Lye Meng Markillie

Lye Meng Markillie
Staff Member Title: 
Scientist
Contact Email: 
meng.markillie@pnnl.gov
Overview: 

Markillie has more than twenty five years of experience in molecular biology, immunology and protein biochemistry techniques and research, experimental design and implementation, and laboratory management.  Her experience covers a wide array of experimental techniques, independent analyses, and management practices in a number of diverse settings, including industry, university, and national laboratory.

Recently, as part of the Cell Isolation and Systems Analysis (CISA) capability development, Ms. Markillie successfully deployed two massively parallel next-generation sequencing SOLiD™ platforms that support a wide range of applications including whole transcriptome analysis, single-cell transcriptome analysis, gene expression profiling, small RNA analysis, and novel transcript identification as well as genome and epigenome sequencing. She implements and oversees the workflow for sample preparation, library construction and data acquisition on the SOLiD™ platform. Ms. Markillie also supports multiple EMSL user projects in which she facilitates the progression and generation of transcriptomic and genomic data. In addition, she supports the PNNL FSFA project studying the dynamic microbial population in Hot Lake mats and evaluating how autotrophic and heterotrophic microorganisms interact with each other in response to environment perturbations.

Previously, Ms. Markillie managed the OBER project, funded by DOE, that established the cell-free high throughput proteins production capability using wheat germ extract and E. coli extract to express toxic/lethal proteins (to living cells) and proteins that are difficult to clone using traditional techniques. With this new cell-free protein production capability, she assisted the EDRN phase II task to express and purify cancer related proteins both in eukaryotic and prokaryotic systems. She also initiated the DOE-funded GTL phase I task to implement and oversee the workflow of cloning high-priority proteins and purifying recombinant proteins for complex protein isolation. Ms. Markillie manages the BSL2 virus laboratory that utilizes retrovirus, lentivirus and adenovirus systems to express and silence genes of interest in mammalian cell systems. In addition, Ms. Markillie mentors undergraduate and graduate student interns in fulfillment of the laboratory’s mission to educate future scientists and engineers of the nation.

History—Research Associate, School of Medicine, University of California, San Diego, La Jolla, CA, 1990-1991; Research Associate, Committee of Vascular Biology, The Scripps Research Institute, La Jolla, CA, 1991-1992; Associate Scientist, Corvas International, Inc., La Jolla, CA, 1992-1993; Scientist, Washington State University, Department of Microbiology, 1994-1997; Research Scientist, PNNL, 1997-present.

Publications—Markillie has authored or co-authored more than 30 peer-reviewed scientific journal publications and two invention reports.

Professional Societies/Service—Member of the American Society for Microbiology.

Education: 

B.S., Microbiology, Washington State University, Pullman, WA, 1990

Capabilities: 
Cell Isolation and Systems Analysis
Key Research Areas: 
molecular biology
immunology and protein biochemistry

Publications

2016

  • HC Bernstein, RS McClure, EA Hill, LMeng Markillie, WB Chrisler, MF Romine, JE McDermott, MC Posewitz, DA Bryant, A Konopka, JK Fredrickson, AS Beliaev. 2016. "Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth." mBio 7(4)Article No. e00949-16. 10.1128/mBio.00949-16

2015

  • C Castelle, KC Wrighton, BC Thomas, LA Hug, CT Brown, MJ Wilkins, KR Frischkorn, SG Tringe, A Singh, LMeng Markillie, RC Taylor, KH Williams, JF Banfield. 2015. "Genomic expansion of Domain Archaea highlights roles for organisms from new phyla in anaerobic carbon cycling." Current Biology 25(6)690-701. 10.1016/j.cub.2015.01.014
  • HC Bernstein, MA Charania, RS McClure, NC Sadler, MR Melnicki, EA Hill, LMeng Markillie, CD Nicora, AT Wright, MF Romine, AS Beliaev. 2015. "Multi-omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-mediated H2 production in Cyanothece sp. ATCC 51142." Scientific Reports 5Article No. 16004. 10.1038/srep16004

2014

  • MJ Wilkins, DW Hoyt, MJ Marshall, PA Alderson, AE Plymale, LMeng Markillie, AE Tucker, ED Walter, BE Linggi, A Dohnalkova, RC Taylor. 2014. "CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough." Frontiers in Microbiology 5Article No. 507. 10.3389/fmicb.2014.00507
  • AS Beliaev, MF Romine, M Serres, HC Bernstein, BE Linggi, LMeng Markillie, NG Isern, WB Chrisler, LA Kucek, EA Hill, G Pinchuk, DA Bryant, HS Wiley, JK Fredrickson, A Konopka. 2014. "Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing." The ISME Journal 8(11)2243-2255. 10.1038/ismej.2014.69
  • JM Eraso, LMeng Markillie, HD Mitchell, RC Taylor, G Orr, W Margolin. 2014. "The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli." Journal of Bacteriology 196(11)2053-2066. 10.1128/JB.01370-13
  • M Croken, YF Ma, LMeng Markillie, RC Taylor, G Orr, LM Weiss, K Kim. 2014. "Distinct Strains of Toxoplasma gondii Feature Divergent Transcriptomes Regardless of Developmental Stage." PLoS One 9(11)Article No. e111297. 10.1371/journal.pone.0111297
  • DG Welkie, X Zhang, LMeng Markillie, RC Taylor, G Orr, JM Jacobs, K Bhide, J Thimmapuram, MA Gritsenko, HD Mitchell, RD Smith, LA Sherman. 2014. "Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle." BMC Genomics 15Article No. 1185.

