biological environment. Biomimetic functionalities on nanotubes could facilitate effective nano-bio interactions enabling nanoscale biological probes, sensors, and imaging agents. Synthetic polymers that facilitate aqueous solubility, biocompatibility and molecular recognition via biomimicry are highly preferred for multifunctional carbon nanotube-based biological probes. In this talk, we will introduce carbon nanotubes cloaked in synthetic mimics of biopolymers and uses of those nanoscale probes in optical sensing of target biomolecules.}, number={10}, booktitle={ECS Meeting Abstracts}, publisher={The Electrochemical Society}, author={Budhathoki-Uprety, Januka and Dewey, Hannah and Sultana, Nigar and Chen, Yu and Jones, Jaron}, year={2021}, month={May}, pages={513–513} }
 @article{williams_chen_langenbacher_galassi_harvey_jena_budhathoki-uprety_luo_heller_2021, title={Harnessing nanotechnology to expand the toolbox of chemical biology}, volume={17}, ISSN={["1552-4469"]}, url={https://doi.org/10.1038/s41589-020-00690-6}, DOI={10.1038/s41589-020-00690-6}, abstractNote={Although nanotechnology often addresses biomedical needs, nanoscale tools can also facilitate broad biological discovery. Nanoscale delivery, imaging, biosensing, and bioreactor technologies may address unmet questions at the interface between chemistry and biology. Currently, many chemical biologists do not include nanomaterials in their toolbox, and few investigators develop nanomaterials in the context of chemical tools to answer biological questions. We reason that the two fields are ripe with opportunity for greater synergy. Nanotechnologies can expand the utility of chemical tools in the hands of chemical biologists, for example, through controlled delivery of reactive and/or toxic compounds or signal-binding events of small molecules in living systems. Conversely, chemical biologists can work with nanotechnologists to address challenging biological questions that are inaccessible to both communities. This Perspective aims to introduce the chemical biology community to nanotechnologies that may expand their methodologies while inspiring nanotechnologists to address questions relevant to chemical biology.}, number={2}, journal={NATURE CHEMICAL BIOLOGY}, author={Williams, Ryan M. and Chen, Shi and Langenbacher, Rachel E. and Galassi, Thomas V. and Harvey, Jackson D. and Jena, Prakrit V. and Budhathoki-Uprety, Januka and Luo, Minkui and Heller, Daniel A.}, year={2021}, month={Feb}, pages={129–137} }
 @article{horoszko_schnatz_budhathoki-uprety_rao-pothuraju_koder_heller_2021, title={Non-Covalent Coatings on Carbon Nanotubes Mediate Photosensitizer Interactions}, volume={13}, ISSN={["1944-8252"]}, url={https://doi.org/10.1021/acsami.1c14266}, DOI={10.1021/acsami.1c14266}, abstractNote={Carbon nanotube-based donor-acceptor devices are used in applications ranging from photovoltaics and sensors to environmental remediation. Non-covalent contacts between donor dyes and nanotubes are often used to optimize sensitization and scalability. However, inconsistency is often observed despite donor dye studies reporting strong donor-acceptor interactions. Here, we demonstrate that the dye binding location is an important factor in this process: we used coated-acceptor chromatic responses and find that dye binding is affected by the coating layer. The emission response to free- and protein-sequestered porphyrin was tested to compare direct and indirect dye contact. An acceptor complex that preferentially red-shifts in response to sequestered porphyrin was identified. We observe inconsistent optical signals that suggest porphyrin-dye interactions are best described as coating-centric; therefore, the coating interface must be considered in application and assay design.}, number={43}, journal={ACS APPLIED MATERIALS & INTERFACES}, publisher={American Chemical Society (ACS)}, author={Horoszko, Christopher P. and Schnatz, Peter J. and Budhathoki-Uprety, Januka and Rao-Pothuraju, Rahul V and Koder, Ronald L. and Heller, Daniel A.}, year={2021}, month={Nov}, pages={51343–51350} }
