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Bioenergy & Defense

Jerilyn A. Timlin, Ph.D.

Photo of Jeri Timlin

Distinguished Member of the Technical Staff
Bioenergy and Defense Technologies Department

(505) 844-7932

Research Interests

Optical microscopy, spectroscopy, and spectral imaging (including fluorescence, Raman, and Fourier transform infrared [FTIR]), high-throughput imaging, superresolution techniques, multiplexed microscopy, multivariate image analysis, image preprocessing, spectral unmixing, and multivariate classification for applications in the early detection of disease/damage, immune response, signal transduction, energy transfer in photosynthetic pigments, and biomarker discovery.

Research Summary

My research focuses on developing and applying novel analytical-imaging and multivariate-analysis tools to elucidate complex spatial-temporal relationships of a variety of biomolecules that drive key biological processes. The work in our lab crosses traditional boundaries of chemistry, physics, and biology and often covers multiple spatial scales from single molecules on up to single cells, communities, and tissues. A main component of our work is spectral imaging - a method whereby spectrally resolved information is obtained at every two-dimensional pixel or three dimensional voxel. I have been developing and applying various spectral imaging technologies (also called chemical imaging) since my graduate work which pioneered the use of hyperspectral Raman microscopy with near-infrared excitation to elucidate the dynamic chemical composition of bone without the use of labels. Most recently, my group has employed both hyperspectral Raman and fluorescence microscopy to a variety of applications looking at single molecules to intact tissue, including the visualization of subcellular pigment distribution in photosynthetic organisms such as cyanobacteria and green algae (Figure 1).

The addition of a spectral dimension can result in a three-, four-, or five-dimension image data set (2-3 spatial, 1 spectral, and 1 temporal) that is beyond human visualization capabilities. For this reason we utilize sophisticated multivariate analysis tools to mathematically extract the underlying spectral signatures and create quantitative spatial-temporal profiles of biomolecules.

In keeping with the multicolor theme, our lab has developed multi-color, optical super resolution capabilities. Building from our unique capabilities in dual-color, video rate, total internal reflection fluorescence (TIRF) microscopy, we have constructed a simultaneous, dual-color single molecule, stochastic optical super-resolution (STORM) microscope. With spatial resolutions approaching those of electron microscopy (~30-40 nm), this technology is opening our eyes to a variety of biological processes never before seen. For example, Figure 2 highlights receptor reorganization at the membrane during immune response.

Figure 1: Hyperspectral confocal Raman image of carotenoids and chlorophyll in living Haematococcus pluvialis cells. Upper panel: component spectra. Lower panel: pigment localization, pseudo-colored corresponding to spectra in upper panel. Figure generated by Aaron Collins in collaboration with Thomas Beechem, and Howland Jones at SNL and Dr. Qiang Hu's group at ASU.

Figure 2: Nanoscale organization of Toll-like Receptor 4 (TLR4) and E. coli lipopolysaccharide (LPS) at the plasma membrane of mouse macrophage cells as visualized with simultaneous, dual-color stochastic optical reconstruction microscopy (STORM). Figure generated by Jesse Aaron, work in collaboration wtih Bryan Carson at SNL.

Our work interfaces analytical chemistry and optical physics with molecular and cellular biology and has direct impact on human health, plant science, and renewable energy research. We work collaboratively with researchers from different scientific disciplines to tackle complex bioscience problems.

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Select Research Projects

Multiplexed Measurements of Protein Dynamics and Interactions at Extreme Resolutions

This project was funded under the National Institutes of Health (NIH) Director’s New Innovator Award in 2009. When successful, this project will provide an unprecedented view of protein interactions in the living cell through the development of novel spectrally resolved superresolution microscopy methods.

Analyzing and Understanding of Transporters to Control Lignin Transformation into Fuel

The overall goal of this project is to understand the fundamental relationships that govern lignin transport in order to control transport in a way that will provide an increase in the range and kinetics of transport into cells. We will develop analytical tools for assessing lignin uptake and kinetics in bulk and at the single cell/single molecule level. Combining experimental measurements with computational modeling, we hope to identify the types of transporters are active on lignin and their substrate specificity as well the kinetics of lignin transport in natural and engineered hosts.

Photosynthetic Antennae Research Center (PARC)

PARC is one of 46 Energy Frontier Research Centers (EFRCs) established nationally at universities, national laboratories, nonprofit organizations, and private firms by the U.S. Department of Energy’s Office of Science. A multi-institutional collaboration, PARC seeks to understand the basic scientific principles that underpin the efficient functioning of natural photosynthetic antenna systems. These principles will then be used as a basis for man-made systems to convert sunlight into fuels. Our specific work within PARC will use advanced spectral imaging and analysis methodologies to isolate fluorescent signatures from natural and bio-inspired photosynthetic pigments to increase our understanding of the spatial distribution and abundance of these critical components in the energy transfer cascade.

