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Item Lateral Flow-Based Skin Patch for Rapid Detection of Protein Biomarkers in Human Dermal Interstitial Fluid(American Chemical Society, 2024) Wilkirson, Elizabeth C.; Li, Danika; Lillehoj, Peter B.Rapid diagnostic tests (RDTs) offer valuable diagnostic information in a quick, easy-to-use and low-cost format. While RDTs are one of the most commonly used tools for in vitro diagnostic testing, they require the collection of a blood sample, which is painful, poses risks of infection and can lead to complications. We introduce a blood-free point-of-care diagnostic test for the rapid detection of protein biomarkers in dermal interstitial fluid (ISF). This device consists of a lateral flow immunochromatographic assay (LFIA) integrated within a microfluidic skin patch. ISF is collected from the skin using a microneedle array and vacuum-assisted extraction system integrated in the patch, and transported through the lateral flow strip via surface tension. Using this skin patch platform, we demonstrate in situ detection of anti-tetanus toxoid IgG and SARS-CoV-2 neutralizing antibodies, which could be accurately detected in human ISF in <20 min. We envision that this device can be readily modified to detect other protein biomarkers in dermal ISF, making it a promising tool for rapid diagnostic testing.Item Development and characterization of a low intensity vibrational system for microgravity studies(Springer Nature, 2024) Khan, Omor M.; Gasperini, Will; Necessary, Chess; Jacobs, Zach; Perry, Sam; Rexroat, Jason; Nelson, Kendall; Gamble, Paul; Clements, Twyman; DeLeon, Maximilien; Howard, Sean; Zavala, Anamaria; Farach-Carson, Mary; Blaber, Elizabeth; Wu, Danielle; Satici, Aykut; Uzer, GunesExtended-duration human spaceflight necessitates a better understanding of the physiological impacts of microgravity. While the ground-based microgravity simulations identified low intensity vibration (LIV) as a possible countermeasure, how cells may respond to LIV under real microgravity remain unexplored. In this way, adaptation of LIV bioreactors for space remains limited, resulting in a significant gap in microgravity research. In this study, we introduce an LIV bioreactor designed specifically for the usage in the International Space Station. Our research covers the bioreactor’s design process and evaluation of the short-term viability of cells encapsulated in hydrogel-laden 3D printed scaffolds under 0.7 g, 90 Hz LIV. An LIV bioreactor compatible with the operation requirements of space missions provides a robust platform to study cellular effects of LIV under real microgravity conditions.Item Exploration of the hierarchical assembly space of collagen-like peptides beyond the triple helix(Springer Nature, 2024) Yu, Le Tracy; Kreutzberger, Mark A. B.; Bui, Thi H.; Hancu, Maria C.; Farsheed, Adam C.; Egelman, Edward H.; Hartgerink, Jeffrey D.The de novo design of self-assembling peptides has garnered significant attention in scientific research. While alpha-helical assemblies have been extensively studied, exploration of polyproline type II helices, such as those found in collagen, remains relatively limited. In this study, we focus on understanding the sequence-structure relationship in hierarchical assemblies of collagen-like peptides, using defense collagen Surfactant Protein A as a model. By dissecting the sequence derived from Surfactant Protein A and synthesizing short collagen-like peptides, we successfully construct a discrete bundle of hollow triple helices. Amino acid substitution studies pinpoint hydrophobic and charged residues that are critical for oligomer formation. These insights guide the de novo design of collagen-like peptides, resulting in the formation of diverse quaternary structures, including discrete and heterogenous bundled oligomers, two-dimensional nanosheets, and pH-responsive nanoribbons. Our study represents a significant advancement in the understanding and harnessing of collagen higher-order assemblies beyond the triple helix.Item Electronic relaxation pathways in thio-acridone and thio-coumarin: two heavy-atom-free photosensitizers absorbing visible light(Royal Society of Chemistry, 2024) Acquah, Chris; Hoehn, Sean; Krul, Sarah; Jockusch, Steffen; Yang, Shudan; Seth, Sourav Kanti; Lee, Eric; Xiao, Han; Crespo-Hernández, Carlos E.; SynthX CenterHeavy-atom-free photosensitizers (HAF-PSs) have emerged as a new class of photosensitizers aiming to broaden their applicability and versatility across various