 @article{langenbacher_budhathoki-uprety_jena_roxbury_streit_zheng_heller_2021, title={Single-Chirality Near-Infrared Carbon Nanotube Sub-Cellular Imaging and FRET Probes}, volume={21}, ISSN={["1530-6992"]}, url={https://doi.org/10.1021/acs.nanolett.1c01093}, DOI={10.1021/acs.nanolett.1c01093}, abstractNote={Applications of single-walled carbon nanotubes (SWCNTs) in bioimaging and biosensing have been limited by difficulties with isolating single-chirality nanotube preparations with desired functionalities. Unique optical properties, such as multiple narrow near-infrared bands and several modes of signal transduction, including solvatochromism and FRET, are ideal for live cell/organism imaging and sensing applications. However, internanotube FRET has not been investigated in biological contexts. We developed single-chirality subcellular SWCNT imaging probes and investigated their internanotube FRET capabilities in live cells. To functionalize SWCNTs, we replaced the surfactant coating of aqueous two-phase extraction-sorted single-chirality nanotubes with helical polycarbodiimide polymers containing different functionalities. We achieved single-chirality SWCNT targeting of different subcellular structures, including the nucleus, to enable multiplexed imaging. We also targeted purified (6,5) and (7,6) chiralities to the same structures and observed internanotube FRET within these organelles. This work portends the use of single-chirality carbon nanotube optical probes for applications in biomedical research.}, number={15}, journal={NANO LETTERS}, publisher={American Chemical Society (ACS)}, author={Langenbacher, Rachel and Budhathoki-Uprety, Januka and Jena, Prakrit V and Roxbury, Daniel and Streit, Jason and Zheng, Ming and Heller, Daniel A.}, year={2021}, month={Aug}, pages={6441–6448} }
 @article{heller_antman-passig_baker_budhathoki-uprety_chen_cupo_jena_kim_langenbacher_shah_et al._2020, title={Carbon Nanotube and Organic Color Center Solvatochromism in Biomedicine}, volume={MA2020-02}, url={https://doi.org/10.1149/MA2020-02673409mtgabs}, DOI={10.1149/MA2020-02673409mtgabs}, abstractNote={Optical sensor technologies for vivo use often run into difficulties when attempting to relay quantitative information. Fluorescence transmission from within tissues may be variable depending on depth and tissue heterogeneity. Modulation of the fluorescence emission band position may mitigate some of these difficulties. We developed sensors that modulate the near-infrared emission of single-walled carbon nanotubes and organic color centers (carbon nanotubes with covalent sp 3 defects). We developed methods to control solvatochromic behavior to improve sensor responses, and we developed tools to observe solvatochromism within live cells and live animals. We found that nanotube solvatochromism extends to variations of local electrostatic charge, induced by adsorption/desorption of polyelectrolytes on the nanotube surface, such as proteins and nucleic acids. We also found that dielectric and charge-mediated solvatochromism can be compounded to exacerbate the response. Upon triggered desorption of a polyelectrolyte, amphiphilic molecules can adsorb to the recently-uncovered nanotube surface. This work has enabled the detection of disease biomarkers, drugs, and metabolites, and nucleic acids, including virus RNA, facilitating improvements in disease detection, drug development, and biomedical research.}, number={67}, journal={ECS Meeting Abstracts}, publisher={The Electrochemical Society}, author={Heller, Daniel A. and Antman-Passig, Merav and Baker, Hanan and Budhathoki-Uprety, Januka and Chen, Chen and Cupo, Christian and Jena, Prakrit Vaibhav and Kim, Mijin and Langenbacher, Rachel E and Shah, Janki and et al.}, year={2020}, month={Nov}, pages={3409–3409} }
 @article{williams_harvey_budhathoki-uprety_heller_2020, title={Glutathione-S-transferase Fusion Protein Nanosensor}, volume={20}, ISSN={["1530-6992"]}, url={https://doi.org/10.1021/acs.nanolett.0c02691}, DOI={10.1021/acs.nanolett.0c02691}, abstractNote={Fusion protein tags are widely used to capture and track proteins in research and industrial bioreactor processes. Quantifying fusion-tagged proteins normally requires several purification steps coupled with classical protein assays. Here, we developed a broadly applicable nanosensor platform that quantifies glutathione-S-transferase (GST) fusion proteins in real-time. We synthesized a glutathione-DNA-carbon nanotube system to investigate glutathione-GST interactions via semiconducting single-walled carbon nanotube (SWCNT) photoluminescence. We found that SWCNT fluorescence wavelength and intensity modulation occurred specifically in response to GST and GST-fusions. The sensor response was dependent on SWCNT structure, wherein mod(n - m, 3) = 1 nanotube wavelength and intensity responses correlated with nanotube diameter distinctly from mod(n - m, 3) = 2 SWCNT responses. We also found broad functionality of this sensor to diverse GST-tagged proteins. This work comprises the first label-free optical sensor for GST and has implications for the assessment of protein expression in situ, including in imaging and industrial bioreactor settings.