Contact information Lawrence Livermore National Laboratory 7000 East Avenue, L-452 Livermore, CA 94550 Email: jiao1@llnl.gov Phone: 925-422-4482

Education

Ph.D.   California Institute of Technology, 2007, Geobiology
B.S.      University of Science and Technology of China, 2001, Geophysics

Awards

• Global Security Gold Award, Lawrence Livermore National Laboratory, 2018
• Laboratory’s Early and Mid-Career Recognition Program, Lawrence Livermore National Laboratory, 2017
• DOE Early Career Research Award, “Systems Level Investigation of Uranium Resistance andRegulation by Caulobacter Crescentus”, 2011
• Student and Postdoctoral Travel Grants, American Society for Microbiology, 2006.
• Li Ming Scholarship, California Institute of Technology, 2006.

Research

My research interest lies in the interface of environmental microbiology and geochemistry, focusing on the systems biology-enabled biosystems design of microbes for clean energy and environment.  I joined LLNL as a postdoc in 2007 after completing a PhD in Geobiology from Caltech.  I use systems biology tools to examine how microbes sense, respond and adapt to environmental cues, and discover foundational design rules that govern the complex biological systems behaviors.  I use synthetic biology tools for rational re-design of organisms with desired traits for environmental applications for clean energy and environment.  I am the lead PI on several DOE funded projects focusing on systems and synthetic biology studies of environmental microorganisms for environmental and energy applications.   A few examples include:  

• Bioengineering of microbial surface display of rare earth binding ligands with environmental microbes to enable biomass-based column purification for rare earth metal recovery from low grade sources.  
• Bioengineering of cement-curing bacteria and interface design of microbe-material interactions for biomineralization and biocement production
• Systems biology studies of microbial stress response and metal sensing in Caulobacter for uranium bioremediation

Expertise include Synthetic biology, Systems biology, Biogeochemistry, Microbiology, Biochemistry, and Electron microscopy.

