This report summarizes a virtual workshop on early lessons from the COVID-19 pandemic as they pertain to proactively addressing future biological threats. Co-hosted by Sandia National Laboratory (Sandia) and the Council on Strategic Risks (CSR) in August 2020, the discussion involved experts who at that time were leading innovative efforts in various U.S. government agencies, industry, and academia sharing observations from their ongoing pandemic response efforts. Based on the input by these expert participants, it is clear that even though the pandemic response is ongoing, the following recommendations will be important to consider for more successfully addressing biological threats in the future: Continue building on the cross-sector collaboration and agility shown in the COVID-19 response; Expand capabilities for detecting biological threats early; Prioritize ways to create and disseminate medical countermeasures even faster; Create the U.S. bio industrial base needed for rapid response to biological threats, and keep it healthy; and, Major government reorganization may not be needed if there is effective work to form coalitions, improve coordination, and expand steady-state and surge capacities.
This report is based on discussions held during an unclassified workshop hosted by Sandia National Laboratories (SNL) and the Council on Strategic Risks (CSR) on August 29, 2019. The first in a planned series, this workshop brought together experts from government, national laboratories, academia, industry, and the policy and entrepreneur communities to examine the potential to use strategy, technology advances, policy, and other tools to make bioweapons obsolete. The workshop provided participants with a rare opportunity to step back from their day-to-day jobs and think strategically about how to achieve this goal more effectively and rapidly. The conversation was held under the Chatham House Rule. The objective was to generate and share ideas and identify questions that will be critical to answer in pursuit of making bioweapons obsolete. Its purpose was not to create consensus. This report does not represent consensus among participants, nor does it assign specific perspectives to any individual participant or represent the official views of any United States (U.S.) government agency or the organizing institutions namely, SNL and CSR.
The challenges of diagnosing infectious disease, especially in the developing world, and the shortcomings of available instrumentation have exposed the need for portable, easy-to-use diagnostic tools capable of detecting the wide range of causative microbes while operating in low resource settings. We present a centrifugal microfluidic platform that combines ultrasensitive immunoassay and isothermal amplification-based screening for the orthogonal detection of both protein and nucleic acid targets at the point-of-care. A disposable disc with automatic aliquoting inlets is paired with a non-contact heating system and precise rotary control system to yield an easy-to-use, field-deployable platform with versatile screening capabilities. The detection of three enterotoxins (cholera toxin, Staphylococcal enterotoxin B, and Shiga-like toxin 1) and three enteric bacteria (C. jejuni, E. coli, and S. typhimurium) were performed independently and shown to be highly sensitive (limit of detection = 1.35–5.50 ng/mL for immunoassays and 1–30 cells for isothermal amplification), highly exclusive in the presence of non-specific targets, and capable of handling a complex sample matrix like stool. The full panel of toxins and bacteria were reliably detected simultaneously on a single disc at clinically relevant sample concentrations in less than an hour. The ability of our technology to detect multiple analyte types in parallel at the point-of-care can serve a variety of needs, from routine patient care to outbreak triage, in a variety of settings to reduce disease impact and expedite effective treatment.
Harmon, Brooke N.; Chylek, Lily A.; Liu, Yanli; Mitra, Eshan D.; Mahajan, Avanika; Saada, Edwin A.; Schudel, Benjamin R.; Holowka, David A.; Baird, Barbara A.; Wilson, Bridget S.; Hlavacek, William S.; Singh, Anup K.
The high-Affinity receptor for IgE expressed on the surface of mast cells and basophils interacts with antigens, via bound IgE antibody, and triggers secretion of inflammatory mediators that contribute to allergic reactions. To understand how past inputs (memory) influence future inflammatory responses in mast cells, a microfluidic device was used to precisely control exposure of cells to alternating stimulatory and non-stimulatory inputs. We determined that the response to subsequent stimulation depends on the interval of signaling quiescence. For shorter intervals of signaling quiescence, the second response is blunted relative to the first response, whereas longer intervals of quiescence induce an enhanced second response. Through an iterative process of computational modeling and experimental tests, we found that these memory-like phenomena arise from a confluence of rapid, short-lived positive signals driven by the protein tyrosine kinase Syk; slow, long-lived negative signals driven by the lipid phosphatase Ship1; and slower degradation of Ship1 co-factors. This work advances our understanding of mast cell signaling and represents a generalizable approach for investigating the dynamics of signaling systems.
Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility. Liquid handling robotics may reduce labor and improve reproducibility, but are themselves expensive and thus inaccessible to most researchers. Microfluidic platforms offer a lower entry price point alternative to robotics, and maintain high throughput and reproducibility while further reducing operating costs through diminished reagent volume requirements. Droplet microfluidics have shown exceptional promise for synthetic biology experiments, including DNA assembly, transformation/transfection, culturing, cell sorting, phenotypic assays, artificial cells and genetic circuits.
Infection with Mycobacterium Tuberculosis represents a significant threat to people with immune disorders, such as HIV-positive individuals, and can result in significant health complications or death if not diagnosed and treated early. We present a centrifugal microfluidic platform for multiplexed detection of tuberculosis and HIV biomarkers in human whole blood with minimal sample preparation and a sample-to-answer time of 30 minutes. This multiplexed assay was developed for the detection of two M.tuberculosis secreted proteins, whose secretion represents an active and ongoing infection, as well as detection of HIV p24 protein and human anti-p24 antibodies. The limit of detection for this multiplex assay is in the pg/mL range for both HIV and M.tuberculosis proteins, making this assay potentially useful in the clinical diagnosis of both HIV and Tuberculosis proteins indicative of active infection. Antigen detection for the HIV assay sensitivity was 89%, the specificity 85%. Serological detection had 100% sensitivity and specificity for the limited sample pool. The centrifugal microfluidic platform presented here offers the potential for a portable, fast and inexpensive multiplexed diagnostic device that can be used in resource-limited settings for diagnosis of TB and HIV.
Multiple displacement amplification (MDA) is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples) before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA) technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet), ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli) compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.
Waterborne pathogens pose significant threat to the global population and early detection plays an important role both in making drinking water safe, as well as in diagnostics and treatment of water-borne diseases. We present an innovative centrifugal sedimentation immunoassay platform for detection of bacterial pathogens in water. Our approach is based on binding of pathogens to antibody-functionalized capture particles followed by sedimentation of the particles through a density-media in a microfluidic disk. Beads at the distal end of the disk are imaged to quantify the fluorescence and determine the bacterial concentration. Our platform is fast (20 min), can detect as few as ~10 bacteria with minimal sample preparation, and can detect multiple pathogens simultaneously. The platform was used to detect a panel of enteric bacteria (Escherichia coli, Salmonella typhimurium, Shigella, Listeria, and Campylobacter) spiked in tap and ground water samples.
Enteric and diarrheal diseases are a major cause of childhood illness and death in countries with developing economies. Each year, more than half of a million children under the age of five die from these diseases. We have developed a portable, microfluidic platform capable of simultaneous, multiplexed detection of several of the bacterial pathogens that cause these diseases. This platform can perform fast, sensitive immunoassays directly from relevant, complex clinical matrices such as stool without extensive sample cleanup or preparation. Using only 1 μL of sample per assay, we demonstrate simultaneous multiplexed detection of four bacterial pathogens implicated in diarrheal and enteric diseases in less than 20 min.
Koh, Chung-Yan K.; Schaff, Ulrich Y.; Piccini, Matthew E.; Stanker, Larry H.; Cheng, Luisa W.; Ravichandran, Easwaran; Singh, Bal R.; Sommer, Greg J.; Singh, Anup K.
