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Anup Singh, Ph.D

Senior Manager, Biological Science and Technology

RESEARCH INTERESTS

The major theme of my group’s work is development of novel microfluidic assays and devices for biochemical and biological analysis to provide significant improvements over the macro-scale counterparts with respect to speed, resolution, sensitivity and multiplexing. Emerging research areas in biology and biotechnology increasingly require large number of experiments performed in smaller amount of time. Moreover, in most instances, these ever-increasing number of experiments need to be performed using a limiting amount of starting biological sample. This requires scaling down of the analysis methods and analogous to the integrated microelectronic-chip revolution, “microfluidic chips” are starting to transform the field of biochemical analysis. Many bio/chemical processes such as mixing, dilution, concentration, transport, separation, and reaction can be integrated and automated in a single chip. The microfluidic assays are typically 10-100 times faster; use 100-1000 times lower sample and reagents, and offer 2-10 times better separation resolution and efficiency than their conventional counterparts.

My group is involved in developing innovative microfluidic assays and integrated devices for many applications including:

  • MicroBioanalytical Systems—Microscale separation methods for cells, protein, nucleic acids, and metabolites
  • Systems Biology & Cell Signaling—Development of tools for analysis of genome, metagenome, transcriptome and proteome of microbial and mammalian cells at single-cell resolution
  • Medical Diagnostics-- Development of fully-integrated point-of-care devices for infectious diseases and biodefense
  • Bioenergy—High throughput platforms for applications in synthetic biology, plant biology and biomass deconstruction

(A) MicroBioanalytical Systems:

Our group, over the last 12 years, has focused on adapting many workhorse biochemical assays to microfluidic chips including slab-gel electrophoretic techniques, chromatography, and immunoassays. One of our specialty has been in developing microfluidic chips with integrated functional materials made in situ by photopolymerization. These polymeric monoliths, crosslinked gels or membranes are formed in minutes and can be easily tailored to obtain desired pore-size (10 nm- 1 micron), surface chemistry and function. Use of light allows exquisite control over spatial patterning of these materials in a microchip, analogous to photolithography, using a mask and a UV-source. The patterned material could be mobile and used as a valve or could be fixed in a channel to act as separation media, a filter, a dialysis membrane or an immobilized reactor. It is also possible to make many of these elements in the same chip to allow integration of the corresponding functions. For example, a microchip containing a photopolymerized size-exclusion membrane upstream of a photopolymerized polyacrylamide gel can be used to perform sample clean up or concentration prior to SDS-PAGE or immunoassay. Microfluidic chips containing functional polymers have found widespread applications and have been used in my laboratory to adapt many biochemical techniques to the microfluidic format as listed below. These are also described in the these review articles (Singh, 2008; Meagher and Singh, 2007)

Microchip SDS-PAGE

Han, J; Singh, AK "Rapid protein separations in ultra-short microchannels: Microchip sodium dodecyl sulfate-polyacrylamide gel electrophoresis and isoelectric focusing" Journal of Chromatography A; 1049, 205-209, 2004.

Herr, A.E.; Singh, A.K. "Photopolymerized cross-linked polyacrylamide gels for on-chip protein sizing," Analytical Chemistry; 76(16), 4727-4733, 2004.

AV Hatch, AE Herr, DJ Throckmorton, JS Brennan, and AK Singh. "Integrated Preconcentration SDS-PAGE of Proteins in Microchips Using Photopatterned Cross-Linked Polyacrylamide Gels." Analytical Chemistry, 78(14), 4976 – 4984, 2006.

C. T. Lo, D. J. Throckmorton, A. K. Singh & A. E. Herr. "Photopolymerized Diffusion-Defined Polyacrylamide Gradient Gels for On-chip Protein Sizing." Lab Chip, 8, 1273-1279, 2008.

Microchip Isoelectric Focusing

Han, J; Singh, AK "Rapid protein separations in ultra-short microchannels: Microchip sodium dodecyl sulfate-polyacrylamide gel electrophoresis and isoelectric focusing" Journal of Chromatography A; 1049, 205-209, 2004.

G. Sommer; A. K. Singh; A. V. Hatch "On-chip Isoelectric Focusing Using Photopolymerized Immobilized pH Gradients", Analytical Chemistry, 80: 3327-33, 2008.

Microchip Chromatography

(Cover article) Throckmorton, D.J.; Shepodd, T.J.; Singh, A.K. "Electrochromatography in Microchips: Reversed-phase Separation of Peptides and Amino Acids Using Photo-Patterned Rigid Polymer Monoliths", Analytical Chemistry, 74, 784-789, 2002.

Shediac, R.; Ngola, S.M.; Throckmorton, D.J.; Anex, D.S.; Shepodd, T.J.; Singh, A.K. "Reverse-Phase Electrochromatography of Amino Acids and Peptides Using Porous Polymer Monoliths", Journal of Chromatography A, 925, 251-262, 2001.

Microfluidic Immunoassays

Herr, A.E.; Throckmorton, D.J.; Davenport, A.A.; Singh, A.K. "On-chip native gel electrophoresis-based immunoassays for tetanus antibody and toxin," Analytical Chemistry, 77(2), 585-590, 2005.

A.E. Herr, A. V. Hatch, D.J. Throckmorton, H.M. Tran, J.S. Brennan, W. V. Giannobile, A.K. Singh. "A Rapid Bioassay for Endogenous Matrix Metalloproteinase-8 in Saliva", Proceedings of the National Academy of Sciences of the USA, 104, 5268-73, 2007.

A.E. Herr, A. V. Hatch, D.J. Throckmorton, H.M. Tran, J.S. Brennan, W. V. Giannobile, A.K. Singh. "Integrated Microfluidic Platform for Oral Diagnostics", Ann N Y Acad Sci, 1098:362-74, 2007.

David Reichmuth, Serena Wang, Louise Barrett, Dan Throckmorton, Wayne Einfeld, and Anup Singh, "Rapid Microchip-Based Electrophoretic Immunoassays For The Detection Of Swine Influenza Virus", Lab Chip, 8,1319-1324, 2008.