}, number={10}, journal={NANO LETTERS}, publisher={American Chemical Society (ACS)}, author={Williams, Ryan M. and Harvey, Jackson D. and Budhathoki-Uprety, Januka and Heller, Daniel A.}, year={2020}, month={Oct}, pages={7287–7295} }
 @inproceedings{budhathoki-uprety_chen_drago_godthi_sultana_2020, title={Polymer Functionalized Nanocarbons for Biomedical Applications}, volume={MA2020-02}, ISSN={2151-2043}, url={http://dx.doi.org/10.1149/MA2020-02673411mtgabs}, DOI={10.1149/MA2020-02673411mtgabs}, abstractNote={Nanocarbons such as photoluminescent single-walled carbon nanotubes are promising materials in biomedical field as molecular imaging agents, optical probes, and biosensors. These carbon-only nanomaterials lack active surface functional moieties to interact effectively with select biomolecules of interest, which limits their potential applications. Tailored surface functionalization is essential for anticipated functions and bio-compatibility. Polymer adsorption on nanocarbons through multivalent interactions provides a versatile platform to develop functional materials with tunable surface chemistry. Herein, we investigate on biomimetic polymer scaffolds for carbon nanotubes to modulate their physiochemical properties and bio-molecular interactions.}, number={67}, booktitle={ECS Meeting Abstracts}, publisher={The Electrochemical Society}, author={Budhathoki-Uprety, Januka and Chen, Yu and Drago, Julia and Godthi, Nidhi and Sultana, Nigar}, year={2020}, month={Nov}, pages={3411–3411} }
 @article{budhathoki-uprety_shah_korsen_wayne_galassi_cohen_harvey_jena_ramanathan_jaimes_et al._2019, title={Synthetic molecular recognition nanosensor paint for microalbuminuria}, volume={10}, ISSN={["2041-1723"]}, url={http://dx.doi.org/10.1038/s41467-019-11583-1}, DOI={10.1038/s41467-019-11583-1}, abstractNote={Abstract Microalbuminuria is an important clinical marker of several cardiovascular, metabolic, and other diseases such as diabetes, hypertension, atherosclerosis, and cancer. The accurate detection of microalbuminuria relies on albumin quantification in the urine, usually via an immunoturbidity assay; however, like many antibody-based assessments, this method may not be robust enough to function in global health applications, point-of-care assays, or wearable devices. Here, we develop an antibody-free approach using synthetic molecular recognition by constructing a polymer to mimic fatty acid binding to the albumin, informed by the albumin crystal structure. A single-walled carbon nanotube, encapsulated by the polymer, as the transduction element produces a hypsochromic (blue) shift in photoluminescence upon the binding of albumin in clinical urine samples. This complex, incorporated into an acrylic material, results in a nanosensor paint that enables the detection of microalbuminuria in patient samples and comprises a rapid point-of-care sensor robust enough to be deployed in resource-limited settings.}, journal={NATURE COMMUNICATIONS}, author={Budhathoki-Uprety, Januka and Shah, Janki and Korsen, Joshua A. and Wayne, Alysandria E. and Galassi, Thomas V and Cohen, Joseph R. and Harvey, Jackson D. and Jena, Prakrit V and Ramanathan, Lakshmi V and Jaimes, Edgar A. and et al.}, year={2019}, month={Aug} }