We present an innovative centrifugal microfluidic immunoassay platform (SpinDx) to address the urgent biodefense and public health need for ultrasensitive point-of-care/incident detection of botulinum toxin. The simple, sample-to-answer centrifugal microfluidic immunoassay approach is based on binding of toxins to antibody-laden capture particles followed by sedimentation of the particles through a density-media in a microfluidic disk and quantification by laser-induced fluorescence. A blind, head-to-head comparison study of SpinDx versus the gold-standard mouse bioassay demonstrates 100-fold improvement in sensitivity (limit of detection = 0.09 pg/mL), while achieving total sample-to-answer time of <30 min with 2-∼L required volume of the unprocessed sample. We further demonstrate quantification of botulinum toxin in both exogeneous (human blood and serum spiked with toxins) and endogeneous (serum from mice intoxicated via oral, intranasal, and intravenous routes) samples. SpinDx can analyze, without any sample preparation, multiple sample types including whole blood, serum, and food. It is readily expandable to additional analytes as the assay reagents (i.e., the capture beads and detection antibodies) are disconnected from the disk architecture and the reader, facilitating rapid development of new assays. SpinDx can also serve as a general-purpose immunoassay platform applicable to diagnosis of other conditions and diseases.
Sandia journal manuscript; Not yet accepted for publication
Koh, Chung-Yan K.; Piccini, Matthew E.; Schaff, Ulrich Y.; Stanker, Larry H.; Cheng, Luisa W.; Ravichandran, Easwaran; Singh, Bal-Ram; Sommer, Greg J.; Singh, Anup K.
Multiple cases of attempted bioterrorism events using biotoxins have highlighted the urgent need for tools capable of rapid screening of suspect samples in the field (e.g., mailroom and public events). We present a portable microfluidic device capable of analyzing environmental (e.g., white powder), food (e.g., milk) and clinical (e.g., blood) samples for multiplexed detection of biotoxins. The device is rapid (<15-30 min sample-to-answer), sensitive (< 0.08 pg/mL detection limit for botulinum toxin), multiplexed (up to 64 parallel assays) and capable of analyzing small volume samples (< 20 μL total sample input). The immunoassay approach (SpinDx) is based on binding of toxins in a sample to antibody-laden capture particles followed by sedimentation of particles through a density-media in a microfluidic disk and quantification using a laser-induced fluorescence detector. A direct, blinded comparison with a gold standard ELISA revealed a 5-fold more sensitive detection limit for botulinum toxin while requiring 250-fold less sample volume and a 30 minute assay time with a near unity correlation. A key advantage of the technique is its compatibility with a variety of sample matrices with no additional sample preparation required. Ultrasensitive quantification has been demonstrated from direct analysis of multiple clinical, environmental and food samples, including white powder, whole blood, saliva, salad dressing, whole milk, peanut butter, half and half, honey, and canned meat. We believe that this device can met an urgent need in screening both potentially exposed people as well as suspicious samples in mail-rooms, airports, public sporting venues and emergency rooms. The general-purpose immunodiagnostics device can also find applications in screening of infectious and systemic diseases or serve as a lab device for conducting rapid immunoassays.
Cell signaling is a dynamic and complex process. A typical signaling pathway may begin with activation of cell surface receptors, leading to activation of a kinase cascade that culminates in induction of messenger RNA (mRNA) and noncoding microRNA (miRNA) production in the nucleus, followed by modulation of mRNA expression by miRNAs in the cytosol, and end with production of proteins in response to the signaling pathway. Signaling pathways involve proteins, miRNA, and mRNAs, along with various forms of transient posttranslational modifications, and detecting each type of signaling molecule requires categorically different sample preparation methods such as Western blotting for proteins, PCR for nucleic acids, and flow cytometry for posttranslational modifications. Since we know that cells in populations behave heterogeneously,1 especially in the cases of stem cells, cancer, and hematopoiesis, there is need for a new technology that provides capability to detect and quantify multiple categories of signaling molecules in intact single cells to provide a comprehensive view of the cell’s physiological state. In this Technology Brief, we describe our automated microfluidic platform with a portfolio of customized molecular assays that can detect nucleic acids, proteins, and posttranslational modifications in single intact cells with >95% reduction in reagent requirement in under 8 h.