(Cover article) R. J. Meagher, A. V. Hatch, R. F. Renzi, and A. K. Singh, "An Integrated, Portable Platform for Ultrasensitive and Rapid Detection of Biological Toxins". Lab on a Chip, 8, 2046–2053, 2008.

Microchip Dialysis

Song, S.; Singh, A.K.; Shepodd, T.J.; Kirby, B.J. "Microchip Dialysis of Proteins Using in Situ Photopatterned Nanoporous Polymer Membranes" Analytical Chemistry, 76, 2367-2373, 2004.

Preconcentration in Microchips

Song, S; Singh, AK; Kirby, BJ "Electrophoretic concentration of proteins at laser-patterned nanoporous membranes in microchips ", Analytical Chemistry, 76 (15), 4589-4592, 2004.

AV Hatch, AE Herr, DJ Throckmorton, JS Brennan, and AK Singh. "Integrated Preconcentration SDS-PAGE of Proteins in Microchips Using Photopatterned Cross-Linked Polyacrylamide Gels." Analytical Chemistry, 78(14), 4976 – 4984, 2006.

(B) Systems Biology & Cell Signaling

A comprehensive “system-level” understanding of cell signaling pathways is the key to deciphering mechanisms of many diseases (e.g., infections, allergies or cancer) and may lead to improvements in early diagnosis or developing improved therapeutics. We are developing an integrated microfluidic system for real-time interrogation of cells to study intracellular signaling. Cell signaling experiments currently are done using large number of cells and hence provide population-averaged data that in many instances may mask the underlying molecular mechanisms. Our approach takes advantage of assays enabled at microscale to provide spatially- and temporally-resolved measurement of signaling pathways in single cells. The integrated microfluidic platform is capable of high-throughput acquisition of quantitative protein expression, translocation and modification information of single and small population of cells. The platform consists of multiple modules such as single-cell array, cell sorter, and phosphoflow chip to provide confocal imaging, cell sorting, and flow cytometry-based phosphorylation assays. The modules have been integrated into a portable package that can be mounted on a typical inverted microscope. The microfluidic platform allows high-resolution imaging as well as quantitative proteomic measurements with high sensitivity (<pM) and time-resolution (~15 s) in the same population of cells, a feat not achievable by current techniques.

Relevant Publications:

  • Liu Y, Barua D, Zwartz G, Liu P, Wilson BS, Oliver JM, Hlavacek WS and Singh AK, Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform, PLoS ONE 2013, 8(3): e60159.
  • Wu M, Piccini M, Koh CY, Lam KS, Singh AK, Single cell microRNA analysis using microfluidic flow cytometry, PLoS ONE, 2013, 8(1): e55044.
  • Schudel BR, Harmon B, Pruitt BW, Abhyankar VV, Negrete OA, Singh, AK Microfluidic platform for RNA interference screening of virus-host interactions, Lab Chip, 2013,13, 811-817.
  • Wu M, Perroud TD, Srivastava N, Branda CS, Sale KL, Carson BD, Patel KD, Branda SS, Singh AK. Microfluidically-unified cell culture, sample preparation, imaging and flow cytometry for measurement of cell signaling pathways with single cell resolution. Lab Chip. 2012, 12(16):2823-31.
  • (Cover article) Wu, M. and Singh AK, Single cell protein analysis, Current Opinion in Biotechnology, 2012, 23(1):83-8.
  • Yilmaz, S and Singh AK, Single cell genome sequencing, Current Opinion in Biotechnology, 2012, 23(3):437-43.
  • (Cover article) Peng Liu, Robert J. Meagher, Yooli Kim Light, Suzan Yilmaz, Romy Chakraborty, Adam P. Arkin, Terry C. Hazen and Anup K. Singh. Microfluidic fluorescence in situ hybridization and flow cytometry (mFlowFISH), Lab On a Chip, 11(16):2673-9, 2011.

For more information, please refer to the Fact Sheet.

(C) Medical Diagnostics:

SpinDxTM: A Point-of-Care Medical Diagnostic Device

SpinDx is an innovative platform for conducting simultaneous multiplexed immunoassays from a single sample with < 15 minute total sample-to-answer time. The technique is based on sedimentation principles within a disposable microfluidic disk, in which all sample processing and detection is automated by centrifugal force. SpinDxTM is highly flexible enabling customized assay development and consolidated disk prototyping with rapid turnaround time. The device requires no manual sample preparation step for complex specimen such as food (milk, juice etc.), white powder samples, and water.

 

For more information, please refer to the Fact Sheet.

RapiDx — Rapid, Automated, Point-of-Care Diagnostic System

apiDx is a hand-held device that can analyze drops of blood or saliva in a primary care setting for low-cost and rapid diagnosis of a disease. The device performs rapid microfluidic chip-based immunoassays (<3–10 min) with low sample volume requirements (10 μL) and appreciable sensitivity (nM–pM). Our microfluidic method facilitates hands-free saliva analysis by integrating sample pretreatment (filtering, enrichment, mixing) with electrophoretic immunoassays to quickly measure analyte concentrations in minimally pretreated saliva samples. The microfluidic chip has been integrated with miniaturized electronics, optical elements, such as diode lasers, fluid-handling components, and data acquisition software to develop a portable, self-contained device.

Specific advantages enabled by the technology include:

  • Fast analysis of fluids samples (5-30 minutes), making clinical or field measurements realistic
  • Quantitation of minute biomarker content, as is especially relevant to complex illnesses
  • Fully-automated analysis – including sample preparation steps and diagnostic tests
  • Analysis of multiple disease indicators, allowing simultaneous measurement of panels of markers.

For more information, please refer to the Fact Sheet.