2013

  • KM DeAngelis, D Sharma, R Varney, BA Simmons, NG Isern, LMeng Markillie, CD Nicora, AD Norbeck, RC Taylor, JT Aldrich, EW Robinson. 2013. "Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1." Frontiers in Microbiology 4Article No. 280.
  • RC Taylor, BJM Webb-Robertson, LMeng Markillie, MH Serres, BE Linggi, JT Aldrich, EA Hill, MF Romine, MS Lipton, HS Wiley. 2013. "Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria." Integrative Biology 5(11)1393-1406. 10.1039/C3IB40120K
  • BM Hess, J Xue, LMeng Markillie, RC Taylor, HS Wiley, BK Ahring, BE Linggi. 2013. "Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics." PLoS One 8(6)e66104. 10.1371/journal.pone.0066104
  • T Tomita, DJ Bzik, YF Ma, BA Fox, LMeng Markillie, RC Taylor, K Kim, LM Weiss. 2013. "The Toxoplasma gondii cyst wall protein CST1 is critical for cyst wall integrity and promotes bradyzoite persistence." PLoS Pathogens 9(12)e1003823. 10.1371/journal.ppat.1003823
  • RW Walker, LMeng Markillie, AHA Colotelo, ME Gay, CM Woodley, RS Brown. 2013. "The Efficacy of Ultraviolet Radiation for Sterilizing Tools Used for Surgically Implanting Transmitters into Fish ."
  • RW Walker, LMeng Markillie, AHA Colotelo, DR Geist, ME Gay, CM Woodley, MB Eppard, RS Brown. 2013. "Ultraviolet radiation as disinfection for fish surgical tools." Animal Biotelemetry 1Article No. 4. 10.1186/2050-3385-1-4
  • H Piao, LMeng Markillie, DE Culley, RI Mackie, M Hess. 2013. "Improved Method for Isolation of Microbial RNA from Biofuel Feedstock for Metatranscriptomics." Advances in Microbiology 3(1)101-107. 10.4236/aim.2013.31016
  • ES Suvorova, M Croken, S Kratzer, LM Ting, M Conde de Felipe, B Balu, LMeng Markillie, LM Weiss, K Kim, MW White. 2013. "Discovery of a Splicing Regulator Required for Cell Cycle Progression." PLoS Genetics 9(2)Article No. e1003305. 10.1371/journal.pgen.1003305

2012

  • F Yang, KM Waters, BJM Webb-Robertson, MB Sowa, CH Freiin von Neubeck, JT Aldrich, LMeng Markillie, RM Wirgau, MA Gristenko, R Zhao, DG Camp, RD Smith, DL Stenoien. 2012. "Quantitative Phosphoproteomics Identifies Filaggrin and other Targets of Ionizing Radiation in a Human Skin Model." Experimental Dermatology 21(5)352–357. 10.1111/j.1600-0625.2012.01470.x

2011

  • G Orr, WB Chrisler, KJ Cassens, R Tan, BJ Tarasevich, LMeng Markillie, RC Zangar, BD Thrall. 2011. "Cellular Recognition and Trafficking of Amorphous Silica Nanoparticles by Macrophage Scavenger Receptor A." Nanotoxicology 5(3)296-311. 10.3109/17435390.2010.513836
  • PP Labaj, GG Leparc, BE Linggi, LMeng Markillie, HS Wiley, DP Kreil. 2011. "Characterization and Improvement of RNA-Seq Precision in Quantitative Transcript Expression Profiling." Bioinformatics 27(13)I383-I391. 10.1093/bioinformatics/btr247
  • RC Zangar, N Bollinger, TJ Weber, R Tan, LMeng Markillie, NJ Karin. 2011. "Reactive Oxygen Species Alter Autocrine and Paracrine Signaling." Free Radical Biology & Medicine 51(11)2041-2047. 10.1016/j.freeradbiomed.2011.09.001

2007

  • B Chen, LMeng Markillie, Y Xiong, MUljana Mayer, TC Squier. 2007. "Increased Catalytic Efficiency Following Gene Fusion of Bifunctional Methionine Sulfoxide Reductase Enzymes from Shewanella oneidensis." Biochemistry 46(49)14153-14161. 10.1021/bi701151t