 @article{quantitative self-assembly prediction yields targeted nanomedicines_2018, url={http://dx.doi.org/10.1038/s41563-017-0007-z}, DOI={10.1038/s41563-017-0007-z}, abstractNote={Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of sulfated indocyanines into particles with ultrahigh drug loadings of up to 90%. We devised quantitative structure-nanoparticle assembly prediction (QSNAP) models to identify and validate electrotopological molecular descriptors as highly predictive indicators of nano-assembly and nanoparticle size. The resulting nanoparticles selectively targeted kinase inhibitors to caveolin-1-expressing human colon cancer and autochthonous liver cancer models to yield striking therapeutic effects while avoiding pERK inhibition in healthy skin. This finding enables the computational design of nanomedicines based on quantitative models for drug payload selection. Molecular simulations reveal the self-assembly of small molecules into nanoparticle drug carriers. Targeting of colon and liver cancer cells by the nanoparticles via kinase inhibitors is employed in anti-tumour therapy in vivo.}, journal={Nature Materials}, year={2018}, month={Apr} }
 @article{the secondary structures of peg-functionalized random copolymers derived from (r)- and (s)- families of alkyne polycarbodiimides_2018, url={http://dx.doi.org/10.1039/c8py00282g}, DOI={10.1039/c8py00282g}, abstractNote={A series of helical rigid-rod (R)- and (S)-polycarbodiimides having PEG2K, 10K, and 20K groups attached to aromatic or aliphatic side chains have been successfully synthesized from the respective alkyne polycarbodiimide precursors using the CuI-catalyzed azide/alkyne cycloaddition (CuAAC) reaction. The AFM, TEM and SEM studies of this series revealed the formation of different types of aggregated morphologies, i.e., micro- and nanospheres, fiber-like crystallites, and porous aggregates, which can be tailored with the hydrophilic PEG segments in the polymer structure. In general, heavily PEGylated scaffolds comprising ∼44 ethylene oxide segments are prone to form round-shaped secondary structures, especially in the bulk, as evident by SEM measurements. AFM data suggested that spherical aggregates are the preferred motifs in a wide range of concentrations. Moreover, polycarbodiimide-graft-PEG(2K) random copolymers were shown to efficiently suspend SWCNTs in water, leading to novel neutral photoluminescent nanocomposite materials. Overall, these extensive self-assembly studies on various polycarbodiimide platforms featuring a hydrophobic rigid rod main chain and a flexible hydrophilic periphery may provide a basic layout for prospective biomedical applications, such as controlled drug delivery and enhanced dispersibility properties of SWCNTs.}, journal={Polymer Chemistry}, year={2018} }
 @article{a carbon nanotube optical reporter maps endolysosomal lipid flux_2017, url={http://dx.doi.org/10.1021/acsnano.7b04743}, DOI={10.1021/acsnano.7b04743}, abstractNote={Lipid accumulation within the lumen of endolysosomal vesicles is observed in various pathologies including atherosclerosis, liver disease, neurological disorders, lysosomal storage disorders, and cancer. Current methods cannot measure lipid flux specifically within the lysosomal lumen of live cells. We developed an optical reporter, composed of a photoluminescent carbon nanotube of a single chirality, that responds to lipid accumulation via modulation of the nanotube's optical band gap. The engineered nanomaterial, composed of short, single-stranded DNA and a single nanotube chirality, localizes exclusively to the lumen of endolysosomal organelles without adversely affecting cell viability or proliferation or organelle morphology, integrity, or function. The emission wavelength of the reporter can be spatially resolved from within the endolysosomal lumen to generate quantitative maps of lipid content in live cells. Endolysosomal lipid accumulation in cell lines, an example of drug-induced phospholipidosis, was observed for multiple drugs in macrophages, and measurements of patient-derived Niemann-Pick type C fibroblasts identified lipid accumulation and phenotypic reversal of this lysosomal storage disease. Single-cell measurements using the reporter discerned subcellular differences in equilibrium lipid content, illuminating significant intracellular heterogeneity among endolysosomal organelles of differentiating bone-marrow-derived monocytes. Single-cell kinetics of lipoprotein-derived cholesterol accumulation within macrophages revealed rates that differed among cells by an order of magnitude. This carbon nanotube optical reporter of endolysosomal lipid content in live cells confers additional capabilities for drug development processes and the investigation of lipid-linked diseases.}, journal={ACS Nano}, year={2017}, month={Nov} }