(D) Bioenergy Applications:

The environmental and economic security of the nation relies on the development of transportation fuels that meet future demands while mitigating climate change. As part of the Joint Bio-Energy Institute (JBEI), we are engaged in advancing research to accelerate solutions to converting lignocellulosic biomass into renewable fuels. My group’s aim is to create specialized technologies to support the scientific research in feedstock development, biomass degradation, and fuel conversion for efficient conversion of biomass to biofuels. These technologies include high-throughput approaches for surveying enzyme diversity and screening of thousands of natural and modified enzyme variants and chips for assembly and cloning of genes.

For more information, visit the JBEI web site.

Relevant Publications:

  • Chang C, Sustarich J, Bharadwaj, R., Adams PD, Singh AK, Droplet-based microfluidic platform for heterogeneous enzymatic assays, Lab Chip, 2013, 13(9):1817-22.
  • Chandrasekaran A, Singh AK. One-Pot, Microscale Cell-Free Enzyme Expression and Screening, Methods in Molecular Biology, in press.
  • (Cover article) Aarthi Chandrasekaran, Kai Deng,  Chung-Yan Koh, Taichi Takasuka, Lai F. Bergeman, Brian G. Fox, Paul D. Adams, and Singh AK, A Universal Flow Cytometry Assay for Screening Carbohydrate-Active Enzymes Using Glycan Microspheres, Chem. Commun., 2013,49, 5441-5443.
  • 10.       Kai Deng, Kevin W. George, Wolfgang Reindl, Jay D. Keasling, Paul D. Adams, Taek Soon Lee, Anup K. Singh, Trent R. Northen, Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme, Rapid Communications of Mass Spectrometry, 2011.
  • Wolfgang Reindl, Cheng S, Kai Deng, Anup K. Singh, Blake A. Simmons, Paul D. Adams, and Trent R. Northen “Nanostructure-Initiator Mass Spectrometry (NIMS) for the Analysis of Enzyme Activities”, Current Opinions in Chemical Biology, 2011.
  • Wolfgang Reindl, Kai Deng, John M. Gladden, Gang Cheng, April Wong, Steven W. Singer, Seema Singh, Jinq-Chyi Lee, Chun-Hsu Yao, Terry C. Hazen, Anup K. Singh, Blake A. Simmons, Paul D. Adams, and Trent R. Northen. Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities, Energy & Environmental Science, 2011. 4(8): p. 2884-2893.
  • Chandrasekaran A, Bharadwaj R, Park JI, Sapra R, Adams PD, Singh AK. A microscale platform for integrated cell-free expression and activity screening of cellulases. J Proteome Res. 2010 Nov 5;9(11):5677-83.
  • Bharadwaj, R., A. Wong, B. Knierim, S. Singh, B.M. Holmes, M. Auer, B.A. Simmons, P.D. Adams, A.K. Singh, “High-Throughput Enzymatic Hydrolysis of Lignocellulosic Biomass via In-Situ Regeneration,” Bioresource Technology, 2010.
  • (Cover Article) Bharadwaj, R., Z. Chen, S. Datta, B.M. Holmes, R. Sapra, B.A. Simmons, P.D. Adams, A.K. Singh, “Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuels Conversion,” Analytical Chemistry, 82 (22), 9135-9592, 2010.
  • Achyuthan KE, Adams PD, Datta S, Simmons BA, Singh AK, “Hitherto unrecognized fluorescence properties of coniferyl alcohol”, Molecules. 2010 Mar 11;15(3):1645-67.
  • Achyuthan KE, Adams PD, Simmons BA, Singh AK, “Spectroscopic analyses of the biofuels-critical phytochemical coniferyl alcohol and its enzyme-catalyzed oxidation products” Molecules. 2009 23;14(11):4758-78
  • K.E. Achyuthan, P.D. Adams, B.A. Simmons & A. K. Singh, "Multimode Spectroscopic Highthroughput Screening of Unmodified Coniferyl Alcohol and its Laccase-catalyzed Oxidation Products", Molecules, 2009, 14(11):4758-78.

RESEARCH PROJECTS

  • Microfluidic Platform for Multiplexed Diagnostics, Funded by National Institute of Allergy and Infectious Diseases, National Institutes of Health

Urgent need exists for developing next-generation clinical diagnostics devices for screening individuals exposed to and/or intoxicated with biological threat agents. These devices need to be capable of rapid, sensitive, and specific diagnosis to enable effective countermeasures including therapeutic intervention. Such systems must also be easy-to-use, automated and self-contained, and preferably, have a small footprint to allow use in point-of-care and point-of-incident settings.

Our goal is to develop, with our partners, a manufacturable device (SpinDx) in preparation for 510(k) submission to the FDA. The device is intended for use in primary care facilities, public health labs, and military clinics overseas for detection of NIAID priority pathogens and toxins botulinum toxins, ricin toxin, shiga-like toxins, Staphyloccocus enterotxn B (SEB), and Anthrax in clinical samples. Invetech will design and develop Beta prototypes ready for field-testing at Sandia and two independent laboratories using spiked human samples as well as serum and nasal swabs from intoxicated/infected mice.

A test-bed version of the device has already been demonstrated with ultra-sensitive detection of a number of analytes including biotoxins (e.g., our assay for botulinum toxin A is ~100 more sensitive than the gold-standard mouse bioassay). The device uses centrifugal force-driven flow to implement bead-based sandwich immunoassays and activity assays in a plastic disk, and can rapidly (<10 min) and sensitively (~ fM) detect multiple analytes using a few μL of clinical sample. The diagnostic device, owing to its bead-based assay format, is readily adaptable to detection of other pathogens and disease markers. The device requires no off-device sample preparation and is compatible with multiple bodily fluids including whole blood, serum, saliva, and urine.

We have assembled a multidisciplinary team for development, manufacturing and testing of SpinDx which includes, in addition to Sandia, United States Department of Agriculture‘s Western Regional Research Center (USDA-WRRC) in Albany, CA and University of Texas Medical Branch (UTMB) at Galveston, TX; and two sites for independent, blind testing of the device at UTMB Allied Health hospital lab and USDA-WRRC.