Publications

1. Chang E., Brewer A., Park, D.M., Jiao, Y., Lammers L.N. (2020), “Surface complexation model of rare earth element adsorption onto bacterial surfaces with lanthanide binding tags” Applied Chemistry, Vol 112:10448. Doi: 10.1016/j.apgeochem.2019.104478
2. Brewer, A., Dohnalkova A, Shutthanandan V, Kovarik L, Chang E, Sawvel A.M., Mason H.E., Reed D, Ye C., Hynes W.F., Lammers LN, Park D.M., Jiao Y. (2019) “Microbe Encapsulation for Selective Rare-Earth Recovery from Electronic Waste Leachates”. Environ Sci Technol, 53(23): p. 13888-13897. doi: 10.1021/acs.est.9b04608.
3. Antonick, P. J.;  Hu, Z. C.;  Fujita, Y.;  Reed, D. W.;  Das, G.;  Wu, L. L.;  Shivaramaiah, R.;  Kim, P.;  Eslamimanesh, A.;  Lencka, M. M.;  Jiao, Y.;  Anderko, A.;  Navrotsky, A.; Riman, R. E., Bio- and mineral acid leaching of rare earth elements from synthetic phosphogypsum Paul. J Chem Thermodyn 2019, 132, 491-496.
4. Navid A, Jiao Y, Wong SE, Pett-Ridge J., System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris, BMC Bioinformatics. 2019 May 9;20(1):233. doi: 10.1186/s12859-019-2844-z
5. Brewer A, Chang E, Park DM, Kou T, Li Y, Lammers LN, Jiao Y., Recovery of Rare Earth Elements from Geothermal Fluids through Bacterial Cell Surface Adsorption, Environ Sci Technol. 2019 Jul 2;53(13):7714-7723. doi: 10.1021/acs.est.9b00301
6. Park DM, Overton KW, Jiao Y., The UzcRS two-component system in Caulobacter crescentus integrates regulatory input from diverse auxiliary regulators. Mol Microbiol. 2019 Mar;111(3):678-699. doi: 10.1111/mmi.14180
7. Jin H, Reed DW, Thompson VS, Fujita Y, Jiao Y, Grain-Zamora M, Fisher J, Scalzone K, Griffel M, Hartley D, Sutherland JW. Sustainable Bioleaching of Rare Earth Elements from Industrial Waste Materials Using Agricultural Wastes, ACS Sustainable Chem. Eng. 2019, DOI: 10.1021/acssuschemeng.9b02584
8. Morrison, K., Jiao, Y., Kersting, A. and Zavarin, M., Reduction of Plutonium(VI) to (V) by Hydroxamate Compounds at Environmentally Relevant pH.  Environ. Sci. Technol., 2018, 52 (11), pp 6448–6456. DOI: 10.1021/acs.est.8b00164
9. Thompson, V., Gupta, M., Jin, H., Vahidi, E., Jindra, M., Nguyen, V., Fujita, Y., Sutherland, J., Jiao, Y. and Reed, D. (2018) Techno-Economic and Life Cycle Analysis for Bioleaching Rare Earth Elements from Waste Materials.  ACS Sustainable Chem. Eng., 2018, 6 (2), pp 1602–1609.  DOI: 10.1021/acssuschemeng.7b02771
10. Park, D. M., Overton, K. W., Liou, M. and Y. Jiao (2017) Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus.  Molecular Microbiology. 104(1), 46–64. doi:10.1111/mmi.13615
11. Park, D. M.; Brewer, A.; Reed, D. W.; Lammers, L. N.; Jiao, Y.  (2017) Recovery of Rare Earth Elements from Low-Grade Feedstock Leachates Using Engineered Bacteria. Environ. Sci. Technol., 51 (22), pp 13471–13480.  DOI: 10.1021/acs.est.7b02414
12. Jin, H.; Park, D. M.; Gupta, M.; Brewer, A. W.; Ho, L.; Singer, S. L.; Bourcier, W. L.; Woods, S.; Reed, D. W.; Lammers, L. N.; Sutherland, J. W.; Jiao, Y. (2017) Techno-economic Assessment for Integrating Biosorption into Rare Earth Recovery Process. ACS Sustainable Chem. Eng., 2017, 5 (11), pp 10148–10155.  DOI: 10.1021/acssuschemeng.7b02147
13. Overton KW, Park DM, Yung MC, Smit J, Jiao Y (2016), Two outer membrane proteins contribute to cellular fitness in Caulobacter crescentus by preventing intracellular S-layer protein accumulation.  Appl Environ Microbiol 82 (23):6961-72. doi:10.1128/AEM.02479-16.
14. Reed, D. W.; Fujita, Y.; Daubaras, D. L.; Jiao, Y.; Thompson, V. S. (2016) Bioleaching of Rare Earth Elements from Waste Phosphors and Cracking Catalysts. Hydrometallurgy 166, 34–40. DOI: 10.1016/j.hydromet.2016.08.006
15. Joseph, C., Mibus, J., Trepte, P., Müller, C., Brendler, V., Park, D. M., Jiao, Y., Kersting, A. B. and Zavarin, M. (2016) Long-term diffusion of U(VI) in bentonite: Dependence on density. Sci. Total Environ. 575, 207-218.
16. Reed, D.W., Y. Fujita, D.L. Daubaras, D.F. Bruhn, J.H. Reiss, V.S. Thompson and Y. Jiao. (2016) Microbially Mediated Leaching of Rare Earth Elements from Recyclable Materials. Proc XXVIII Int Min Proc Congr, 2016, ISBN: 978-1-926872-29-2