 @article{a carbon nanotube optical sensor reports nuclear entry via a noncanonical pathway_2017, url={http://dx.doi.org/10.1021/acsnano.7b00176}, DOI={10.1021/acsnano.7b00176}, abstractNote={Single-walled carbon nanotubes are of interest in biomedicine for imaging and molecular sensing applications and as shuttles for various cargos such as chemotherapeutic drugs, peptides, proteins, and oligonucleotides. Carbon nanotube surface chemistry can be modulated for subcellular targeting while preserving photoluminescence for label-free visualization in complex biological environments, making them attractive materials for such studies. The cell nucleus is a potential target for many pathologies including cancer and infectious diseases. Understanding mechanisms of nanomaterial delivery to the nucleus may facilitate diagnostics, drug development, and gene-editing tools. Currently, there are no systematic studies to understand how these nanomaterials gain access to the nucleus. Herein, we developed a carbon nanotube based hybrid material that elucidate a distinct mechanism of nuclear translocation of a nanomaterial in cultured cells. We developed a nuclear-targeted probe via cloaking photoluminescent single-walled carbon nanotubes in a guanidinium-functionalized helical polycarbodiimide. We found that the nuclear entry of the nanotubes was mediated by the import receptor importin β without the aid of importin α and not by the more common importin α/β pathway. Additionally, the nanotube photoluminescence exhibited distinct red-shifting upon entry to the nucleus, potentially functioning as a reporter of the importin β-mediated nuclear transport process. This work delineates a noncanonical mechanism for nanomaterial delivery to the nucleus and provides a reporter for the study of nucleus-related pathologies.}, journal={ACS Nano}, year={2017}, month={Apr} }
 @article{jena_roxbury_galassi_akkari_horoszko_iaea_budhathoki-uprety_pipalia_haka_harvey_et al._2017, title={A carbon nanotube optical reporter maps endolysosomal lipid flux}, volume={5}, url={https://doi.org/10.1101/134999}, DOI={10.1101/134999}, abstractNote={Lipid accumulation within the lumen of endolysosomal vesicles is observed in various pathologies including atherosclerosis, liver disease, neurological disorders, lysosomal storage disorders, and cancer. Current methods cannot measure lipid flux specifically within the lysosomal lumen of live cells. We developed an optical reporter, composed of a photoluminescent carbon nanotube of a single chirality, which responds to lipid accumulation via modulation of the nanotube’s optical bandgap. The engineered nanomaterial, composed of short-single stranded DNA and a single nanotube chirality, localizes exclusively to the lumen of endolysosomal organelles without adversely affecting cell viability or proliferation, or organelle morphology, integrity, or function. The emission wavelength of the reporter can be spatially resolved from within the endolysosomal lumen to generate quantitative maps of lipid content in live cells. Endolysosomal lipid accumulation in cell lines, an example of drug-induced phospholipidosis (DIPL), was observed for multiple drugs in macrophages, and measurements of patient-derived Niemann-Pick type C fibroblasts identified lipid accumulation and phenotypic reversal of this lysosomal storage disease. Single-cell measurements using the reporter discerned sub-cellular differences in equilibrium lipid content, illuminating significant intracellular heterogeneity among endolysosomal organelles of differentiating bone marrow-derived monocytes. Single-cell kinetics of lipoprotein-derived cholesterol accumulation within macrophages revealed rates that differed among cells by an order of magnitude. This carbon nanotube optical reporter of endolysosomal lipid content in live cells confers new capabilities for drug development processes and the investigation of lipid-linked diseases.}, publisher={Cold Spring Harbor Laboratory}, author={Jena, Prakrit V. and Roxbury, Daniel and Galassi, Thomas V. and Akkari, Leila and Horoszko, Christopher P. and Iaea, David B. and Budhathoki-Uprety, Januka and Pipalia, Nina H. and Haka, Abigail S. and Harvey, Jackson D. and et al.}, year={2017}, month={May} }
