Optical Biosensor Platforms Display Varying Sensitivity for the Direct Detection of Influenza RNA.

Detection methods that do not require nucleic acid amplification are advantageous for viral diagnostics due to their rapid results. These platforms could provide information for both accurate diagnoses and pandemic surveillance. Influenza virus is prone to pandemic-inducing genetic mutations, so there is a need to apply these detection platforms to influenza diagnostics. Here, we analyzed the Fast Evaluation of Viral Emerging Risks (FEVER) pipeline on ultrasensitive detection platforms, including a waveguide-based optical biosensor and a flow cytometry bead-based assay. The pipeline was also evaluated in silico for sequence coverage in comparison to the U.S. Centers for Disease Control and Prevention's (CDC) influenza A and B diagnostic assays. The influenza FEVER probe design had a higher tolerance for mismatched bases than the CDC's probes, and the FEVER probes altogether had a higher detection rate for influenza isolate sequences from GenBank. When formatted for use as molecular beacons, the FEVER probes detected influenza RNA as low as 50 nM on the waveguide-based optical biosensor and 1 nM on the flow cytometer. In addition to molecular beacons, which have an inherently high background signal we also developed an exonuclease selection method that could detect 500 pM of RNA. The combination of high-coverage probes developed using the FEVER pipeline coupled with ultrasensitive optical biosensors is a promising approach for future influenza diagnostic and biosurveillance applications.

Interaction of amphiphilic lipoarabinomannan with host carrier lipoproteins in tuberculosis patients: Implications for blood-based diagnostics.

Lipoarabinomannan (LAM), an amphiphilic lipoglycan of the Mycobacterium tuberculosis cell wall, is a diagnostic target for tuberculosis. Previous work from our laboratory and others suggests that LAM is associated with host serum lipoproteins, which may in turn have implications for diagnostic assays. Our team has developed two serum assays for amphiphile detection: lipoprotein capture and membrane insertion. The lipoprotein capture assay relies on capture of the host lipoproteins, exploiting the biological association of host lipoprotein with microbial amphiphilic biomarkers to "concentrate" LAM. In contrast, the membrane insertion assay is independent of the association between pathogen amphiphiles and host lipoprotein association, and directly captures LAM based on its thermodynamic propensity for association with a supported lipid membrane, which forms the functional surface of an optical biosensor. In this manuscript, we explored the use of these assays for the detection of LAM in sera from adults whose tuberculosis status had been well-characterized using conventional microbiological tests, and endemic controls. Using the lipoprotein capture assay, LAM signal/noise ratios were >1.0 in 29/35 (83%) individuals with culture-confirmed active tuberculosis, 8/13 (62%) individuals with tuberculosis symptoms, but no positive culture for M. tuberculosis, and 0/6 (0%) symptom-free endemic controls. To evaluate serum LAM levels without bias associated with potential differences in circulating host lipoprotein concentrations between individuals, we subsequently processed available samples to liberate LAM from associated host lipoprotein assemblies followed by direct detection of the pathogen biomarker using the membrane insertion approach. Using the membrane insertion assay, signal/noise for detection of serum LAM was greater than that observed using the lipoprotein capture method for culture-confirmed TB patients (6/6), yet remained negative for controls (2/2). Taken together, these results suggest that detection of serum LAM is a promising TB diagnostic approach, but that further work is required to optimize assay performance and to decipher the implications of LAM/host lipoprotein associations for diagnostic assay performance and TB pathogenesis.

Comparative genomic and phenotypic characterization of invasive non-typhoidal Salmonella isolates from Siaya, Kenya.