17. Park D. M., Reed D. W., Yung M. C., Eslamimanesh A., Lencka M. M., Anderko A., Fujita Y., Riman R. E., Navrotsky A. and Y. Jiao (2016) Bioadsorption of rare earth elements through cell surface display of lanthanide binding tags. Environ. Sci. Technol., 50 (5), pp 2735–2742. DOI: 10.1021/acs.est.5b06129
18. Boggs, M. A. Jiao, Y. Dai, Z. Zavarin, M. Kersting, A. B. (2016). "Interactions of Plutonium with Pseudomonas sp. Strain EPS-1W and Its Extracellular Polymeric Substances." Appl Environ Microbiol 82(24): 7093-7101
19. Yung, M. C., Park, D. M., Overton, K. W., Blow, M. J., Hoover, C. A., Smit, J., Murray, S. R., Ricci, D. P., Christen, B., Bowman, G. R., & Jiao, Y. (2015) Transposon mutagenesis paired with deep sequencing of Caulobacter crescentus under uranium stress reveals genes essential for detoxification and stress tolerance. J. Bacteriol. 197, 3160-72. doi: 10.1128/JB.00382-15
20. Park, D. M. and Y. Jiao (2014). "Modulation of medium pH by Caulobacter crescentus facilitates recovery from uranium-induced growth arrest." Applied and Environmental Microbiology 80(18): 5680-5688. DOI: 10.1128/AEM.01294-14.
21. Yung, M. C. and Y. Jiao (2014). "Biomineralization of uranium by PhoY phosphatase activity aids cell survival in Caulobacter crescentus." Applied and Environmental Microbiology 80(16): 4795-4804. DOI:10.1128/AEM.01050-14 
22. Yung, M.C., Ma, M. R. Salemi, B. S. Phinney, G. R. Bowman, and Y. Jiao. (2014) “Shotgun proteomic analysis unveils survival and detoxification strategies by Caulobacter crescentus during exposure to uranium, chromium, and cadmium”. J Proteome Res. 13(4): 1833-1847. DOI: 10.1021/pr400880s
23. Wang, H., F. Qian, G. Wang, Y. Jiao, Z. He and Y. Li (2013) “Self-biased solar-microbial device for sustainable hydrogen generation.” ACS Nano 7(10):8728-8735. DOI: 10.1021/nn403082m
24. Jiao Y., A. Navid, B.J. Stewart, J.B. McKinlay, M. Thelen and J. Pett-Ridge. “Syntrophic metabolism of a co-culture containing Clostridium cellulolyticum with Rhodopseudomonas palustris on cellulose”.  International Journal of Hydrogen Energy, 37: 11719-726 (2012). DOI: 10.1016/j.ijhydene.2012.05.100
25. Jiao, Y., F. Qian, Y. Li, G. Wang, C.W. Saltikov, J.A. Granick, “Deciphering the electron transport pathway for graphene oxide reduction by Shewanella oneidensis MR-1”, Journal of Bacteriology, 193(14): 3662-3665 (2011). DOI: 10.1128/​JB.00201-11
26. Jiao, Y., P. D'haeseleer, B.D. Dill, M. Shah, N.C. Verberkmoes, R.L. Hettich, J.F. Banfield, M.P. Thelen, “Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community.” Applied and Environmental Microbiology, 77(15): 5230-5237 (2011). DOI: 10.1128/​AEM.03005-10
27. Wang, G., F. Qian, C.W. Saltikov, Y. Jiao, Y. Li, “Microbial reduction of graphene oxide by Shewanella”, Nano Research, pp. 1-8, (2011). DOI: 10.1007/s12274-011-0112-2
28. Wheeler, K.E., A. Zemla, Y. Jiao, D.S. Goltsman, S.W. Singer, J.F. Banfield and M.P. Thelen “Functional insights from Computational Modeling of Orphan Proteins Expressed in a Microbial Community.” Journal of Proteomics & Bioinformatics, 3: 266-274 (2010).  DOI:10.4172/jpb.1000150
29. Jiao, Y., G.D. Cody, A.K. Harding, P. Wilmes, M. Schrenk, K.E. Wheeler, J.F. Banfield, M.P. Thelen, “Characterization of extracellular polymeric substances from acidophilic microbial biofilms.” Applied and Environmental Microbiology, 76: 2916-2922 (2010). DOI: 10.1128/​AEM.02289-09
30. Jiao, Y.*, L.R. Croal*, A. Kappler, D.K. Newman, “Phototrophic Fe(II) oxidation in an atmosphere of H₂: implications for Archean banded iron formations”, *co-first authors. Geobiology, 7 (1): 21-4 (2009). DOI: 10.1111/j.1472-4669.2008.00185.x
31. Jiao, Y., D.K. Newman “The pio operon is essential for phototrophic Fe(II) oxidation in Rhodopseudomonas palustris TIE-1”, Journal of Bacteriology, 189 (5): 1765-1773 (2006). DOI: 10.1128/​JB.00776-06  
32. Croal, L.R., Y. Jiao, D.K. Newman, “The fox Operon from Rhodobacter Strain SW2 Promotes Phototrophic Fe(II) Oxidation in Rhodobacter capsulatus SB1003”, Journal of Bacteriology, 189 (5): 1774-1782 (2006). DOI: 10.1128/JB.01395-06
33. Jiao, Y., A.K. Kappler, L.R. Croal, D.K. Newman, “Isolation and Characterization of a Genetically Tractable Photoautotrophic Fe(II)-Oxidizing Bacterium, Rhodopseudomonas palustris Strain TIE-1.  Applied and Environmental Microbiology 71: 4487-4496 (2005). DOI: 10.1128/​AEM.71.8.4487-4496.2005

