Research

Bioscience Leadership

Anup Singh

Doctor Anup Singh
Dr. Anup Singh is the Director of the Biological and Engineering Sciences at Sandia National Laboratories, Livermore, CA. The Center is comprised of four groups and ten departments with approximately 145 staff, technologists and postdoctoral researchers working at three geographically distributed locations - Albuquerque, NM, Emeryville, CA and Livermore, CA. The center performs exploratory science and develops technology to address pressing national needs in energy security, homeland security, and radiological and nuclear security. Key sponsors include the DOE- NNSA; DOE Office of Science (BER and BES), DOE Office of Energy Efficiency and Renewable Energy, ARPA-E, DoD, the Defense Threat Reduction Agency, DHS, the NIH, and the Sandia Laboratory Directed Research and Development (LDRD) Program.
Dr. Singh also holds the positions of Director of Microfluidics at the Joint BioEnergy Institute (JBEI) located in Emeryville, CA and Adjunct Professor at University of Texas Medical Branch in Galveston, TX. He has published over 80 peer-reviewed publications, delivered over 150 presentations at national and international conferences, and his inventions have led to over 40 patents and patent applications. Many of his inventions have been licensed to companies engaged in medical diagnostics and sensor technology development.

Research Interests

My major scientific contributions have been in the development of novel microfluidic assays and devices for biochemical and biological analysis that 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 and molecular biology. 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 and reactions 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.
We are involved in developing innovative microfluidic assays and integrated devices for many applications including:
  • Medical Diagnostics

    My group has developed a number of innovative assays and devices for applications in infectious diseases and biodefense. A few of these are described below.

    SpinDx™ is an innovative platform for conducting simultaneous multiplexed immunoassays from a single sample with < 30 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. The device requires no manual sample preparation step for complex specimen such as whole blood, serum, saliva, food (milk, juice etc.), white powder samples (dissolved in water or buffer), and water. Sensitive and rapid detection has been demonstrated for bio-toxins (e.g., ricin and botulinum), immunoglobulins, cardiac markers, and pathogens. This innovative, patented technology has been licensed to multiple companies for various applications such as water monitoring, at-home male fertility testing, and drugs-of-abuse testing. More information is available in the SpinDx factsheet.
    Representative publication includes:

    • Chung-Yan Koh, Ulrich Y. Schaff, Matthew E. Piccini, Larry H. Stanker, Luisa W. Cheng, Easwaran Ravichandran, Bal-Ram Singh, Greg J. Sommer, and Anup K. Singh. Centrifugal Microfluidic Platform for Ultrasensitive Detection of Botulinum Toxin, Anal Chem, 2015, 922-928.

    RapiDx (Rapid, Automated, Point-of-Care Diagnostic System) 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.

    Representative publications include:
    • 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, 2007, 104: 5268–5273.
    • (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
  • High-throughput Platforms for Synthetic Biology

    Engineering of biological organisms requires combinatorial optimization of genes and genetic pathways. Advances in sequencing and gene synthesis have made it possible to have thousands of variants of a gene or hundreds of thousands of combinations of genes to be tried. Such large-scale optimization experiments using traditional molecular biology methods are cost-prohibitive, labor-intensive, and suffer from poor reproducibility. Robotics liquid handling stations can reduce manual labor and improve reproducibility but are expensive and not affordable by most researchers. We have developed droplet microfluidic platforms as a promising alternative as they can reduce the cost drastically by lower reagent consumption while maintaining the throughput and reproducibility. Many genetic engineering steps have been adapted to a microfluidic format, including DNA assembly, transformation/transfection, culturing, cell sorting, and phenotypic assays.
    A key driver for our efforts in this area has been optimization of pathways in microbes to produce biofuels. This research is being carried out at the Joint Bio-Energy Institute (JBEI), where I lead the Microfluidics group. More information can be found here.

    Representative publications include:

    • C Gach, Philip, Iwai, Kosuke, Kim, Peter, Hillson, Nathan, & Singh, Anup. (2017). Droplet Microfluidics for Synthetic Biology, Lab Chip, 2017.
    • Philip Charles Gach, Steve C.C. Shih, Jess Sustarich, Jay D Keasling, Nathan J Hillson, Paul D. Adams, and Anup K Singh. (2016) A Droplet Microfluidic Platform for Automating Genetic Engineering. ACS Synthetic Biology, 2016. DOI:10.1021/acssynbio.6b00011
    • (Cover article) Steve C. C. Shih, Garima Goyal, Peter W. Kim, Nicolas Koutsoubelis, Jay D. Keasling, Paul D. Adams, Nathan J. Hillson, and Anup K. Singh, Versatile Microfluidic Device for Automating Synthetic Biology, ACS Synthetic Biology, 2016.
  • Single Cell Analysis

    A comprehensive “system-level” understanding of cellular pathways is the key to deciphering how cells work and how they interact with other cells in a tissue or microbial com community. Cellular pathway 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. We are developing innovative assays and platforms to measure analytes (DNA, RNA, protein) at the level of single cells.

    Representative Publications:

    • Brooke Harmon, Lily A. Chylek, Yanli Liu, Eshan D. Mitra, Avanika Mahajan, Edwin A. Saada, Benjamin R. Schudel, David A. Holowka, Barbara A. Baird, Bridget S. Wilson Ϯ, William S. Hlavacek and Anup K. Singh. Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation. In press. Nature Scientific Reports.
    • Brito, I. L., S. Yilmaz, K. Huang, L. Xu, S. D. Jupiter, A. P. Jenkins, W. Naisilisili, M. Tamminen, C. S. Smillie, J. R. Wortman, B. W. Birren, R. J. Xavier, P. C. Blainey, A. K. Singh, D. Gevers and E. J. Alm. "Mobile Genes in the Human Microbiome Are Structured from Global to Individual Scales." Nature 535, no. 7612 (2016): 435-+.
    • 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) 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.
  • 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.

    • 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.
      • 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
    • 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.