 @article{control of carbon nanotube solvatochromic response to chemotherapeutic agents_2017, url={http://dx.doi.org/10.1021/acsami.7b12015}, DOI={10.1021/acsami.7b12015}, abstractNote={Alkylating agents such as cisplatin play an essential role in chemotherapy regimens, but initial and acquired resistance in many cancer types often dampen therapeutic response. The poor understanding of the mechanisms of resistance highlight the need for quantitative measurements of alkylating agent distribution at both the tissue and subcellular levels. Sensors for use in live animals and cells would allow for more effective study of drug action and resistance. Toward this end, single-walled carbon nanotubes suspended with single-stranded DNA have suitable optical properties for in vivo sensors, such as near-infrared emission and sensitivity to the local environment via solvatochromic responses. Currently, solvatochromic changes of such sensors have been limited by the chemical nature of the analyte, making it impossible to control the direction of energy emission changes. Here, we describe a new approach to control the direction and magnitude of solvatochromic responses of carbon nanotubes. We found that the alkylation of DNA on the nanotube surface can result in small changes in DNA conformation that allow the adsorption of amphiphiles to produce large differences (>14 nm) in response to different drugs. The technique surprisingly revealed differences among drugs upon alkylation. The ability to control carbon nanotube solvatochromism as desired may potentially expand the application of nanotube-based optical sensors for new classes of analytes.}, journal={ACS Applied Materials & Interfaces}, year={2017}, month={Nov} }
 @article{polymer cloaking modulates the carbon nanotube protein corona and delivery into cancer cells_2017, url={http://dx.doi.org/10.1039/c7tb00695k}, DOI={10.1039/c7tb00695k}, abstractNote={Carbon nanotube-based molecular probes, imaging agents, and biosensors in cells and in vivo continue to garner interest as investigational tools and clinical devices due to their unique photophysical properties. Surface chemistry modulation of nanotubes plays a critical role in determining stability and interaction with biological systems both in vitro and in vivo. Among the many parameters that influence the biological fate of nanomaterials, surface charge is particularly influential due to direct electrostatic interactions with components of the cell membrane as well as proteins in the serum, which coat the nanoparticle surface in a protein corona and alter nanoparticle-cell interactions. Here, we modulated functional moieties on a helical polycarbodiimide polymer backbone that non-covalently suspended the nanotubes in aqueous media. By derivatizing the polymer with either primary amine or carboxylic acid side chains, we obtained nanotube complexes that present net surface charges of opposite polarity at physiological pH. Using these materials, we found that the uptake of carbon nanotubes in these cells is highly dependent on charge, with cationic nanotubes efficiently internalized into cells compared to the anionic nanotubes. Furthermore, we found that serum proteins drastically influenced cell uptake of the anionic nanotubes, while the effect was not prominent for the cationic nanotubes. Our findings have implications for improved engineering of drug delivery devices, molecular probes, and biosensors.}, journal={J. Mater. Chem. B}, year={2017} }
 @article{helical polycarbodiimide cloaking of carbon nanotubes enables inter-nanotube exciton energy transfer modulation_2014, url={http://dx.doi.org/10.1021/ja505529n}, DOI={10.1021/ja505529n}, abstractNote={The use of single-walled carbon nanotubes (SWCNTs) as near-infrared optical probes and sensors require the ability to simultaneously modulate nanotube fluorescence and functionally derivatize the nanotube surface using noncovalent methods. We synthesized a small library of polycarbodiimides to noncovalently encapsulate SWCNTs with a diverse set of functional coatings, enabling their suspension in aqueous solution. These polymers, known to adopt helical conformations, exhibited ordered surface coverage on the nanotubes and allowed systematic modulation of nanotube optical properties, producing up to 12-fold differences in photoluminescence efficiency. Polymer cloaking of the fluorescent nanotubes facilitated the first instance of controllable and reversible internanotube exciton energy transfer, allowing kinetic measurements of dynamic self-assembly and disassembly.}, journal={Journal of the American Chemical Society}, year={2014}, month={Nov} }