  • FISH "N" Chips: A Microfluidic Processor for Isolating and Analyzing Microbes, funded by National Institute of Dental and Craniofacial Research, National Institutes of Health.
    • Since uncultivable microorganisms comprise a large percentage of the microbiome, and are likely to play a major role in the ecology at all sites within the body, it is critical to develop new approaches to obtain samples of these microorganisms for genomic analysis.  In this proposal we focus on one anatomic site, the mouth, and propose to develop a technology to extract single bacterial cells from saliva. To attain these goals, we have formed a collaboration between Sandia (with expertise in integrated microfluidic technology for biological analysis), NYU College of Dentistry (with expertise in oral microbiomics and oral-based diagnostics), and the Joint Genome Institute (with expertise in microbial ecology and sequencing). The technological approach is to build an integrated microfluidic cell processor that will identify, select, and isolate into discrete microdroplets single bacteria from a mixture of oral bacteria from human saliva.  The microfluidic processor will have multiple modules to 1) perform fluorescence in situ hybridization on a mixture of bacteria, 2) sort single cells using fluorescence activated photonic-force deflection, and 3) encapsulate sorted cells in microdroplets before depositing them on an array. The input to the device will be bacterial cells from saliva and the output will be arrayed droplets containing no more than one bacterium. We expect this technique to be used to extract sequence-quality genomic DNA from individual microorganism and can be used as a diagnostic to identify bacterial signatures obtained from healthy versus diseases subjects.
  • Microscale Immune Studies Laboratory (for more information, please visit http://www.ca.sandia.gov/mica/)
    • As part of a multi-institutional and multidisciplinary effort, we are developing novel microfluidic and imaging tools and computational models to elucidate the molecular mechanisms of innate immunity with unprecedented speed, resolution, and throughput. This project involves researchers in both the California and New Mexico laboratories and at two academic partners, the University of Texas Medical Branch and the University of California at San Francisco. Our overarching goal is to develop technologies to understand how immune cells respond to pathogens, such as bacteria and viruses, in the first few minutes and hours after exposure. We are especially interested in the molecular mechanisms used by pathogens to subvert an organism’s innate immunity and thus cause greater harm To achieve this goal, we are developing an integrated, high-throughput experimental and computational approach that provides “system-level,” quantitative, spatio-temporal data at single-cell resolution for an innate-immunity pathway — specifically, the toll-like receptor (TLR) signaling pathway. Our miniaturized measurement and analysis system will detect protein concentrations, states, and interactions in both individual host cells and a population of such cells. We will validate this system by integrating biological experimentation, microengineered platforms, imaging tools, and predictive models to quantify the response of the TLR signaling pathway in macrophages and epithelial cells that have been challenged with lipopolysaccharide and bacteria.
  • Integrated Microfluidic System for Oral Diagnostics, Funded by National Institute of Dental and Craniofacial Research, National Institutes of Health

In addition, I am an Investigator on the following projects.

RECENT PUBLICATIONS (1999 - PRESENT)

Chang C, Sustarich J, Bharadwaj, R., Adams PD, Singh AK, Droplet-based microfluidic platform for heterogeneous enzymatic assays, Lab Chip, 2013, 13(9):1817-22.

Chandrasekaran A, Singh AK. One-Pot, Microscale Cell-Free Enzyme Expression and Screening, Methods in Molecular Biology, in press.

(Cover article) Aarthi Chandrasekaran,Kai Deng,  Chung-Yan Koh, Taichi Takasuka,Lai F. Bergeman,Brian G. Fox,Paul D. Adams,and Singh AK, A Universal Flow Cytometry Assay for Screening Carbohydrate-Active Enzymes Using Glycan Microspheres, Chem. Commun., 2013,49, 5441-5443.

Liu Y, Barua D, Zwartz G, Liu P, Wilson BS, Oliver JM, Hlavacek WS and Singh AK, Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform, PLoS ONE 2013, 8(3): e60159.

Wu M, Piccini M, Koh CY, Lam KS, Singh AK, Single cell microRNA analysis using microfluidic flow cytometry, PLoS ONE, 2013, 8(1): e55044.

Schudel BR, Harmon B, Pruitt BW, Abhyankar VV, Negrete OA, Singh, AK Microfluidic platform for RNA interference screening of virus-host interactions, Lab Chip, 2013,13, 811-817.

Wu M, Perroud TD, Srivastava N, Branda CS, Sale KL, Carson BD, Patel KD, Branda SS, Singh AK. Microfluidically-unified cell culture, sample preparation, imaging and flow cytometry for measurement of cell signaling pathways with single cell resolution. Lab Chip. 2012, 12(16):2823-31.

(Cover article) Wu, M. and Singh AK, Single cell protein analysis, Current Opinion in Biotechnology, 2012, 23(1):83-8.

Yilmaz, S and Singh AK, Single cell genome sequencing, Current Opinion in Biotechnology, 2012, 23(3):437-43.

Kai Deng, Kevin W. George, Wolfgang Reindl, Jay D. Keasling, Paul D. Adams, Taek Soon Lee, Anup K. Singh, Trent R. Northen, Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme, Rapid Communications of Mass Spectrometry, 2011.

Wolfgang Reindl, Cheng S, Kai Deng, Anup K. Singh, Blake A. Simmons, Paul D. Adams, and Trent R. Northen “Nanostructure-Initiator Mass Spectrometry (NIMS) for the Analysis of Enzyme Activities”, Current Opinions in Chemical Biology, 2011.

(Cover article) Peng Liu, Robert J. Meagher, Yooli Kim Light, Suzan Yilmaz, Romy Chakraborty, Adam P. Arkin, Terry C. Hazen and Anup K. Singh. Microfluidic fluorescence in situ hybridization and flow cytometry (mFlowFISH), Lab On a Chip, 11(16):2673-9, 2011.

Chhabra SR, Joachimiak MP, Petzold CJ, Zane GM, Price MN, Reveco SA, Fok V, Johanson AR, Batth TS, Singer M, Chandonia JM, Joyner D, Hazen TC, Arkin AP, Wall JD, Singh AK, Keasling JD. Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough. PLoS ONE 6(6), 2011.