fields of the photodynamic therapy of cancers. The strategy involves replacing the exocyclic oxygen atoms of the carbonyl groups of established biocompatible organic fluorophores with sulfur, thereby bathochromically shifting their absorption spectra and enhancing their intersystem crossing efficiencies. Despite these advancements, the photophysical attributes and electronic relaxation mechanisms of many of these HAF-PSs remain inadequately elucidated. In this study, we investigate the excited state dynamics and photochemical properties of two promising HAF-PSs, thio-coumarin and thio-acridone. Employing a combination of steady-state and time-resolved techniques from femtoseconds to microseconds, coupled with quantum chemical calculations, we unravel the electronic relaxation mechanisms that give rise to the efficient population of long-lived and reactive triplet states in these HAF-PSs.Item Directed evolution of an orthogonal transcription engine for programmable gene expression in eukaryotes(Elsevier, 2025) Kar, Shaunak; Gardner, Elizabeth C.; Javanmardi, Kamyab; Boutz, Daniel R.; Shroff, Raghav; Horton, Andrew P.; Segall-Shapiro, Thomas H.; Ellington, Andrew D.; Gollihar, JimmyT7 RNA polymerase (RNAP) has enabled orthogonal control of gene expression and recombinant protein production across diverse prokaryotic host chassis organisms for decades. However, the absence of 5′ methyl guanosine caps on T7 RNAP-derived transcripts has severely limited its utility and widespread adoption in eukaryotic systems. To address this shortcoming, we evolved a fusion enzyme combining T7 RNAP with the single subunit capping enzyme from African swine fever virus using Saccharomyces cerevisiae. We isolated highly active variants of this fusion enzyme, which exhibited roughly two orders of magnitude higher protein expression compared to the wild-type enzyme. We demonstrate the programmable control of gene expression using T7 RNAP-based genetic circuits in yeast and validate enhanced performance of these engineered variants in mammalian cells. This study presents a robust, orthogonal gene regulatory system applicable across diverse eukaryotic hosts, enhancing the versatility and efficiency of synthetic biology applications.Item Divergent Syntheses of Near-Infrared Light-Activated Molecular Jackhammers for Cancer Cell Eradication(Wiley, 2024) Li, Bowen; Ayala-Orozco, Ciceron; Si, Tengda; Zhou, Lixin; Wang, Zicheng; Martí, Angel A.; Tour, James M.; Smalley-Curl Institute;NanoCarbon Center;Rice Advanced Materials InstituteAminocyanines incorporating Cy7 and Cy7.5 moieties function as molecular jackhammers (MJH) through vibronic-driven action (VDA). This mechanism, which couples molecular vibrational and electronic modes, results in picosecond-scale concerted stretching of the entire molecule. When cell-associated and activated by near-infrared light, MJH mechanically disrupts cell membranes, causing rapid necrotic cell death. Unlike photodynamic and photothermal therapies, the ultrafast vibrational action of MJH is unhindered by high concentrations of reactive oxygen species scavengers and induces only a minimal temperature increase. Here, the efficient synthesis of a library of MJH is described using a practical approach to access a key intermediate and facilitating the preparation of various Cy7 and Cy7.5 MJH with diverse side chains in moderate to high yields. Photophysical characterization reveals that structural modifications significantly affect molar extinction coefficients and quantum yields while maintaining desirable absorption and emission wavelengths. The most promising compounds, featuring dimethylaminoethyl and dimethylcarbamoyl substitutions, demonstrate up to sevenfold improvement in phototherapeutic index compared to Cy7.5 amine across multiple cancer cell lines. This synthetic strategy provides a valuable platform for developing potent, light-activated therapeutic agents for cancer treatment, with potentially broad applicability across various cancer types.Item Transcriptional responses to direct and indirect TGFB1 stimulation in cancerous and noncancerous mammary epithelial cells(Springer Nature, 2024) Janus, Patryk; Kuś, Paweł; Jaksik, Roman; Vydra, Natalia; Toma-Jonik, Agnieszka; Gramatyka, Michalina; Kurpas, Monika; Kimmel, Marek; Widłak, WiesławaTransforming growth factor beta (TGFβ) is important for the morphogenesis and secretory function of the mammary gland. It is one of the main activators of the epithelial–mesenchymal transition (EMT), a process important for tissue