Non-typhoidal Salmonella (NTS) is a major global health concern that often causes bloodstream infections in areas of the world affected by malnutrition and comorbidities such as HIV and malaria. Developing a strategy to control the emergence and spread of highly invasive and antimicrobial resistant NTS isolates requires a comprehensive analysis of epidemiological factors and molecular pathogenesis. Here, we characterize 11 NTS isolates that caused bloodstream infections in pediatric patients in Siaya, Kenya from 2003-2010. Nine isolates were identified as S. Typhimurium sequence type 313 while the other two were S. Enteritidis. Comprehensive genotypic and phenotypic analyses were performed to compare these isolates to those previously identified in sub-Saharan Africa. We identified a S. Typhimurium isolate referred to as UGA14 that displayed novel plasmid, pseudogene and resistance features as compared to other isolates reported from Africa. Notably, UGA14 is able to ferment both lactose and sucrose due to the acquisition of insertion elements on the pKST313 plasmid. These findings show for the first time the co-evolution of plasmid-mediated lactose and sucrose metabolism along with cephalosporin resistance in NTS further elucidating the evolutionary mechanisms of invasive NTS phenotypes. These results further support the use of combined genomic and phenotypic approaches to detect and characterize atypical NTS isolates in order to advance biosurveillance efforts that inform countermeasures aimed at controlling invasive and antimicrobial resistant NTS.

Pediatric Tuberculosis: The Impact of "Omics" on Diagnostics Development.

Tuberculosis (TB) is a major public health concern for all ages. However, the disease presents a larger challenge in pediatric populations, partially owing to the lack of reliable diagnostic standards for the early identification of infection. Currently, there are no biomarkers that have been clinically validated for use in pediatric TB diagnosis. Identification and validation of biomarkers could provide critical information on prognosis of disease, and response to treatment. In this review, we discuss how the "omics" approach has influenced biomarker discovery and the advancement of a next generation rapid point-of-care diagnostic for TB, with special emphasis on pediatric disease. Limitations of current published studies and the barriers to their implementation into the field will be thoroughly reviewed within this article in hopes of highlighting future avenues and needs for combating the problem of pediatric tuberculosis.

Stamped multilayer graphene laminates for disposable in-field electrodes: application to electrochemical sensing of hydrogen peroxide and glucose.

A multi-step approach is described for the fabrication of multi-layer graphene-based electrodes without the need for ink binders or post-print annealing. Graphite and nanoplatelet graphene were chemically exfoliated using a modified Hummers' method and the dried material was thermally expanded. Expanded materials were used in a 3D printed mold and stamp to create laminate electrodes on various substrates. The laminates were examined for potential sensing applications using model systems of peroxide (H2O2) and enzymatic glucose detection. Within the context of these two assay systems, platinum nanoparticle electrodeposition and oxygen plasma treatment were examined as methods for improving sensitivity. Electrodes made from both materials displayed excellent H2O2 sensing capability compared to screen-printed carbon electrodes. Laminates made from expanded graphite and treated with platinum, detected H2O2 at a working potential of 0.3 V (vs. Ag/AgCl [0.1 M KCl]) with a 1.91 µM detection limit and sensitivity of 64 nA·µM-1·cm-2. Electrodes made from platinum treated nanoplatelet graphene had a H2O2 detection limit of 1.98 µM (at 0.3 V), and a sensitivity of 16.5 nA·µM-1·cm-2. Both types of laminate electrodes were also tested as glucose sensors via immobilization of the enzyme glucose oxidase. The expanded nanographene material exhibited a wide analytical range for glucose (3.7 µM to 9.9 mM) and a detection limit of 1.2 µM. The sensing range of laminates made from expanded graphite was slightly reduced (9.8 µM to 9.9 mM) and the detection limit for glucose was higher (18.5 µM). When tested on flexible substrates, the expanded graphite laminates demonstrated excellent adhesion and durability during testing. These properties make the electrodes adaptable to a variety of tests for field-based or wearable sensing applications. Graphical abstract Expanded graphite (eGR) and expanded nanoplatelet graphene (nGN) were chemically exfoliated, thermally expanded, and manually stamped into flexible multi-layer graphene laminate electrodes. Hydrogen peroxide amperometric testing of eGR laminates compared to nGN laminates and a screen printed carbon (SPC) electrode.

Direct detection of bacteremia by exploiting host-pathogen interactions of lipoteichoic acid and lipopolysaccharide.