Wolfgang Reindl, Kai Deng, John M. Gladden, Gang Cheng, April Wong, Steven W. Singer, Seema Singh, Jinq-Chyi Lee, Chun-Hsu Yao, Terry C. Hazen, Anup K. Singh, Blake A. Simmons, Paul D. Adams, and Trent R. Northen. Colloid-based multiplexed screening for plant biomass-degrading glycoside hydrolase activities in microbial communities, Energy & Environmental Science, 2011. 4(8): p. 2884-2893.

Sommer, G. J.; Mai J, Singh, A. K.; Hatch, A. V. Microscale Isoelectric Fractionation Using Photopolymerized Membranes, Analytical Chemistry 2011 83 (8), pp 3186–3191.

Smruti Pushalkar, Shrinivasrao P. Mane, Xiaojie Ji, Yihong Li, Clive Evans, Oswald R. Crasta,, Douglas Morse, Robert Meagher, Anup Singh & Deepak Saxena, Microbial diversity in saliva of oral squamous cell carcinoma. FEMS Immunol Med Microbiol, (2011) 1–9

J.S. Kinney, T. Morelli, T. Braun, C.A. Ramseier, A.E. Herr, J.V. Sugai, C.E. Shelburne, L.A. Rayburn, A.K. Singh, and W.V. Giannobile, Saliva and Pathogen biomarker Signatures and Periodontal Disease Progression. J Dent Res. 90(6):752-8, 2011.

Chandrasekaran A, Bharadwaj R, Park JI, Sapra R, Adams PD, Singh AK. A microscale platform for integrated cell-free expression and activity screening of cellulases. J Proteome Res. 2010 Nov 5;9(11):5677-83.

Bharadwaj, R., A. Wong, B. Knierim, S. Singh, B.M. Holmes, M. Auer, B.A. Simmons, P.D. Adams, A.K. Singh, “High-Throughput Enzymatic Hydrolysis of Lignocellulosic Biomass via In-Situ Regeneration,” Bioresource Technology, 2010.

(Cover Article) Bharadwaj, R., Z. Chen, S. Datta, B.M. Holmes, R. Sapra, B.A. Simmons, P.D. Adams, A.K. Singh, “Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuels Conversion,” Analytical Chemistry, 82 (22), 9135-9592, 2010.

Hecht AH, Sommer GJ, Durland RH, Yang X, Singh AK, Hatch AV, “Aptamers as Affinity Reagents in an Integrated Electrophoretic Lab-on-a-Chip Platform”, Anal Chem, 2010.

Achyuthan KE, Adams PD, Datta S, Simmons BA, Singh AK, “Hitherto unrecognized fluorescence properties of coniferyl alcohol”, Molecules. 2010 Mar 11;15(3):1645-67.

James CD, Moorman MW, Carson BD, Branda CS, Lantz JW, Manginell RP, Martino A, Singh AK, “Nuclear translocation kinetics of NF-kappaB in macrophages challenged with pathogens in a microfluidic platform”, Biomed Microdevices. 2009,11(3):693-700.

Achyuthan KE, Adams PD, Simmons BA, Singh AK, “Spectroscopic analyses of the biofuels-critical phytochemical coniferyl alcohol and its enzyme-catalyzed oxidation products” Molecules. 2009 23;14(11):4758-78

K.E. Achyuthan, P.D. Adams, B.A. Simmons & A. K. Singh, "Multimode Spectroscopic Highthroughput Screening of Unmodified Coniferyl Alcohol and its Laccase-catalyzed Oxidation Products", Molecules, 2009, 14(11):4758-78.

G. J. Sommer, A. K. Singh and A. V. Hatch Enrichment and fractionation of proteins via microscale pore limit electrophoresis. Lab on a Chip, June 2009.

N. Srivastava, J. S. Brennan, R. F. Renzi, M. Wu, S. S. Branda, A. K. Singh, and A. E. Herr Fully Integrated Microfluidic Platform Enabling Automated Phosphoprofiling of Macrophage Response. Anal. Chem., 81, 3261–3269, 2009.

C.A. Ramseier, J.S. Kinney, A.E. Herr, T. Braun, J.V. Sugai, C.A. Shelburne, L.A. Rayburn, H.M. Tran, A.K. Singh, W.V. Giannobile, “Identification of pathogen and host-response markers correlated with periodontal disease”, J Periodontol, 2009, 80, 3, 436-446.

G. J. Sommer, A. K. Singh and A. V. Hatch, Enrichment and fractionation of proteins via microscale pore limit electrophoresis. Lab on a Chip, 2009.

N. Srivastava, J. S. Brennan, R. F. Renzi, M. Wu, S. S. Branda, A. K. Singh, and A. E. Herr, Fully Integrated Microfluidic Platform Enabling Automated Phosphoprofiling of Macrophage Response. Anal. Chem., 81, 3261–3269, 2009.

Perroud, TD, RJ Meagher,MP Kanouff, RF Renzi, M Wu, AK Singh, KD Patel, Isotropically etched radial micropore for cell concentration, immobilization, and picodroplet generation. Lab on a Chip, 2009.

(Cover article) R. J. Meagher, A. V. Hatch, R. F. Renzi, and A. K. Singh, "An Integrated, Portable Platform for Ultrasensitive and Rapid Detection of Biological Toxins". Lab on a Chip, 8, 2046–2053, 2008.

Perroud, Thomas; Kaiser, Julia; Sy, Jay; Lane, Todd; Branda, Catherine; Singh, A. K.; Patel, Kamlesh, “Microfluidic-Based Cell Sorting of Francisella tularensis Infected Macrophages using Optical Forces", Analytical Chemistry, 80, 6365-6372, 2008.

C. T. Lo, D. J. Throckmorton, A. K. Singh & A. E. Herr, "Photopolymerized Diffusion-Defined Polyacrylamide Gradient Gels for On-chip Protein Sizing." Lab Chip, 8, 1273-1279, 2008.