remodeling and regeneration. It also provides cells with the plasticity to form metastases during tumor progression. Noncancerous and cancer cells respond differently to TGFβ. However, knowledge of the cellular signaling cascades triggered by TGFβ in various cell types is still limited.Item Persistent tailoring of MSC activation through genetic priming(Elsevier, 2024) Beauregard, Michael A.; Bedford, Guy C.; Brenner, Daniel A.; Sanchez Solis, Leonardo D.; Nishiguchi, Tomoki; Abhimanyu; Longlax, Santiago Carrero; Mahata, Barun; Veiseh, Omid; Wenzel, Pamela L.; DiNardo, Andrew R.; Hilton, Isaac B.; Diehl, Michael R.Mesenchymal stem/stromal cells (MSCs) are an attractive platform for cell therapy due to their safety profile and unique ability to secrete broad arrays of immunomodulatory and regenerative molecules. Yet, MSCs are well known to require preconditioning or priming to boost their therapeutic efficacy. Current priming methods offer limited control over MSC activation, yield transient effects, and often induce the expression of pro-inflammatory effectors that can potentiate immunogenicity. Here, we describe a genetic priming method that can both selectively and sustainably boost MSC potency via the controlled expression of the inflammatory-stimulus-responsive transcription factor interferon response factor 1 (IRF1). MSCs engineered to hyper-express IRF1 recapitulate many core responses that are accessed by biochemical priming using the proinflammatory cytokine interferon-γ (IFN-γ). This includes the upregulation of anti-inflammatory effector molecules and the potentiation of MSC capacities to suppress T cell activation. However, we show that IRF1-mediated genetic priming is much more persistent than biochemical priming and can circumvent IFN-γ-dependent expression of immunogenic MHC class II molecules. Together, the ability to sustainably activate and selectively tailor MSC priming responses creates the possibility of programming MSC activation more comprehensively for therapeutic applications.Item Two photon imaging probe with highly efficient autofluorescence collection at high scattering and deep imaging conditions(Optica Publishing Group, 2024) Camli, Berk; Andrus, Liam; Roy, Aditya; Mishra, Biswajit; Xu, Chris; Georgakoudi, Irene; Tkaczyk, Tomasz; Ben-Yakar, AdelaIn this paper, we present a 2-photon imaging probe system featuring a novel fluorescence collection method with improved and reliable efficiency. The system aims to miniaturize the potential of 2-photon imaging in the metabolic and morphological characterization of cervical tissue at sub-micron resolution over large imaging depths into a flexible and clinically viable platform towards the early detection of cancers. Clinical implementation of such a probe system is challenging due to inherently low levels of autofluorescence, particularly when imaging deep in highly scattering tissues. For an efficient collection of fluorescence signals, our probe employs 12 0.5 NA collection fibers arranged around a miniaturized excitation objective. By bending and terminating a multitude of collection fibers at a specific angle, we increase collection area and directivity significantly. Positioning of these fibers allows the collection of fluorescence photons scattered away from their ballistic trajectory multiple times, which offers a system collection efficiency of 4%, which is 55% of what our bench-top microscope with 0.75 NA objective achieves. We demonstrate that the collection efficiency is largely maintained even at high scattering conditions and high imaging depths. Radial symmetry of arrangement maintains uniformity of collection efficiency across the whole FOV. Additionally, our probe can image at different tissue depths via axial actuation by a dc servo motor, allowing depth dependent tissue characterization. We designed our probe to perform imaging at 775 nm, targeting 2-photon autofluorescence from NAD(P)H and FAD molecules, which are often used in metabolic tissue characterization. An air core photonic bandgap fiber delivers laser pulses of 100 fs duration to the sample. A miniaturized objective designed with commercially available lenses of 3 mm diameter focuses the laser beam on tissue, attaining lateral and axial imaging resolutions of 0.66 µm and 4.65 µm, respectively. Characterization results verify that our probe achieves collection efficiency comparable to our optimized bench-top 2-photon imaging microscope, minimally affected by imaging depth and radial positioning. We validate autofluorescence