Director of Biological and Engineering Sciences
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.
Singh's 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.
Sandia is involved in developing innovative microfluidic assays and integrated devices for many applications including:
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 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.
- 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.
Nature abounds with intricate composite architectures composed of hard and soft materials synergistically intertwined to provide both useful functionality and mechanical integrity. Recent synthetic efforts to mimic such natural designs have focused on nanocomposites. In this area we have investigated the mechanically responsive behavior of polydiacetylene films and have developed novel functionalized diacetylene amphiphiles that self-assemble into hexagonal, cubic, or lamellar structures in silica sol-gel materials. The resultant conjugated polymer/silica nanocomposite films offer unique insights into the interplay between the dynamic organic structural agents and the static inorganic scaffold that they organize. For example, one of our nanocomposite materials exhibits unique thermal-, mechano-, and solvato-chromic properties resulting in rapid and reversible optical behavior previously unreported for polydiacetylene materials.
- “Polydiacetylene Films: A Review of Recent Investigations into Chromogenic Transitions and Nanomechanical Properties” R. W. Carpick, D. Y. Sasaki, M. S. Marcus, M. A. Ericksson, A. R. Burns, J. Phys.: Cond. Matt. 2004, 16, R679 – R697.
- “Functional Nanocomposites Prepared by Self-Assembly and Polymerization of Diacetylene Surfactants and Silicic Acid” Yang, Y., Y. Lu, M. Lu, J. Huang, R. Haddad, G. Xomeritakis, N. Liu, A. P. Malanoski, D. Sturmayr, H. Fan, D. Y. Sasaki, R. A. Assink, J. A. Shelnutt, F. v. Swol, G. P. Lopez, A. R. Burns, and C. J. Brinker. J. Am. Chem. Soc. 2003,125(5),1269 - 1277.
- “Self-assembly of mesoscopically ordered chromatic polydiacetylene/silica nanocomposites” Yunfeng Lu, Yi Yang, Alan Sellinger, Mengcheng Lu, Jinman Huang, Hongyou Fan, Raid Haddad, Gabriel Lopez, Alan R. Burns, Darryl Y. Sasaki, John Shelnutt, C. Jeffrey Brinker, Nature 2001, 410, 913 – 917.
- “High Molecular Orientation in Mono- and Trilayer Polydiacetylene Films Imaged by Atomic Force Microscopy” Darryl Y. Sasaki, Robert W. Carpick, Alan R. Burns, J. Coll. Interface Sci. 2000, 229, 490.