G. Sommer; A. K. Singh; A. V. Hatch, "On-chip Isoelectric Focusing Using Photopolymerized Immobilized pH Gradients", Analytical Chemistry, 80: 3327-33, 2008.

S. Gaucher, A. Redding, A.M. Mukhopadhyay, J.D. Keasling, A.K. Singh, “Proteins in the Sulfate Reduction Pathway of Desulfovibrio vulgaris Hildenborough are Highly Modified”, Journal of Proteome Research, 7, 2320-2331, 2008.

(Cover article) R. J. Meagher, Y. K. Light and A. K. Singh, “Rapid, continuous purification of proteins in a microfluidic device using genetically-engineered partition tags”, Lab Chip, 8, 527-32, 2008.

David Reichmuth, Serena Wang, Louise Barrett, Dan Throckmorton, Wayne Einfeld, and Anup Singh, ”Rapid Microchip-Based Electrophoretic Immunoassays For The Detection Of Swine Influenza Virus”, Lab Chip, 8,1319-1324, 2008.

A.E. Herr, A. V. Hatch, D.J. Throckmorton, H.M. Tran, J.S. Brennan, W. V. Giannobile, A.K. Singh, “Integrated Microfluidic Platform for Oral Diagnostics”, Ann N Y Acad Sci, 1098:362-74, 2007.

A.E. Herr, A.V. Hatch, D.J. Throckmorton, H.M. Tran , J.S. Brennan, W.V. Giannobile, A.K. Singh. "Microfluidic Immunoassays as Rapid Saliva-based Clinical Diagnostics." Proc Natl Acad Sci USA, 2007, 104(13), 5268-5273. PDF file

R. Sapra , S.P. Gaucher, J.S. Lachmann, G.M. Buffleben , G. S. Chirica , J.E. Comer, J.W. Peterson, and A.K. Chopra and A.K. Singh, Proteomic analyses of murine macrophages treated with Bacillus anthracis lethal toxin Microbial Pathogenesis, In press.

AV Hatch, AE Herr, DJ Throckmorton, JS Brennan, and AK Singh. "Integrated Preconcentration SDS-PAGE of Proteins in Microchips Using Photopatterned Cross-Linked Polyacrylamide Gels." Analytical Chemistry, 2006, 78(14), 4976 - 4984.

S.R. Chhabra, Q. He, K.H. Huang, S.P. Gaucher, E.J. Alm, Z. He, M.Z. Hadi, T.C. Hazen, J.D. Wall, J. Zhou, A.P. Arkin, A.K. Singh, Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough, Journal of Bacteriology, Mar. 2006; Vol. 188, No. 5, p. 1817-1828.

Song, S; Singh, AK On-chip sample preconcentration for integrated microfluidic analysis, Analytical and Bioanalytical Chemistry; January 2006; v.384, no.1, p.41-43.

Barrett, L.M.; Skulan, A.J.; Singh, A.K.; Cummings, E.B.; Fiechtner, G.J. Dielectrophoretic Manipulation of Particles and Cells Using Insulating Ridges in Faceted Prism Microchannels Anal. Chem. 2005, 2005, Nov 1 2005; v.77, no.21, p.6798-6804.

Skulan, A.J.; Barrett, L.M.; Singh, A.K.; Cummings, E.B.; Fiechtner, G.J. Fabrication and Analysis of Spatially Uniform Field Electrokinetic Flow Devices: Theory and Experiment Anal. Chem. 2005, Nov 1 2005; v.77, no.21, p.6790-6797.

Diana Yu, Joanne Volponi, Swapnil Chhabra, C. Jeffrey Brinker, Ashok Mulchandani and Anup K. Singh
Aqueous sol-gel encapsulation of genetically engineered Moraxella spp. cells for the detection of organophosphates,
Biosensors & Bioelectronics, 20(7), 1433-1437, 2005.

Jose M. Moran-Mirabal, Joshua B. Edel, Grant D. Meyer, Daniel J. Throckmorton, Anup K. Singh, and Harold G. Craighead, "Micrometer-Sized Supported Lipid Bilayer Arrays for Bacterial Toxin Binding Studies through Total Internal Reflection Fluorescence Microscopy", Biophysical Journal, July 2005; vol.89, no.1, p.296-305.

AE Herr, DJ Throckmorton, AA Davenport, AK Singh, "On-chip native gel electrophoresis-based immunoassays for tetanus antibody and toxin," Analytical Chemistry, Jan 15 2005; 77(2), 585-590

Amy E. Herr, Anup K. Singh
Photopolymerized Cross-Linked Polyacrylamide Gels for On-Chip Protein Sizing
Analytical Chemistry, 77, 585-590, 2005.

Simon Song, Anup K Singh, Timothy J. Shepodd, Brian J Kirby
Electrophoretic Concentration of Proteins at Laser-Patterned Nanoporous Membranes in Microchips Anaytical Chemistry, 76(15), 4589-4592, 2004.

Jongyoon Han and Anup K Singh,
Miniaturized Isoelectric Focusing and SDS-PAGE Protein Separation
Journal of Chromatography A., 1049 (1-2), 205-209, 2004.

Pathak, S; Singh, AK; McElhanon, JR; Dentinger, PM,
Dendrimer-activated surfaces for high density and high activity protein chip applications, Langmuir, 20(15), 6075-6079, 2004.

Y.J. Song, Y. Yang, C. Medforth, E. Pereira, A.K. Singh, H. Xu, Y. Jiang, C. J. Brinker, F. van Swol, J. A. Shelnutt.
Controlled Synthesis of 2-D and 3-D Platinum Dendrites Using Porphyrin
Photocatalysts, Journal of the American Chemical Society, 126(2), 635-645, 2004.

Simon Song, Anup K Singh, Timothy J. Shepodd, Brian J Kirby
Microchip dialysis of proteins using in situ photopatterned nanoporous polymer
membranes, Analytical Chemistry, 76(8), 2367-2373, 2004.