Bacteremia is a leading cause of death in sub-Saharan Africa where childhood mortality rates are the highest in the world. The early diagnosis of bacteremia and initiation of treatment saves lives, especially in high-disease burden areas. However, diagnosing bacteremia is challenging for clinicians, especially in children presenting with co-infections such as malaria and HIV. There is an urgent need for a rapid method for detecting bacteremia in pediatric patients with co-morbidities to inform treatment. In this manuscript, we have developed and clinically validated a novel method for the direct detection of amphiphilic pathogen biomarkers indicative of bacteremia, directly in aqueous blood, by mimicking innate immune recognition. Specifically, we have exploited the interaction of amphiphilic pathogen biomarkers such as lipopolysaccharides (LPS) from Gram-negative bacteria and lipoteichoic acids (LTA) from Gram-positive bacteria with host lipoprotein carriers in blood, in order to develop two tailored assays - lipoprotein capture and membrane insertion - for their direct detection. Our assays demonstrate a sensitivity of detection of 4 ng/mL for LPS and 2 ng/mL for LTA using a waveguide-based optical biosensor platform that was developed at LANL. In this manuscript, we also demonstrate the application of these methods for the detection of LPS in serum from pediatric patients with invasive Salmonella Typhimurium bacteremia (n = 7) and those with Staphylococcal bacteremia (n = 7) with 100% correlation with confirmatory culture. Taken together, these results demonstrate the significance of biochemistry in both our understanding of host-pathogen biology, and development of assay methodology, as well as demonstrate a potential new approach for the rapid, sensitive and accurate diagnosis of bacteremia at the point of need.

CIP2A immunosensor comprised of vertically-aligned carbon nanotube interdigitated electrodes towards point-of-care oral cancer screening.

Vertically aligned carbon nanotube array (VANTA) coatings have recently garnered significant attention due in part to their unique material properties including light absorption, chemical inertness, and electrical conductivity. Herein we report the first use of VANTAs grown via chemical vapor deposition in a 2D interdigitated electrode (IDE) footprint with a high height-to-width aspect ratio (3:1 or 75:25 µm). The VANTA-IDEs were functionalized with an antibody (Ab) specific to the human cancerous inhibitor PP2A (CIP2A)-an oncoprotein that is associated with a variety of malignancies such as oral, breast, and multiple myeloma cancers. The resultant label-free immunosensor was capable of detecting CIP2A across a wide linear sensing range (1-100 pg/mL) with a detection limit of 0.24 pg/mL within saliva supernatant-a range that is more sensitive than the corresponding CIP2A enzyme linked immunosorbent assay (ELISA). These results help pave the way for rapid cancer screening tests at the point-of-care (POC) such as for the early-stage diagnosis of oral cancer at a dentist's office.

Presentation matters: Impact of association of amphiphilic LPS with serum carrier proteins on innate immune signaling.

Recognition of Pathogen-associated Molecular Patterns (PAMPs) by Toll-like receptors is central to innate immunity. Many bacterial PAMPs such as lipopolysaccharide (LPS) and lipoteichoic acid have amphiphilic properties. The hydrophobicity of amphiphilic PAMPs contributes to increasing entropy and causes these molecules to self-aggregate or bind host carrier proteins in aqueous physiological environments. The goal of this work was to determine how innate immune signaling is impacted by physical presentation and association of amphiphilic PAMPs with serum carrier proteins, using LPS as an example molecule. Specifically, we measured LPS-induced cytokine profiles in murine macrophages when the antigen was presented associated with the various serum carrier proteins in serum versus a serum-depleted system. Our study demonstrates that the observed cytokine profiles are dramatically different when LPS is presented in buffer, versus in serum when it is associated with proteins, specifically with respect to inhibition of pro-inflammatory cytokines in the latter. These studies suggest that LPS-mediated cytokine expression is dependent on its presentation in physiological systems. The amphiphilicity of bacterial PAMPs and consequent association with lipoproteins is a feature, which should be taken into account in the design of in vitro experiments. Further studies of the interdependencies of different serum carriers can identify pathways for drug delivery and diagnostics.

Superhydrophobic inkjet printed flexible graphene circuits via direct-pulsed laser writing.