2006

  • TJ Weber, HS Smallwood, LE Kathmann, LMeng Markillie, TC Squier, BD Thrall. 2006. "Functional link between TNF biosynthesis and CaM-dependent activation of inducible nitric oxide synthase in RAW 264.7 macrophages ." American Journal of Physiology. Cell Physiology 290(6)C1512-C1520. 10.1152/ajpcell.00527.2005
  • Y Xiong, B Chen, HS Smallwood, RJ Urbauer, LMeng Markillie, NA Galeva, TD Williams, TC Squier. 2006. " High-Affinity and Cooperative Binding of Oxidized Calmodulin by Methionine Sulfoxide Reductase." Biochemistry 45(49)14642-14654. 10.1021/bi0612465

2005

  • LMeng Markillie, CTso Lin, JN Adkins, DL Auberry, EA Hill, BS Hooker, PA Moore, RJ Moore, L Shi, HS Wiley, V Kery. 2005. "Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks." Journal of Proteome Research 4(2)268-274. 10.1021/pr049847a
  • L Shi, CTso Lin, LMeng Markillie, TC Squier, BS Hooker. 2005. "Over-expression of Multi-heme C-type Cytochromes." BioTechniques 38(2)297-299.
  • TJ Weber, RW Siegel, LM Markillie, WB Chrisler, XC Lei, NH Colburn. 2005. "A paracrine signal mediates the cell transformation response to low dose gamma radiation in JB6 cells ." Molecular Carcinogenesis 43(1)31-37.
  • B Chen, MUljana Mayer, LMeng Markillie, DL Stenoien, TC Squier. 2005. "Dynamic Motion of Helix A in the Amino-terminal Domain of Calmodulin is Stabilized Upon Calcium Activation." Biochemistry 44(3)905-914.
  • B Chen, MUljana Mayer, LMeng Markillie, DL Stenoien, TC Squier. 2005. "Dynamic Motion of Helix A in the Amino-terminal Domain of Calmodulin is Stabilized Upon Calcium Activation." Biochemistry 44905-914.
  • NA Galeva, SW Esch, TD Williams, LMeng Markillie, TC Squier. 2005. "Rapid Method for Quantifying the Extent of Methionine Oxidation in Intact Calmodulin." Journal of the American Society for Mass Spectrometry 16(9)1470-80.

2004

  • M Jasionowski, KJ Krzyminski, WB Chrisler, LMeng Markillie, JE Morris, A Gutowska. 2004. "Thermally-reversible gels for 3D cell culture of chondrocytes." Journal of Materials Science. Materials in Medicine 15(5)575-582.

2003

  • TJ Weber, LMeng Markillie. 2003. "Regulation of Activator Protein-1 by 8-iso-Prostaglandin E2 in a Thromboxane A2 Receptor-Dependent and -Independent Manner ." Molecular Pharmacology 63(5)1075-81.
  • TJ Weber, LMeng Markillie. 2003. "Regulation of activator protein-1 by 8-iso-prostaglandin E2 in a thromboxane A2 receptor-dependent and -independent manner." Molecular Pharmacology 63(5)1075-1081.

2002

  • MS Lipton, L Pasa-Tolic, GA Anderson, DJ Anderson, DL Auberry, JR Battista, MJ Daly, JK Fredrickson, KK Hixson, HM Kostandarithes, CD Masselon, LMeng Markillie, RJ Moore, MF Romine, Y Shen, EF Strittmatter, N Tolic, HR Udseth, A Venkateswaran, KK Wong, R Zhao, RD Smith. 2002. "Global Analysis of Deinococcus Radiodurans Proteome by Csing Accurate Mass Tags." Proceedings of the National Academy of Sciences of the United States of America 99(17)11049-11054.
  • TJ Weber, LMeng Markillie, WB Chrisler, GA Vielhauer, JW Regan. 2002. "Modulation of JB6 Mouse Epidermal Cell Transformation Response by the Prostaglandin F2 Alpha Receptor." Molecular Carcinogenesis 35(4)163-172.
  • TJ Weber, LMeng Markillie, WB Chrisler, GA Vielhauer, JW Regan. 2002. "Modulation of JB6 Mouse Epidermal Cell Transformation Response by the Prostaglandin F2 alpha Receptor." Molecular Carcinogenesis 35(4)163-172.

1999

  • LMeng Markillie, SM Varnum, PB Hradecky, KK Wong. 1999. "Targeted mutagenesis by duplication insertion in the radioresistant bacterium Deinococcus radiodurans: radiation sensitivities of catalase (katA) and superoxide dismutase (sodA) mutants.." Journal of Bacteriology 181(2)666-669.