 

Contact information Lawrence Livermore National Laboratory 7000 East Avenue, L-367 Livermore, CA 94550 email: dhaeseleer2@llnl.gov phone: 925 422 9717

Education

Post-doctoral researcher, Harvard Medical School, 2001-2004

Ph.D. in Computer Science, University of New Mexico, 2000

M.S. in Computer Science, Stanford University, 1993

M.S. in Electrical Engineering, Ghent University, Belgium, 1991

M.E. in Electrical Engineering, KIHO, Belgium, 1988

Research

My research focuses on systems biology of bacterial pathogens, and the study of microbial communities through metagenomics and other meta-omics data. Systems biology attempts to achieve a whole-system understanding of an organism, rather than focusing on a single gene at a time. I enjoy highly interdisciplinary research, working closely with experimental biologists, and linking them to computational analyses. After hours, I am involved in the local citizen science and DIYbio community, acting as the community projects coordinator at BioCurious in Sunnyvale, and  co-founder and chair of Counter Culture Labs in the East Bay.

Selected Publications

Griesemer M, Kimbrel J, Zhou CE, Navid A, D'haeseleer P. (2018) Combining multiple functional annotation tools increases coverage of metabolic annotation. BMC Genomics 19:948

Franco M, D'haeseleer PM, Branda SS, Liou MJ, Haider Y, Segelke BW, El-Etr SH. (2018) Proteomic Profiling of Burkholderia thailandensis During Host Infection Using Bio-Orthogonal Noncanonical Amino Acid Tagging (BONCAT). Front Cell Infect Microbiol. 8:370.

D'haeseleer P, Lee JZ, Prufert-Bebout L, Burow LC, Detweiler AM, Weber PK, Karaoz U, Brodie EL, Glavina Del Rio T, Tringe SG, Bebout BM, Pett-Ridge J. (2017) Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate. Stand Genomic Sci. 12:67.

D'haeseleer P, Johnson SL, Davenport KW, Chain PS, Schoeniger J, Ray D, Sinha A, Williams KP, Peña J, Branda SS, El-Etr S. (2016) Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6. Genome Announc. 4(3). pii: e00649-16.

Simmons CW, Reddy AP, D'haeseleer P, Khudyakov J, Billis K, Pati A, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS. . (2014) Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnol Biofuels 7(1):495.

Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S. (2014) Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol 9(9):2082-91.

Gladden JM, Park JI, Bergmann J, Reyes-Ortiz V, D'haeseleer P, Quirino BF, Sale KL, Simmons BA, Singer SW. (2014) Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community. Biotechnol Biofuels 7(1):15.

Bergmann J, Costa OY, Gladden J, Singer S, Heins R, D´haeseleer P, Simmons B, Quirino B (2014) Discovery of two novel β-glucosidases from an Amazon soil metagenomic library. FEMS Microbiol Lett. 351(2):147-55. .

Reddy AP, Simmons CW, D'haeseleer P, Khudyakov J, Burd H, Hadi M, Simmons BA, Singer SW, Thelen MP, Vandergheynst JS. (2013) Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses. PLoS One 8(10):e77985.