Eric Cummings and Anup K Singh
Dielectrophoresis in Microchips Containing Arrays of Insulating Posts: Theoretical and Experimental Results
Analytical Chemistry, 75(18), 4724-4731, 2003.

(Ke Wang, Anup K. Singh and John H. van Zanten),
Aggregation Rate Measurements by Zero Angle Time-Resolved Multiangle Laser Light Scattering, Langmuir, 18(6); 2421-2425, 2002.

Daniel J. Throckmorton, Timothy J. Shepodd, Anup K. Singh
Electrochromatography in Microchips: Reversed-phase Separation of Peptides and Amino Acids Using Photo-Patterned Rigid Polymer Monoliths, Analytical Chemistry, 74, 784-789, 2002.

Renèe Shediac, Sarah M. Ngola, Dan J. Throckmorton, Deon S. Anex, Timothy J. Shepodd, Anup K. Singh
Reverse-Phase Electrochromatography of Amino Acids and Peptides Using Porous Polymer Monoliths, Journal of Chromatography A, 925, 251-262, 2001.

(Lital Alfonta, Itamar Willner, Daniel J. Throckmorton and Anup K. Singh),
Electrochemical and Quartz-Crystal-Microbalance Detection of the Cholera Toxin Employing Horseradish Peroxidase- and GM1-functionalized Liposomes, Analytical Chemistry, 73, 5287-5295, 2001.

Anup K. Singh, Eric B. Cummings, Daniel J. Throckmorton
Fluorescent Liposome Flow Markers for Microscale Particle-Image Velocimetry, Analytical Chemistry, 73, 1057-1061, 2001.

Lital Alfonta, Anup K. Singh, Itamar Willner
Liposomes Labeled with Biotin and Horseradish Peroxidase: A Probe for the Enhanced Amplification of Antigen-Antibody or Oligonucleotide-DNA Sensing Processes by the Precipitation of an Insoluble Product on Electrodes, Analytical Chemistry, 73, 91-102, 2001

Anup K. Singh, Suzanne H. Harrison, and Joseph S. Schoeniger
Gangliosides as Receptors for Biological Toxins: Development of Sensitive Fluoroimmunoassays Using Ganglioside-Bearing Liposomes, Analytical Chemistry, 72, 6019-6024, 2000.

R. B. Bhatia, C. J. Brinker, A. K. Gupta, A. K. Singh
An Aqueous Sol-Gel Process for Protein Encapsulation, Chemistry of Materials, 12, 2434-2441, 2000.

Felice C. Lightstone, Maria C. Prieto, Anup K. Singh, Mari Carmen Piqueras, Randy M. Whittal, Mark S. Knapp, Rod Balhorn, and Diana C. Roe
The Identification of Novel Small Molecule Ligands that Bind to Tetanus Toxin, Chemical Research in Toxicology, 13, 356-362, 2000.

A K Singh, A W Flounders, J V Volponi, C S Ashley, K Wally, J S Schoeniger
Development of Sensors for Direct Detection of Organophosphates, Part I: Immobilization, Characterization & Stabilization of Enzymes Acetylcholineesterase & Organophosphate Hydrolase on Silica Supports, Biosensors & Bioelectronics, 14, 703-713, 1999.

A W Flounders, A K Singh, J V Volponi, S C Carichner, K. Wally, A S Simonian, J R Wild, J S Schoeniger
Development of Sensors for Direct Detection of Organophosphates, Part II: Sol-Gel Modified Field Effect Transistor with Immobilized Organophosphate Hydrolase, Biosensors & Bioelectronics, 14, 715-722, 1999.

PATENTS

  1. “Microfluidic Devices, Systems, and Methods for Quantifying Particles Using Centrifugal Force”, US patent 12/891,956 filed 09/28/2010.
  2. “Devices, Systems, and Methods for Conducting Sandwich Assays Using Sedimentation”, US patent 12/891,977 filed 09/28/2010.
  3. “Devices, Systems, and Methods for Conducting Assays with Improved Sensitivity Using Sedimentation”, US patent 13/423,050 filed 03/16/2012.
  4. “Systems, Devices, and Methods for Agglutination Assays Using Sedimentation”, US patent 13/423,073 filed 03/16/2012.
  5. “Microfluidic Platform for Synthetic Biology Applications”, US patent 61/471,027 filed April 2011.
  6. “Colloid-based Multiplexed Screening for Glycoside Hydrolase Activities in Microbial Communities using Nanostructure Initiator Mass Spectrometry”, US patent application filed 2011.
  7. “Portable modular detection system”, US Patent 7602307, 2011.
  8. “Microfluidic devices and methods for integrated flow cytometry”, US Patent 7999937, 2010.
  9. Method for forming polymerized microfluidic devices, US Patent 8047829, 2011.
  10. “Microscale isoelectric fractionation membranes”, US Patent Application, filed Oct 2008.
  11. “Sandwich-method polymerized microfluidic devices”, US Patent Application, filed Oct 2008.
  12. “Methods for Providing and Using Solution Gradients in Microchannels”, US patent Application, filed Jul 2008.
  13. “Method for voltage gated protein fractionation”, US Patent Application, filed July 2007.
  14. “Concentration and Separation of molecules using photopolymerized gels”, US patent appl filed Aug, 2006.
  15. “Method for Gel Electrophoretic Immunoassays”, US patent Application filed Mar, 2005
  16. “Apparatus for Gel Electrophoretic Immunoassays”, US patent Application filed Mar, 2005
  17. “Apparatus for Selective Particle Detection,” United States Patent Application No. 10/969,137 (2004).
  18. “Planar Micromixer,” United States Patent Application No. 10/960,324 (2004).
  19. “Apparatus and Method for Concentrating and Filtering Particles Suspended in a Fluid,” United States Patent Application No. 10/956,446 (2004).
  20. Dialysis on Microchips using thin porous polymer membranes”.  US Patent 7,264,723, Sep4, 2007.
  21. “Dielectrophoretic Systems without Embedded Electrodes”, U.S Patent 7,014,747, Mar 21, 2006.
  22. “Sol-Gel Method for Encapsulating Molecules”, U.S Patent 6, 495, 352, Dec 17, 2002.
  23. “Electrokinetic Concentration of Charged Molecules”, US Patent 6,428, 666, Aug 6, 2002.
  24. “Immunodiagnostic Assays Using Liposomes Carrying Labels Thereof On Outer Liposome Surface", US Patent 5,494,803, Feb. 27, 1996