Flow cytometry in combination with fluorescent in situ hybridization (flow-FISH) is a powerful technique that can be utilized to rapidly detect nucleic acids at single-cell resolution without the need for homogenization or nucleic acid extraction. Here, we describe a microfluidic-based method which enables the detection of microRNAs or miRNAs in single intact cells by flow-FISH using locked nucleic acid (LNA)-containing probes. Our method can be applied to all RNA species including mRNA and small noncoding RNA and is suitable for multiplexing with protein immunostaining in the same cell. For demonstration of our method, this chapter details the detection of miR155 and CD69 protein in PMA and ionomycin-stimulated Jurkat cells. Here, we also include instructions on how to set up a microfluidic chip sample preparation station to prepare cells for imaging and analysis on a commercial flow cytometer or a custom-built micro-flow cytometer.
A microfluidic RNA interference screening device was designed to study which genes are involved in Rift Valley Fever Virus (RVFV) infection. Spots of small interfering RNA (siRNA) are manually spotted onto a glass microscope slide, and aligned to a screening device designed to accommodate cell seeding, siRNA transfection, cell culture, virus infection and imaging analysis. This portable and disposable PDMS-based microfluidic device for RNAi screening was designed for a 96-well library of transfection against variety of gene targets. Current results show transfection of GFP-22 siRNA within the device, as compared to controls, which inhibit the expression of GFP produced by recombinant RVFV. This technique can be applied to host-pathogen interactions for highly dangerous systems in BSL-3/4 laboratories, where bulky robotic equipment is not ideal.
Uncultivable microorganisms likely play significant roles in the ecology within the human body, with subtle but important implications for human health. Focusing on the oral microbiome, we are developing a processor for targeted isolation of individual microbial cells, facilitating whole-genome analysis without the need for isolation of pure cultures. The processor consists of three microfluidic modules: identification based on 16S rRNA fluorescence in situ hybridization (FISH), fluorescence-based sorting, and encapsulation of individual selected cells into small droplets for whole-genome amplification. We present here a technique for performing microscale FISH and flow cytometry, as a prelude to single cell sorting.
Here we demonstrate the suitability of robust nucleic acid affinity reagents in an integrated point-of-care diagnostic platform for monitoring proteomic biomarkers indicative of astronaut health in spaceflight applications. A model thioaptamer[1] targeting nuclear factor-kappa B (NF-KB) is evaluated in an on-chip electrophoretic gel-shift assay for human serum. Key steps of i) mixing sample with the aptamer, ii) buffer exchange, and iii) preconcentration of sample were successfully integrated upstream of fluorescence-based detection. Challenges due to i) nonspecific interactions with serum, and ii) preconcentration at a nanoporous membrane are discussed and successfully resolved to yield a robust, rapid, and fully-integrated diagnostic system.
We present a platform that combines patterned photopolymerized polymer monoliths with living radical polymerization (LRP) to develop a low cost microfluidic based immunoassay capable of sensitive (low to sub pM) and rapid (<30 minute) detection of protein in 100 μL sample. The introduction of LRP functionality to the porous monolith allows one step grafting of functionalized affinity probes from the monolith surface while the composition of the hydrophilic graft chain reduces non-specific interactions and helps to significantly improve the limit of detection.
We report on the use of thin ({approx}30 micron) photopatterned polymer membranes for on-line preconcentration of single- or double-stranded DNA samples prior to electrophoretic analysis. Shaped UV laser light is used to quickly ({approx}10 seconds) polymerize a highly crosslinked polyacrylamide plug. By applying an electric field across the membrane, DNA from a dilute sample can be concentrated into a narrow zone (<100 micron wide) at the outside edge of the membrane. The field at the membrane can then be reversed, allowing the narrow plug to be cleanly injected into a separation channel filled with a sieving polymer for analysis. Concentration factors >100 are possible, increasing the sensitivity of analysis for dilute samples. We have fabricated both neutral membranes (purely size-based exclusion) as well as anionic membranes (size and charge exclusion), and characterized the rate of preconcentration as well as the efficiency of injection from both types of membrane, for DNA, ranging from a 20 base ssDNA oligonucleotide to >14 kbp dsDNA. We have also investigated the effects of concentration polarization on device performance for the charged membrane. Advantages of the membrane preconcentration approach include the simplicity of device fabrication and operation, and the generic (non-sequence specific) nature of DNA capture, which is useful for complex or poorly characterized samples where a specific capture sequence is not present. The membrane preconcentration approach is well suited to simple single-level etch glass chips, with no need for patterned electrodes, integrated heaters, valves, or other elements requiring more complex chip fabrication. Additionally, the ability to concentrate multiple charged analytes into a narrow zone enables a variety of assay functionalities, including enzyme-based and hybridization-based analyses.