 @article{budhathoki-uprety_reuther_novak_2012, title={Determining the Regioregularity in Alkyne Polycarbodiimides and Their Orthogonal Modification of Side Chains To Yield Perfectly Alternating Functional Polymers}, volume={45}, ISSN={["1520-5835"]}, url={http://dx.doi.org/10.1021/ma301639m}, DOI={10.1021/ma301639m}, abstractNote={To understand the structure–property relationship in functional macromolecules through side chain modulation, both the accurate determination of the position of modifiable groups along the polymer chain and their subsequent modifications using high fidelity methods are crucial. In this report, the polymer microstructure of a helical alkyne polycarbodiimide has directly been probed through 15N NMR spectroscopy on isotopic labeled poly(N-(3-ethynylphenyl)-15N′-hexyl)carbodiimide and found to be a highly regioregular polymer structure. This polymer undergoes facile and quantitative CuAAC “click” chemistry, yielding perfectly alternating functional polymers. Advances have been made through the synthesis of new optically active alkyne polycarbodiimides with two independently modifiable pendant groups per repeat unit of polymers. Orthogonal postmodifications of the pendant groups were then performed to incorporate two different sets of small molecules in the repeat unit of polymers in a controlled manner and un...}, number={20}, journal={MACROMOLECULES}, author={Budhathoki-Uprety, Januka and Reuther, James F. and Novak, Bruce M.}, year={2012}, month={Oct}, pages={8155–8165} }
 @article{budhathoki-uprety_peng_melander_novak_2012, title={Synthesis of Guanidinium Functionalized Polycarbodiimides and Their Antibacterial Activities}, volume={1}, ISSN={["2161-1653"]}, url={http://dx.doi.org/10.1021/mz200116k}, DOI={10.1021/mz200116k}, abstractNote={A family of guanidinium-side-chain functionalized polycarbodiimides has been synthesized by allowing an azido guanidinium salt to react with alkyne polycarbodiimides via the copper catalyzed [3 + 2] cycloaddition (Click) reaction. Poly-2(a-d) are cationic/amphiphilic polymers in which the global hydrophilic/hydrophobic balance has been tailored by local alteration of the length of alkyl side chain in the repeat unit of polymers prior to polymerization. The shorter alkyl chains yield water-soluble polymers, Poly-2c, -2d, and -2e. Antibacterial activities of these cationic polycarbodiimides have been investigated for Gram-positive and Gram-negative bacteria that include Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli, and Acinetobacter baumannii. It was observed that the influence of hydrophobic-hydrophilic balance per repeat unit of these polymers have profound effects for both antimicrobial and hemolytic activities. In addition, these polycarbodiimide-guanidinium-triazole conjugates offered moderate to significant antibacterial activity and rapid interaction with red blood cells causing blood precipitation without significant hemolysis in case of Poly-2(b-e). This latter property has the potential to be exploited in the polymer coatings or wound protection.}, number={3}, journal={ACS MACRO LETTERS}, author={Budhathoki-Uprety, Januka and Peng, LingLing and Melander, Christian and Novak, Bruce M.}, year={2012}, month={Mar}, pages={370–374} }
 @article{walker_budhathoki-uprety_novak_muddiman_2011, title={Stable-Isotope Labeled Hydrophobic Hydrazide Reagents for the Relative Quantification of N-Linked Glycans by Electrospray Ionization Mass Spectrometry}, volume={83}, ISSN={["1520-6882"]}, url={http://dx.doi.org/10.1021/ac201376q}, DOI={10.1021/ac201376q}, abstractNote={This study presents the development of stable-isotope labeled hydrophobic, hydrazide reagents for the relative quantification of N-linked glycans. The P2GPN "light" ((12)C) and "heavy" ((13)C(6)) pair are used to differentially label two N-linked glycan samples. The samples are combined 1:1, separated using HILIC, and then mass differentiated and quantified using mass spectrometry. These reagents have several benefits: (1) impart hydrophobic character to the glycans affording an increase