D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolić L, Hugenholtz P, Simmons BA, Singer SW. (2013) Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. PLoS One. 8(7):e68465.

McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, D'haeseleer P, Northen T, Sale KL, Simmons BA, Adams PD. (2013) From soil to structure, a novel dimeric β-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis. J Biol Chem. 288(21):14985-92.

Chaudhury S, Abdulhameed MD, Singh N, Tawa GJ, D'haeseleer PM, Zemla AT, Navid A, Zhou CE, Franklin MC, Cheung J, Rudolph MJ, Love J, Graf JF, Rozak DA, Dankmeyer JL, Amemiya K, Daefler S, Wallqvist A. (2013) Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PLoS One. 2013 May 21;8(5):e63369

Deangelis KM, D'Haeseleer P, Chivian D, Simmons B, Arkin AP, Mavromatis K, Malfatti S, Tringe S, Hazen TC. (2013) Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. Stand Genomic Sci. 2013 Feb 25;7(3):382-98

Khudyakov JI, D'haeseleer P, Borglin SE, Deangelis KM, Woo H, Lindquist EA, Hazen TC, Simmons BA, Thelen MP. (2012) Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. Proc Natl Acad Sci U S A. 109(32):E2173-82.

Dougherty MJ, D'haeseleer P, Hazen TC, Simmons BA, Adams PD, Hadi MZ. (2012) Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization. BMC Biotechnol. 12:38.

Borglin S, Joyner D, DeAngelis KM, Khudyakov J, D'haeseleer P, Joachimiak MP, Hazen T. (2012) Application of phenotypic microarrays to environmental microbiology. Current opinion in biotechnology. 23(1):41-8

Lu Z, Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A, Lee YJ, Mason OU, Dubinsky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D'haeseleer P, Hazen TC, Zhou J. (2012) Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J. 6(2):451-60.

Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, Batth T, Benke PI, D'haeseleer P, Sun N, Sale KL, Keasling JD, Lee TS, Petzold CJ, Mukhopadhyay A, Singer SW, Simmons BA, Gladden JM. (2012) A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. PLoS One. 7(5):e37010.

Jiao Y, D'haeseleer P, Dill BD, Shah M, Verberkmoes NC, Hettich RL, Banfield JF, Thelen MP. (2011) Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community. Appl Environ Microbiol. 77(15):5230-7.

Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU. (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science. 330(6001):204-8.

Allgaier M, Reddy A, Park JI, Ivanova N, D'haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS, Hugenholtz P. (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One. 5(1):e8812

DeAngelis, KM, JG Gladden, M Allgaier, P D’haeseleer, JL Fortney, A Reddy, P Hugenholtz, S Singer, J Van Der Gheynst, WL Silver, B Simmons, and TC Hazen. (2010) Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities. BioEnergy Research 3:146-158.

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 462(7276):1056-60.

Tamura, M. and D’haeseleer, P. (2008) Microbial genotype-phenotype mapping by class association rule mining. Bioinformatics. 24(13):1523-9.

D'haeseleer, P. (2006) How does DNA sequence motif discovery work? Nat Biotechnol. 24(8):959-61.

D'haeseleer P. (2006) What are DNA sequence motifs? Nat Biotechnol. 24(4):423-5.

Nguyen, D. and D'haeseleer, P. (2006) Deciphering Principles of Transcription Regulation in Eukaryotic Genomes. Mol Syst Biol. 2:2006.0012.

D'haeseleer, P. (2005) How does gene expression clustering work? Nature Biotechnology 23(12):1499-501.

D'haeseleer, P. (2005) Closing the circle of osmoregulation. Nature Biotechnology, 23(8):941-2.

Segrè D, Zucker J, Katz J, Lin X, D'haeseleer P, Rindone WP, Kharchenko P, Nguyen DH, Wright MA, Church GM. (2003) From annotated genomes to metabolic flux models and kinetic parameter fitting. Omics 7(3):301-16.

Steffen M, Petti A, Aach J, D'haeseleer P, Church G. (2002) Automated modelling of signal transduction networks. BMC Bioinformatics. 3:34.

D'haeseleer P, Liang S, Somogyi R. (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics. 16(8):707-26.