The emerging field of metagenomics seeks to assess the genetic diversity of complex mixed populations of bacteria, such as those found at different sites within the human body. A single person's mouth typically harbors up to 100 bacterial species, while surveys of many people have found more than 700 different species, of which {approx}50% have never been cultivated. In typical metagenomics studies, the cells themselves are destroyed in the process of gathering sequence information, and thus the connection between genotype and phenotype is lost. A great deal of sequence information may be generated, but it is impossible to assign any given sequence to a specific cell. We seek non-destructive, culture-independent means of gathering sequence information from selected individual cells from mixed populations. As a first step, we have developed a microfluidic device for concentrating and specifically labeling bacteria from a mixed population. Bacteria are electrophoretically concentrated against a photopolymerized membrane element, and then incubated with a specific fluorescent label, which can include antibodies as well as specific or non-specific nucleic acid stains. Unbound stain is washed away, and the labeled bacteria are released from the membrane. The stained cells can then be observed via epifluorescence microscopy, or counted via flow cytometry. We have tested our device with three representative bacteria from the human microbiome: E. coli (gut, Gram-negative), Lactobacillus acidophilus (mouth, Gram-positive), and Streptococcus mutans (mouth, Gram-positive), with results comparable to off-chip labeling techniques.
Uncultivable microorganisms likely play significant roles in the ecology within the human body, with subtle but important implications for human health. Focusing on the oral microbiome, we are developing a processor for targeted isolation of individual microbial cells, facilitating whole-genome analysis without the need for isolation of pure cultures. The processor consists of three microfluidic modules: identification based on 16S rRNA fluorescence in situ hybridization (FISH), fluorescence-based sorting, and encapsulation of individual selected cells into small droplets for whole genome amplification. We present here a technique for performing microscale FISH and flow cytometry, as a prelude to single cell sorting.
Single-cell analysis offers a promising method of studying cellular functions including investigation of mechanisms of host-pathogen interaction. We are developing a microfluidic platform that integrates single-cell capture along with an optimized interface for high-resolution fluorescence microscopy. The goal is to monitor, using fluorescent reporter constructs and labeled antibodies, the early events in signal transduction in innate immunity pathways of macrophages and other immune cells. The work presented discusses the development of the single-cell capture device, the iCellator chip, that isolates, captures, and exposes cells to pathogenic insults. We have successfully monitored the translocation of NF-κB, a transcription factor, from the cytoplasm to the nucleus after lipopolysaccharide (LPS) stimulation of RAW264.7 macrophages.