in electrospray ionization efficiency and MS detection; (2) indistinguishable chromatographic, MS, and MS/MS performance of the "light" and "heavy" reagents affording relative quantification; and (3) analytical variability is significantly reduced due to the two samples being mixed together after sample preparation. Obtaining these analytical benefits only requires ~4 h of sample preparation time. It is shown that these reagents are capable of quantifying changes in glycosylation in simple mixtures, and the analytical variability of the reagents in pooled plasma samples is shown to be less than ±30%. Additionally, the incorporation of an internal standard allows one to account for the difference in systematic error between the two samples due to the samples being processed in parallel and not mixed until after derivatization.}, number={17}, journal={ANALYTICAL CHEMISTRY}, author={Walker, S. Hunter and Budhathoki-Uprety, Januka and Novak, Bruce M. and Muddiman, David C.}, year={2011}, month={Sep}, pages={6738–6745} }
 @article{budhathoki-uprety_novak_2011, title={Synthesis of Alkyne-Functionalized Helical Polycarbodiimides and their Ligation to Small Molecules using 'Click' and Sonogashira Reactions}, volume={44}, ISSN={["0024-9297"]}, url={http://dx.doi.org/10.1021/ma200960e}, DOI={10.1021/ma200960e}, abstractNote={New terminal alkyne side chain functionalized polycarbodiimides, have been synthesized and “alkyne” ligation tools—“click” (copper-catalyzed Huisgen 1,3-dipolar cycloaddition reaction) and Sonogashira couplings—were utilized to create functional polymers in one step postpolymerization modifications. Polycarbodiimides are interesting synthetic, helical, nanodimensional scaffolds that are capable of presenting a variety of functional groups in highly regular periodic fashion. Herein, we report the synthesis of the first alkyne substituted polycarbodiimides, Poly-1, Poly-2, and Poly-3 and the quantitative coupling of functional azides to the alkyne repeat units of these polymers, as evidenced by IR and 1H NMR and 13C NMR spectra. We are able to couple benzyl azide, carboxylic acid azide, and N-Boc amine azide by “click” and N-Boc-l-phenylalanine by Sonogashira reactions to the alkyne side chain of Poly 1 to provide Poly-1a, -1b, -1c and -1phe, respectively. Poly-1b and Poly-1c provide peptide-coupling sites ...}, number={15}, journal={MACROMOLECULES}, author={Budhathoki-Uprety, Januka and Novak, Bruce M.}, year={2011}, month={Aug}, pages={5947–5954} }
 @article{budhathoki-uprety_novak_2010, title={Synthesis of a pyridine substituted polycarbodiimide and its use as a solid support for chemical reagents}, volume={51}, ISSN={["1873-2291"]}, url={http://dx.doi.org/10.1016/j.polymer.2010.03.011}, DOI={10.1016/j.polymer.2010.03.011}, abstractNote={Abstract Optically active, polycarbodiimides 3(a, b & c) with pyridine pendant groups were synthesized using [(R) – 2,2′- binaphthoxy] (di-isopropoxy) titanium(IV) catalyst. The polymers were characterized by 1H and 13C NMR, and IR. Thermal stability of these polymers (up to 162 °C by TGA), allows thermally demanding chemical transformations on their side chains without decomposition. Advantages include fine-tunability of the other pendant group of the carbodiimide monomer. This allows one to optimize the properties of the polymer without undergoing copolymerization or further post-polymerization modifications. Borane (BH3) was coordinated to poly 3 (a & b) to prepare the functional polymers 4 (a & b) respectively. A strong IR signature peak at 2368 cm−1 supports BH3 coordination. Gravimetric analysis indicates 97–99% borane complexation of the pyridine units. In addition, the thermal stability increased to 194 °C in poly 4a is consistent with the incorporation of BH3 to the pendant pyridine of the helical polycarbodiimide 3a. Poly 4 (a & b) can be used as supported reagents and successfully reduced the carbonyl compounds (5 a–e) in moderate to excellent yields (60–100%) and are shown to be efficient, non-volatile, stable, and mild supported-reducing reagents. Upon completion of the reduction reaction, the polymer support was quantitatively recycled as required for a green solid catalyst support.}, number={10}, journal={POLYMER}, author={Budhathoki-Uprety, Januka and Novak, Bruce M.}, year={2010}, month={May}, pages={2140–2146} }