Solution-phase printing of exfoliated graphene flakes is emerging as a low-cost means to create flexible electronics for numerous applications. The electrical conductivity and electrochemical reactivity of printed graphene has been shown to improve with post-print processing methods such as thermal, photonic, and laser annealing. However, to date no reports have shown the manipulation of surface wettability via post-print processing of printed graphene. Herein, we demonstrate how the energy density of a direct-pulsed laser writing (DPLW) technique can be varied to tune the hydrophobicity and electrical conductivity of the inkjet-printed graphene (IPG). Experimental results demonstrate that the DPLW process can convert the IPG surface from one that is initially hydrophilic (contact angle ∼47.7°) and electrically resistive (sheet resistance ∼21 MΩ â–¡-1) to one that is superhydrophobic (CA ∼157.2°) and electrically conductive (sheet resistance ∼1.1 kΩ â–¡-1). Molecular dynamic (MD) simulations reveal that both the nanoscale graphene flake orientation and surface chemistry of the IPG after DPLW processing induce these changes in surface wettability. Moreover, DPLW can be performed with IPG printed on thermally and chemically sensitive substrates such as flexible paper and polymers. Hence, the developed, flexible IPG electrodes treated with DPLW could be useful for a wide range of applications such as self-cleaning, wearable, or washable electronics.

In Vivo Pulmonary Delivery and Magnetic-Targeting of Dry Powder Nano-in-Microparticles.

This brief communication evaluates the cytotoxicity and targeting capability of a dry powder chemotherapeutic. Nano-in-microparticles (NIMs) are a dry powder drug delivery vehicle containing superparamagnetic iron oxide nanoparticles (SPIONs) and either doxorubicin (w/w solids) or fluorescent nanospheres (w/v during formulation; as a drug surrogate) in a lactose matrix. In vitro cytotoxicity was evaluated in A549 adenocarcinoma cells using MTS and LDH assays to assess viability and toxicity after 48 h of NIMs exposure. In vivo magnetic-field-dependent targeting of inhaled NIMs was evaluated in a healthy mouse model. Mice were endotracheally administered fluorescently labeled NIMs either as a dry powder or a liquid aerosol in the presence of an external magnet placed over the left lung. Quantification of fluorescence and iron showed a significant increase in both fluorescence intensity and iron content to the left magnetized lung. In comparison, we observed decreased targeting of fluorescent nanospheres to the left lung from an aerosolized liquid suspension, due to the dissociation of SPIONs and nanoparticles during pulmonary administration. We conclude that dry powder NIMs maintain the therapeutic cytotoxicity of doxorubicin and can be better targeted to specific regions of the lung in the presence of a magnetic field, compared to a liquid suspension.

High-Resolution Graphene Films for Electrochemical Sensing via Inkjet Maskless Lithography.

Solution-phase printing of nanomaterial-based graphene inks are rapidly gaining interest for fabrication of flexible electronics. However, scalable manufacturing techniques for high-resolution printed graphene circuits are still lacking. Here, we report a patterning technique [i.e., inkjet maskless lithography (IML)] to form high-resolution, flexible, graphene films (line widths down to 20 µm) that significantly exceed the current inkjet printing resolution of graphene (line widths ∼60 µm). IML uses an inkjet printed polymer lacquer as a sacrificial pattern, viscous spin-coated graphene, and a subsequent graphene lift-off to pattern films without the need for prefabricated stencils, templates, or cleanroom technology (e.g., photolithography). Laser annealing is employed to increase conductivity on thermally sensitive, flexible substrates [polyethylene terephthalate (PET)]. Laser annealing and subsequent platinum nanoparticle deposition substantially increases the electroactive nature of graphene as illustrated by electrochemical hydrogen peroxide (H2O2) sensing [rapid response (5 s), broad linear sensing range (0.1-550 µm), high sensitivity (0.21 µM/µA), and low detection limit (0.21 µM)]. Moreover, high-resolution, complex graphene circuits [i.e., interdigitated electrodes (IDE) with varying finger width and spacing] were created with IML and characterized via potassium chloride (KCl) electrochemical impedance spectroscopy (EIS). Results indicated that sensitivity directly correlates to electrode feature size as the IDE with the smallest finger width and spacing (50 and 50 µm) displayed the largest response to changes in KCl concentration (∼21 kΩ). These results indicate that the developed IML patterning technique is well-suited for rapid, solution-phase graphene film prototyping on flexible substrates for numerous applications including electrochemical sensing.

Membrane Insertion for the Detection of Lipopolysaccharides: Exploring the Dynamics of Amphiphile-in-Lipid Assays.