imaging capability with excised porcine vocal fold tissue samples. Images with 120 µm FOV and 0.33 µm pixel sizes collected at 2 fps confirm that the 300 µm imaging depth was achieved.Item Use of topical methylene blue to image nuclear morphometry with a low-cost scanning darkfield microendoscope(SPIE, 2024) Hou, Huayu; Carns, Jennifer; Schwarz, Richard A.; Gillenwater, Ann M.; Anandasabapathy, Sharmila; Richards-Kortum, Rebecca R.SignificanceFiber-optic microendoscopy is a promising approach to noninvasively visualize epithelial nuclear morphometry for early cancer and precancer detection. However, the broader clinical application of this approach is limited by a lack of topical contrast agents available for in vivo use.AimThe aim of this study was to evaluate the ability to image nuclear morphometry in vivo with a novel fiber-optic microendoscope used together with topical application of methylene blue (MB), a dye with FDA approval for use in chromoendoscopy in the gastrointestinal tract.ApproachThe low-cost, high-resolution microendoscope implements scanning darkfield imaging without complex optomechanical components by leveraging programmable illumination and the rolling shutter of the image sensor. We validate the integration of our system and MB staining for visualizing epithelial cell nuclei by performing ex vivo imaging on fresh animal specimens and in vivo imaging on healthy volunteers.ResultsThe results indicate that scanning darkfield imaging significantly reduces specular reflection and resolves epithelial nuclei with enhanced image contrast and spatial resolution compared to non-scanning widefield imaging. The image quality of darkfield images with MB staining is comparable to that of fluorescence images with proflavine staining.ConclusionsOur approach enables real-time microscopic evaluation of nuclear patterns and has the potential to be a powerful noninvasive tool for early cancer detection.Item Phototaxis is a satiety-dependent behavioral sequence in Hydra vulgaris(The Company of Biologists, 2024) Kim, Soonyoung; Badhiwala, Krishna N.; Duret, Guillaume; Robinson, Jacob T.Understanding how internal states such as satiety are connected to animal behavior is a fundamental question in neuroscience. Hydra vulgaris, a freshwater cnidarian with only 12 neuronal cell types, serves as a tractable model system for studying state-dependent behaviors. We found that starved hydras consistently move towards light, while fed hydras do not. By modeling this behavior as a set of three sequences of head orientation, jump distance and jump rate, we demonstrate that the satiety state only affects the rate of the animal jumping to a new position, while the orientation and jump distance are unaffected. These findings yield insights into how internal states in a simple organism, Hydra, affect specific elements of a behavior, and offer general principles for studying the relationship between state-dependent behaviors and their underlying molecular mechanisms.Item Magnetoelectrics for Implantable Bioelectronics: Progress to Date(American Chemical Society, 2024) Alrashdan, Fatima; Yang, Kaiyuan; Robinson, Jacob T.; Applied Physics ProgramConspectusThe coupling of magnetic and electric properties manifested in magnetoelectric (ME) materials has unlocked numerous possibilities for advancing technologies like energy harvesting, memory devices, and medical technologies. Due to this unique coupling, the magnetic properties of these materials can be tuned by an electric field; conversely, their electric polarization can be manipulated through a magnetic field.Over the past seven years, our lab work has focused on leveraging these materials to engineer implantable bioelectronics for various neuromodulation applications. One of the main challenges for bioelectronics is to design miniaturized solutions that can be delivered with minimally invasive procedures and yet can receive sufficient power to directly stimulate tissue or power electronics to perform functions like communication and sensing.Magnetoelectric coupling in ME materials is strongest when the driving field matches a mechanical resonant mode. However, miniaturized ME transducers typically have resonance frequencies >100 kHz, which is too high for direct neuromodulation as neurons only respond to low frequencies (typically <1 kHz). We discuss two approaches that have been proposed to overcome this frequency mismatch: operating off-resonance and rectification. The off-resonance approach is most common for magnetoelectric