RECENT INVITED LECTURES (2002- Present)

New York Academy of Sciences Conference on Oral Based Diagnostics, Oct 2006, Lake Lanier Island, Georgia

Gordon Research Conference 2005, Salivary Glands and Exocrine Secretion, Ventura, California February 6-11, 2005

Gordon Research Conference on the Physics and Chemistry of Microfluidics, August 21 - 26, 2005, Magdalen College, Oxford, UK

Biochemical analysis in microchips using photopatterned porous polymers American Chemical Society (ACS) National Meeting, Anaheim, CA, March 28-April 1, 2004

Microchips Containing Engineered Materials for Biochemical Analysis Materials Research Society (MRS) Spring Meeting, San Francisco, April, 2004

A novel miniaturized protein concentrator, Annual Electrochemical Society Meeting, San Francisco, Nov 2003.

Microfluidic Systems for Proteomics, Nanobiotechnology Center Seminar Series, Cornell University, Ithaca, NY, Sep 9, 2003.

Chromatography and Gel Electrphoresis of Proteins and Peptides in Microchips, BioMEMS 2003, San Jose, CA, June 15-17, 2003.

Electrochromatography and gel electrophoresis of proteins and peptides in microchips using photopatterned polymer matrices, American Chemical Society Nortwest Regional Meeting, Bozeman, June 2003.

Microfluidic Systems for Biochemical Analysis, Analytical Chemistry Invited Seminar, April 17, 2003, UC Riverside.

Microfluidic systems for analysis of biological molecules, Bioengineering Seminar Series, MIT, Cambridge, MA, Oct 10, 2002.

Electrochromatography in Microchips, Small Talk 2002, San Diego, July 28-31, 2002.

RECENT PRESENTATIONS (2002 - Present)

Controlled Synthesis of 2-D and 3-D Platinum Dendrites Using Porphyrin Photocatalysts, Y. Song, Y. Yang, C. Medforth, E. Pereira, A.K. Singh, H. Xu, Y. Jiang, C. J. Brinker, F. van Swol, J. A. Shelnutt, 226th ACS National Meeting, Sept 1-11, NY, NY.

Miniaturized Isoelectric Focusing and SDS-PAGE Protein Separation, Jongyoon Han and Anup K. Singh CSBi Computaional and Systems Biology Conference, January 9-10, 2003, MIT, Cambridge, MA.

Rapid Deduction of Stress Reponse Pathways in Metal/Radionuclide Reducing Bacteria, Adam Arkin, Alex Beliaev, Inna Dubchak, Matthew Field, Terry Hazen, Jay Keasling, Martin Keller, Vincent Martin, Frank Olken, Anup Singh, David Stahl, Dorothea Thompson, Judy Wall, and Jizhong Zhou

A novel miniaturized protein preconcentrator based on electric field-addressable retention and release. Singh, A. K., Throckmorton, D. J., Kirby, B. J., Thompson, A. P., Micro Total Analysis Systems 2002, Nov 10-15, Nara, Japan.

Injection of Sample Bands from Open Channels into Packed Separation Columns, Robert H. Nilson, Stewart K. Griffiths and Anup K. Singh, Micro Total Analysis Systems 2002, Nov 10-15, Nara, Japan.

Electrokinetic Trapping of Proteins in Cast-To-Shape Matrices, Alexander Artau, Anup, K. Singh, and Timothy J. Shepodd, Micro Total Analysis Systems 2002, Nov 10-15, Nara, Japan.

Miniaturization of Protein Separation: Isoelectric Focusing and SDS-PAGE, Jongyoon Han and Anup K. Singh, Micro Total Analysis Systems 2002, Nov 10-15, Nara, Japan.

In-situ Fabrication of Dialysis Membranes in Glass Microchannels Using Laser-induced Phase- Separation Polymerization, Brian J. Kirby, Anup K. Singh, Micro Total Analysis Systems 2002, Nov 10- 15, Nara, Japan.

Electrochromatography In Chips: Reversed-Phase Separation Of Peptides And Amino Acids Using Polymer Monoliths Photopatterned In Channels Of A Glass Microchip" (Anup K. Singh, Daniel J. Throckmorton, and Timothy J. Shepodd), High Performance Capillary Electrophoresis (HPCE 2002), Stockholm, Sweden, April 13-18, 2002.

IN THE NEWS

Sandia researchers take new approach to studying how cells respond to pathogens
Method looks at one cell at a time
, April 13, 2007

Sandia Researchers Develop Portable Device That Can Detect Heart And Gum Disease Instantly,
February 15, 2005

Sandia researchers develop portable device that can detect heart and gum disease instantly.
Technology based on lab-on-a-chip technology, January 17, 2005

Molecular Integrated Microsystems grand challenge pursues revolutionary approach to microsystems

Bay Area scientists get big funding for microbe research

The Daily Californian

Chemical Science and Engineering News

Education:

Ph.D. 1995,
Chemical Engineering, North Carolina State University, Raleigh. Advisors: Prof. Ruben Carbonell and Prof. Peter Kilpatrick

B.Tech. 1990,
Chemical Engineering, Indian Institute of Technology, Bombay, India.

Contact Information

Dr. Anup Singh
Biosystems Research Department
Sandia National Laboratories
MS 9292, PO Box 969
7011 East Avenue
Livermore, CA 94551-0969

aksingh@sandia.gov
phone: 925-294-1260
fax: 925-294-3020