Shiga toxin-producing Escherichia coli is an important cause of foodborne illness, with cases attributable to beef, fresh produce and other sources. Many serotypes of the pathogen cause disease, and differentiating one serotype from another requires specific identification of the O antigen located on the lipopolysaccharide (LPS) molecule. The amphiphilic structure of LPS poses a challenge when using classical detection methods, which do not take into account its lipoglycan biochemistry. Typically, detection of LPS requires heat or chemical treatment of samples and relies on bioactivity assays for the conserved lipid A portion of the molecule. Our goal was to develop assays to facilitate the direct and discriminative detection of the entire LPS molecule and its O antigen in complex matrices using minimal sample processing. To perform serogroup identification of LPS, we used a method called membrane insertion on a waveguide biosensor, and tested three serogroups of LPS. The membrane insertion technique allows for the hydrophobic association of LPS with a lipid bilayer, where the exposed O antigen can be targeted for specific detection. Samples of beef lysate were spiked with LPS to perform O antigen specific detection of LPS from E. coli O157. To validate assay performance, we evaluated the biophysical interactions of LPS with lipid bilayers both in- and outside of a flow cell using fluorescence microscopy and fluorescently doped lipids. Our results indicate that membrane insertion allows for the qualitative and reliable identification of amphiphilic LPS in complex samples like beef homogenates. We also demonstrated that LPS-induced hole formation does not occur under the conditions of the membrane insertion assays. Together, these findings describe for the first time the serogroup-specific detection of amphiphilic LPS in complex samples using a membrane insertion assay, and highlight the importance of LPS molecular conformations in detection architectures.

Purification and characterization of lipopolysaccharides from six strains of non-O157 Shiga toxin-producing Escherichia coli.

Certain Shiga toxin-producing Escherichia coli (STEC) are virulent human pathogens that are most often acquired through contaminated food. The United States Department of Agriculture, Food Safety and Inspection Service has declared several serogroups of STEC as adulterants in non-intact raw beef products. Hence, sensitive and specific tests for the detection of these STEC are a necessity for implementation in food safety programs. E. coli serogroups are identified by their respective O-antigen moiety on the lipopolysaccharide (LPS) macromolecule. We propose that the development of O-antigen-specific immunological assays can facilitate simple and rapid discriminatory detection of STEC in beef. However, the resources (antigens and antibodies) required for such development are not readily available. To overcome this, we extracted and characterized LPS and O-antigen from six STEC strains. Using hot phenol extraction, we isolated the LPS component from each strain and purified it using a series of steps to eliminate proteins, nucleic acids, and lipid A antigens. Antigens and crude LPS extracts were characterized using gel electrophoresis, immunoblotting, and modified Western blotting with commercially available antibodies, thus assessing the serogroup specificity and sensitivity of available ligands as well. The results indicate that, while many commercially available antibodies bind LPS, their activities and specificities are highly variable, and often not as specific as those required for serogroup discrimination. This variability could be minimized by the production of antibodies specific for the O-antigen. Additionally, the antigens generated from this study provide a source of characterized LPS and O-antigen standards for six serogroups of STEC.

Exploiting lipopolysaccharide-induced deformation of lipid bilayers to modify membrane composition and generate two-dimensional geometric membrane array patterns.

Supported lipid bilayers have proven effective as model membranes for investigating biophysical processes and in development of sensor and array technologies. The ability to modify lipid bilayers after their formation and in situ could greatly advance membrane technologies, but is difficult via current state-of-the-art technologies. Here we demonstrate a novel method that allows the controlled post-formation processing and modification of complex supported lipid bilayer arrangements, under aqueous conditions. We exploit the destabilization effect of lipopolysaccharide, an amphiphilic biomolecule, interacting with lipid bilayers to generate voids that can be backfilled to introduce desired membrane components. We further demonstrate that when used in combination with a single, traditional soft lithography process, it is possible to generate hierarchically-organized membrane domains and microscale 2-D array patterns of domains. Significantly, this technique can be used to repeatedly modify membranes allowing iterative control over membrane composition. This approach expands our toolkit for functional membrane design, with potential applications for enhanced materials templating, biosensing and investigating lipid-membrane processes.