nanoparticles (MENPs) that typically have resonance frequencies in the gigahertz range. In vivo experiments on rat models have shown that MENPs could induce changes in neural activity upon excitation with <200 Hz magnetic fields. However, the neural response has latencies of several seconds due to the weak coupling in the off-resonance regime.To stimulate neural responses with millisecond precision, we developed methods to rectify the ME response so that we could drive the materials at their resonant frequency but still produce the slowly varying voltages needed for direct neural stimulation. The first version of the stimulator combined a ME transducer and analog electronics for rectification. To create even smaller solutions, we introduced the first magnetoelectric metamaterial (MNM) that exhibits self-rectification. Both designs have effectively induced neural modulation in rat models with less than 5 ms latency.Based on our experience with in vivo testing of the rectified ME stimulators, we found it challenging to deliver the precisely controlled therapy required for clinical applications, given the ME transducer’s sensitivity to the external transmitter alignment. To overcome this challenge, we developed the ME-BIT (MagnetoElectric BioImplanT), a digitally programmable stimulator that receives wireless power and data through the ME link.We further expanded the utility of this technology to neuromodulation applications that require high stimulation thresholds by introducing the DOT (Digitally programmable Overbrain Therapeutic). The DOT has voltage compliance up to 14.5 V. We have demonstrated the efficacy of these designs through various in vivo studies for applications like peripheral nerve stimulation and epidural cortical stimulation.To further improve these systems to be adaptive and enable a network of coordinated devices, we developed a bidirectional communication system to transmit data to and from the implant. To enable even greater miniaturization, we developed a way to use the same ME transducer for wireless power and data communication by developing the first ME backscatter communication protocol.Item Superhydrophobic Array Devices for the Enhanced Formation of 3D Cancer Models(American Chemical Society, 2024) Lopez-Cavestany, Maria; Wright, Olivia A.; Reckhorn, Noah T.; Carter, Alexandria T.; Jayawardana, Kalana; Nguyen, Tin; Briggs, Dayrl P.; Koktysh, Dmitry S.; Esteban Linares, Alberto; Li, Deyu; King, Michael R.During the metastatic cascade, cancer cells travel through the bloodstream as circulating tumor cells (CTCs) to a secondary site. Clustered CTCs have greater shear stress and treatment resistance, yet their biology remains poorly understood. We therefore engineered a tunable superhydrophobic array device (SHArD). The SHArD-C was applied to culture a clinically relevant model of CTC clusters. Using our device, we cultured a model of cancer cell aggregates of various sizes with immortalized cancer cell lines. These exhibited higher E-cadherin expression and are significantly more capable of surviving high fluid shear stress-related forces compared to single cells and model clusters grown using the control method, helping to explain why clustering may provide a metastatic advantage. Additionally, the SHArD-S, when compared with the AggreWell 800 method, provides a more consistent spheroid-forming device culturing reproducible sizes of spheroids for multiple cancer cell lines. Overall, we designed, fabricated, and validated an easily tunable engineered device which grows physiologically relevant three-dimensional (3D) cancer models containing tens to thousands of cells.Item High throughput and rapid isolation of extracellular vesicles and exosomes with purity using size exclusion liquid chromatography(Elsevier, 2024) Kapoor, Kshipra S.; Harris, Kristen; Arian, Kent A.; Ma, Lihua; Schueng Zancanela, Beatriz; Church, Kaira A.; McAndrews, Kathleen M.; Kalluri, RaghuExtracellular vesicles (EVs) have emerged as potential biomarkers for diagnosing a range of diseases without invasive procedures. Extracellular vesicles also offer advantages compared to synthetic vesicles for delivery of various drugs; however, limitations in segregating EVs from other particles and soluble proteins have led to inconsistent EV retrieval rates with low levels of purity. Here, we report a new high-yield (88.47 %) and rapid (<20 min) EV isolation method termed size exclusion – fast protein liquid chromatography (SE-FPLC). We show SE-FPLC can effectively isolate EVs from multiple