The overarching goal is to develop novel technologies to elucidate molecular mechanisms of the innate immune response in host cells to pathogens such as bacteria and viruses including the mechanisms used by pathogens to subvert/suppress/obfuscate the immune response to cause their harmful effects. Innate immunity is our first line of defense against a pathogenic bacteria or virus. A comprehensive 'system-level' understanding of innate immunity pathways such as toll-like receptor (TLR) pathways is the key to deciphering mechanisms of pathogenesis and can lead to improvements in early diagnosis or developing improved therapeutics. Current methods for studying signaling focus on measurements of a limited number of components in a pathway and hence, fail to provide a systems-level understanding. We have developed a systems biology approach to decipher TLR4 pathways in macrophage cell lines in response to exposure to pathogenic bacteria and their lipopolysaccharide (LPS). Our approach integrates biological reagents, a microfluidic cell handling and analysis platform, high-resolution imaging and computational modeling to provide spatially- and temporally-resolved measurement of TLR-network components. The Integrated microfluidic platform is capable of imaging single cells to obtain dynamic translocation data as well as high-throughput acquisition of quantitative protein expression and phosphorylation information of selected cell populations. The platform consists of multiple modules such as single-cell array, cell sorter, and phosphoflow chip to provide confocal imaging, cell sorting, flow cytomtery and phosphorylation assays. The single-cell array module contains fluidic constrictions designed to trap and hold single host cells. Up to 100 single cells can be trapped and monitored for hours, enabling detailed statistically-significant measurements. The module was used to analyze translocation behavior of transcription factor NF-kB in macrophages upon activation by E. coli and Y. pestis LPS. The chip revealed an oscillation pattern in translocation of NF-kB indicating the presence of a negative feedback loop involving IKK. Activation of NF-kB is preceded by phosphorylation of many kinases and to correlate the kinase activity with translocation, we performed flow cytometric assays in the PhosphoChip module. Phopshorylated forms of p38. ERK and RelA were measured in macrophage cells challenged with LPS and showed a dynamic response where phosphorylation increases with time reaching a maximum at {approx}30-60min. To allow further downstream analysis on selected cells, we also implemented an optical-trapping based sorting of cells. This has allowed us to sort macrophages infected with bacteria from uninfected cells with the goal of obtaining data only on the infected (the desired) population. The various microfluidic chip modules and the accessories required to operate them such as pumps, heaters, electronic control and optical detectors are being assembled in a bench-top, semi-automated device. The data generated is being utilized to refine existing TLR pathway model by adding kinetic rate constants and concentration information. The microfluidic platform allows high-resolution imaging as well as quantitative proteomic measurements with high sensitivity (<pM) and time-resolution ({approx}15 s) in the same population of cells, a feat not achievable by current techniques. Furthermore, our systems approach combining the microfluidic platform and high-resolution imaging with the associated computational models and biological reagents will significantly improve our ability to study cell-signaling involved in host-pathogen interactions and other diseases such as cancer. The advances made in this project have been presented at numerous national and international conferences and are documented in many peer-reviewed publications as listed. Finer details of many of the component technologies are described in these publications. The chapters to follow in this report are also adapted from other manuscripts that are accepted for publication, submitted or in preparation to be submitted to peer-reviewed journals.
We demonstrate the power of our technique for establishing and immobilizing well-defined polymer gradients in microchannels by fabricating two miniaturized analytical platforms: microscale immobilized pH gradients (μIPGs) for rapid and high resolution isoelectric focusing (IEF) applications, and polyacrylamide porosity gradients to achieve microscale pore limit electrophoresis (μPLE) in which species are separated based on molecular size by driving them toward the pore size at which migration ceases. Both separation techniques represent the first microscale implementation of their respective methodologies.
This report describes the continued development of a low-power, portable detector for the rapid identification of pathogens such as B. anthracis and smallpox. Based on our successful demonstration of the continuous filter/concentrator inlet, we believe strongly that the inlet section will enable differentiation between viable and non-viable populations, between types of cells, and between pathogens and background contamination. Selective, continuous focusing of particles in a microstream enables highly selective and sensitive identification using fluorescently labeled antibodies and other receptors such as peptides, aptamers, or small ligands to minimize false positives. Processes such as mixing and lysing will also benefit from the highly localized particle streams. The concentrator is based on faceted prisms to contract microfluidic flows while maintaining uniform flowfields. The resulting interfaces, capable of high throughput, serve as high-, low-, and band-pass filters to direct selected bioparticles to a rapid, affinity-based detection system. The proposed device is superior to existing array-based detectors as antibody-pathogen binding can be accomplished in seconds rather than tens of minutes or even hours. The system is being designed to interface with aerosol collectors under development by the National Laboratories or commercial systems. The focused stream is designed to be interrogated using diode lasers to differentiate pathogens by light scattering. Identification of particles is done using fluorescently labeled antibodies to tag the particles, followed by multiplexed laser-induced fluorescence (LIF) detection (achieved by labeling each antibody with a different dye).