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Book Chapters

  • Timlin, JA, Collins, AM, Shumskaya, M, Wurtzel, ET, Beechem, TA, “Localizing and Quantifying Carotenoids in Intact Cells and Tissues” in Carotenoids. Cvetkovic, D and Nikolic, G. In Tech, 2017, in press.
  • Anthony S, Carroll-Portillo A and Timlin JA, "Dynamics and interactions of individual proteins in the membrane of single, living cells " in Single Cell Protein Analysis. Singh, AK and Chandrasekaran, A, editor(s). Springer New York: 2015, 185-207.
  • Chen W, Han D, Li Y, Jones HDT, Timlin JA, Hu Q, Semi-Quantitative and Absolute Quantitative Analyses of Biochemical Composition of Microalgae. In Handbook of Microalgal Cultures - Second Edition. Hu R, (Ed.), Wiley-Blackwell, 2013.
  • Aaron JS and Timlin JA “Advanced Optical Imaging of Endocytosis,” in Molecular Recognition of Endocytosis, B. Ceresa (Ed.), InTech, 2012.
  • Timlin JA, "Scanning microarrays: Current methods and future directions," In DNA Microarrays, Part B: Databases and Statistics. Kimmel A, Oliver B, editors. Academic Press: New York, 2006: 79-98.
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    Select Publications

    2014 – present
    2011 – 2013

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    2008 –2010

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    2004 – 2007

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    1999 – 2003


    2002 PostDoc, Analytical Chemistry, Sandia National Labs, Albuquerque, NM
    2000 PhD, Analytical Chemistry, University of Michigan, Ann Arbor, MI
    1995 BS, Chemical Engineering, Geneva College, Beaver Falls, PA

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    Postdoctoral Appointees Working in the Timlin Group

    Meghan Dailey
    Postdoctoral Apppointee

    Meghan received her B.S. in Biochemistry from the University of New Mexico in 2008. She attended the University of Virginia for her doctoral studies where she received her Master's and Ph.D. in Biochemistry and Molecular Genetics in 2010 and 2014, respectively. She did her thesis research in Dan Foltz's lab (now at Northwestern University) studying centromeric chromatin establishment and maintenance. She was the recipient of an NIH Molecular Biology Training Grant and UVA Farrow Fellowship, supporting her salary for the first 4 years of her doctoral studies. Upon completion of her doctoral work, she continued in the Foltz lab for 2 years as a post-doctoral fellow studying the role of the Condensin II complex on centromeric chromatin establishment. She then moved to Sandia National Laboratories in 2016 to finish her post-doctoral training under Jeri Timlin in the Biofuel and Biodefense Systems department. She is currently studying lignin transport in biofuel-relevant organisms using LC/MS, super-resolution, confocal, and TIRF microscopy as her primary project. She also performs hyperspectral imaging studies of mammalian, algal, and cyanobacterial cells, with applications ranging from photosynthetic pigment studies to TB drug compound testing. She and her husband enjoy time hiking and running in the sunny New Mexico weather and are looking forward to the arrival of their first baby in April 2017.


    Lateral segregation of photosystem I in cyanobacterial thylakoids.
    Craig MacGregor-Chatwin, Melih Sener, Samuel Barnett, Andrew Hitchcock, Meghan Barnhart-Dailey, Karim Maghlaoui, James Barber, Jerilyn Timlin, Klaus Schulten, and Christopher Hunter.
    The Plant Cell. 2017, In press.

    HJURP interaction with the condensin II complex during G1 promotes CENP-A deposition.
    Barnhart-Dailey MC, Trivedi P, Stukenberg PT, Foltz DR.
    Mol Biol Cell. 2017 Jan 1;28(1):54-64. doi: 10.1091/mbc.E15-12-0843.

    Centromere licensing: Mis18 is required to Polo-ver.
    Barnhart-Dailey MC, Foltz DR.
    Curr Biol. 2014 Sep 8;24(17):R808-10. doi: 10.1016/j.cub.2014.07.026.

    Dimerization of the CENP-A assembly factor HJURP is required for centromeric nucleosome deposition.
    Zasadzinska E, Barnhart-Dailey MC, Kuich PH, Foltz DR.
    EMBO J. 2013 Jul 31;32(15):2113-24. doi: 10.1038/emboj.2013.142.

    HJURP uses distinct CENP-A surfaces to recognize and to stabilize CENP-A/histone H4 for centromere assembly.
    Bassett EA, DeNizio J, Barnhart-Dailey MC, Panchenko T, Sekulic N, Rogers DJ, Foltz DR, Black BE.
    Dev Cell. 2012 Apr 17;22(4):749-62. doi: 10.1016/j.devcel.2012.02.001.

    HJURP is a CENP-A chromatin assembly factor sufficient to form a functional de novo kinetochore.
    Barnhart MC1, Kuich PH, Stellfox ME, Ward JA, Bassett EA, Black BE, Foltz DR .
    J Cell Biol. 2011 Jul 25;194(2):229-43. doi: 10.1083/jcb.201012017. Epub 2011 Jul 18.

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