sources including EVs derived from human and mouse cells and serum samples. The results indicate that SE-FPLC can successfully remove highly abundant protein contaminants such as albumin and lipoprotein complexes, which can represent a major hurdle in large scale isolation of EVs. The high-yield nature of SE-FPLC allows for easy industrial scaling up of EV production for various clinical utilities. SE-FPLC also enables analysis of small volumes of blood for use in point-of-care diagnostics in the clinic. Collectively, SE-FPLC offers many advantages over current EV isolation methods and offers rapid clinical translation.Item Breakdown of Boltzmann-type models for the alignment of self-propelled rods(Elsevier, 2024) Murphy, Patrick; Perepelitsa, Misha; Timofeyev, Ilya; Lieber-Kotz, Matan; Islas, Brandon; Igoshin, Oleg A.; Center for Theoretical Biological PhysicsStudies in the collective motility of organisms use a range of analytical approaches to formulate continuous kinetic models of collective dynamics from rules or equations describing agent interactions. However, the derivation of these kinetic models often relies on Boltzmann’s “molecular chaos” hypothesis, which assumes that correlations between individuals are short-lived. While this assumption is often the simplest way to derive tractable models, it is often not valid in practice due to the high levels of cooperation and self-organization present in biological systems. In this work, we illustrated this point by considering a general Boltzmann-type kinetic model for the alignment of self-propelled rods where rod reorientation occurs upon binary collisions. We examine the accuracy of the kinetic model by comparing numerical solutions of the continuous equations to an agent-based model that implements the underlying rules governing microscopic alignment. Even for the simplest case considered, our comparison demonstrates that the kinetic model fails to replicate the discrete dynamics due to the formation of rod clusters that violate statistical independence. Additionally, we show that introducing noise to limit cluster formation helps improve the agreement between the analytical model and agent simulations but does not restore the agreement completely. These results highlight the need to both develop and disseminate improved moment-closure methods for modeling biological and active matter systems.Item Acoustically targeted measurement of transgene expression in the brain(AAAS, 2024) Seo, Joon Pyung; Trippett, James S.; Huang, Zhimin; Lee, Sangsin; Nouraein, Shirin; Wang, Ryan Z.; Szablowski, Jerzy O.; Applied Physics Program;Systems, Synthetic, and Physical Biology Program;Rice Neuroengineering InitiativeGene expression is a critical component of brain physiology, but monitoring this expression in the living brain represents a major challenge. Here, we introduce a new paradigm called recovery of markers through insonation (REMIS) for noninvasive measurement of gene expression in the brain with cell type, spatial, and temporal specificity. Our approach relies on engineered protein markers that are produced in neurons but exit into the brain’s interstitium. When ultrasound is applied to targeted brain regions, it opens the blood-brain barrier and releases these markers into the bloodstream. Once in blood, the markers can be readily detected using biochemical techniques. REMIS can noninvasively confirm gene delivery and measure endogenous signaling in specific brain sites through a simple insonation and a subsequent blood test. REMIS is reliable and demonstrated consistent improvement in recovery of markers from the brain into the blood. Overall, this work establishes a noninvasive, spatially specific method of monitoring gene delivery and endogenous signaling in the brain.Item Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens(Springer Nature, 2024) Wang, Michael X.; Lou, Esther G.; Sapoval, Nicolae; Kim, Eddie; Kalvapalle, Prashant; Kille, Bryce; Elworth, R. A. Leo; Liu, Yunxi; Fu, Yilei; Stadler, Lauren B.; Treangen, Todd J.Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 15 million complete SARS-CoV-2 genomes are now publicly available, most sequenced and assembled via tiled amplicon sequencing. While computational tools for tiled amplicon design exist, they require downstream manual optimization both computationally and experimentally, which is slow and costly. Here we present Olivar, a first step towards a fully automated, variant-aware design of tiled amplicons for pathogen genomes. Olivar converts each nucleotide of the target genome into a numeric risk score, capturing undesired sequence features that should be avoided. In a direct comparison with PrimalScheme, we show that Olivar has fewer mismatches overlapping with primers and predicted PCR byproducts. We also compare Olivar head-to-head with ARTIC v4.1, the most widely used primer set for SARS-CoV-2 sequencing, and show Olivar yields similar read mapping rates (~90%) and better coverage to the manually designed ARTIC v4.1 amplicons. We also evaluate Olivar on real wastewater samples and found that Olivar has up to 3-fold higher mapping rates while retaining similar coverage. In summary, Olivar automates and accelerates the generation of tiled amplicons, even in situations of high mutation frequency and/or density. Olivar is available online as a web application at https://olivar.rice.edu and can be installed locally as a command line tool with Bioconda. Source code, installation guide, and usage are available at https://github.com/treangenlab/Olivar.Item MethPhaser: methylation-based long-read haplotype phasing of human genomes(Springer Nature, 2024) Fu, Yilei; Aganezov, Sergey; Mahmoud, Medhat; Beaulaurier, John; Juul, Sissel; Treangen, Todd J.; Sedlazeck, Fritz J.The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease. However, phasing is limited by read length and stretches of homozygosity along the genome. To overcome this limitation, we designed MethPhaser, a method that utilizes methylation signals from Oxford Nanopore Technologies to extend Single Nucleotide Variation (SNV)-based phasing. We demonstrate that haplotype-specific methylations extensively exist in Human genomes and the advent of long-read technologies enabled direct report of methylation signals. For ONT R9 and R10 cell line data, we increase the phase length N50 by 78%-151% at a phasing accuracy of 83.4-98.7% To assess the impact of tissue purity and random methylation signals due to inactivation, we also applied MethPhaser on blood samples from 4 patients, still showing improvements over SNV-only phasing. MethPhaser further improves phasing across HLA and multiple other medically relevant genes, improving our understanding of how mutations interact across multiple phenotypes. The concept of MethPhaser can also be extended to non-human diploid genomes. MethPhaser is available at https://github.com/treangenlab/methphaser.Item Microneedle-based sampling of dermal interstitial fluid using a vacuum-assisted skin patch(Elsevier, 2024) Jiang, Xue; Wilkirson, Elizabeth C.; Bailey, Aaron O.; Russell, William K.; Lillehoj, Peter B.Interstitial fluid (ISF) contains a wealth of biomolecules, yet it is underutilized for diagnostic testing due to a lack of rapid and simple techniques for collecting abundant amounts of fluid. Here, we report a simple and minimally invasive technique for rapidly sampling larger quantities of ISF from human skin. A microneedle array is used to generate micropores in skin from which ISF is extracted using a vacuum-assisted skin patch. Using this technique, an average of 20.8 μL of dermal ISF is collected in 25 min, which is an ∼6-fold improvement over existing sampling methods. Proteomic analysis of collected ISF reveals that it has nearly identical protein composition as blood, and >600 medically relevant biomarkers are identified. Toward this end, we demonstrate the detection of SARS-CoV-2 neutralizing antibodies in ISF collected from COVID-19 vaccinees using two commercial immunoassays, showcasing the utility of this technique for diagnostic testing.Item Microscale measurements of protein complexes from single cells(Elsevier, 2024) Dutta, Tanushree; Vlassakis, JuleaProteins execute numerous cell functions in concert with one another in protein–protein interactions (PPI). While essential in each cell, such interactions are not identical from cell to cell. Instead, PPI heterogeneity contributes to cellular phenotypic heterogeneity in health and diseases such as cancer. Understanding cellular phenotypic heterogeneity thus requires measurements of properties of PPIs such as abundance, stoichiometry, and kinetics at the single-cell level. Here, we review recent, exciting progress in single-cell PPI measurements. Novel technology in this area is enabled by microscale and microfluidic approaches that control analyte concentration in timescales needed to outpace PPI disassembly kinetics. We describe microscale innovations, needed technical capabilities, and methods poised to be adapted for single-cell analysis in the near future.