Biology Department Biology Department  


Safiyh Taghavi

Brookhaven National Laboratory - Past Employee

Currently at: Center for Agricultural and Environmental Biotechnology Discovery and Analytical Sciences Research Triangle Institute (RTI) International 3040 Cornwallis Road - PO Box 12194
Research Triangle Park, NC 27709-2194 - USA

Phone: (+1-919.316.3532
Cell Phone: +1-919.491.2009




Recent News

Scientists ID Bacterial Genes that Improve Plant Growth
Plant Microbe Shares Features with Drug-Resistant Pathogen

Research Interests

Characterization and application of plant associated microorganisms to improve plant biomass production and the phytoremediation of heavy metals and organic xenobiotics. The aim of this work is to study the microbial communities associated with plants (rhizosphere bacteria and endophytic bacteria) and to exploit how these organisms can be engineered to improve phytoremediation processes and plant biomass production. We also apply these microorganisms to improve plant biomass production on marginal soils (funded by DOE BER). A brief summary of this work is given in the BNL Press Release of April 11, 2004.

Heavy metal resistance: lead and copper resistance in Cupriavidus metallidurans CH34. The purpose of this project is to further elucidate the functioning of the pbrTRABCD lead resistance operon and the cop copper resistance operons of Cupriavidus metallidurans CH34, and to determine the role and interactions of the different resistance proteins. A short paragraph about the discovery of a lead(II) binding protein is given in the BNL Press Release of April 4, 2005.

Diversity, structure, and functional interdependence of microbial communities. The project's goal is to develop new molecular ecological tools with an open architecture (which do not require a priori genomic knowledge) to study gene expression, and to combine them with state of the art molecular ecological techniques to dramatically extend scientific and technical understanding of the genetic and metabolic diversity of microbial communities, including their association with higher organisms. The model systems we have chosen for this project are linked to biomass production and conversion, and specifically address the microbial communities involved in the decay of poplar biomass, and the rhizosphere of poplar. BNL Press Release of December 19, 2007

Hydrogen production using Thermatoga. This research aims at understanding at the molecular level hydrogen production by different Thermatogales under oxygen limited conditions and applying this knowledge for developing a hydrogen production process. For an update on current initiatives read the BNL Press Release of September 12, 2006.

Nanosciences: application of nucleic acids and proteins for the programmable assembly of nano-objects and the design of biosensor devices. This work is carried out in the context of the Center for Functional Nanomaterials, where Daniel van der Lelie is, together with Oleg Gang, Theme Leader for Biological and Soft Nanomaterials.  In an achievement some see as the "holy grail" of nanoscience, we have for the first time used DNA to guide the creation of three-dimensional, ordered, crystalline structures of nanoparticles (particles with dimensions measured in billionths of a meter). The ability to engineer such 3-D structures is essential to producing functional materials that take advantage of the unique properties that may exist at the nanoscale - for example, enhanced magnetism, improved catalytic activity, or new optical properties. BNL Press Release of January 30, 2008.


Selected Publications

  • Taghavi S, van der Lelie D, Hoffman A, Zhang YB, Walla MD, Vangronsveld J, Newman L, Monchy S.
    Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638.
    PLoS Genetics cover, 13;6(5):e1000943 (May 2010).  PubMed
  • Barac T., Weyens N., Oeyen L., Taghavi S., van der Lelie D., Dubin D., Spliet M., and Vangronsveld J.
    Field Note: Hydraulic containment of a BTEX plume using poplar trees.
    International Journal of Phytoremediation, 11(5):416-424 (February, 2009).
  • Lee, S.-K., Maye, M. M., Zhang, Y.-B., Gang, O., and van der Lelie D.
    Controllable g5p-protein-directed aggregation of ssDNA-gold nanoparticles.
    Langmuir, 25(2):657-660 (January, 2009).  PubMed
  • Li, L.-L., McCorkle, S. R., Monchy, S., Taghavi S., and van der Lelie D.
    Bioprospecting metagenomes: Glycosyl hydrolases for converting biomass. (Review).
    Biotechnology for Biofuels, 2(1):10 (May, 2009).  PubMed
  • Mastretta, C., Taghavi S., van der Lelie D., Mengoni, A., Galardi, F., Gonnelli, C., Barac, T., Boulet, J., Weyens, N., and Vangronsveld, J.
    Endophytic bacteria from seeds of Nicotiana tabacum can reduce cadmium phytotoxicity.
    International Journal of Phytoremediation, 11(3):251-267 (March, 2009).
  • Maye, M. M., Nykypanchuk, D., Cuisinier, M., van der Lelie D., and Gang, O.
    Stepwise surface encoding for high-throughput assembly of nanoclusters.
    Nature Materials 8: 388-391 (May, 2009). [News & Views: Prabhu, V. M. and Hudson, S. D. Nanoparticle assembly: DNA provides control. Nature Materials, 8:365-366 (May, 2009)]  PubMed
  • Ryan, R. P., Monchy, S., Cardinale, M., Taghavi S., Crossman, L., Avison, M. B., Berg, G., van der Lelie D., and Dow, J. M.
    Versatility and adaptation of bacteria from the genus Stenotrophomonas.
    Nature Reviews in Microbiology (accepted).
  • Taghavi S., Garafola, C., Monchy, S., Newman, L., Hoffman, A., Weyens, N., Barac, T., Vangronsveld, J., and van der Lelie D.
    Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees.
    Applied and Environmental Microbiology, 75(3):748-757 (February, 2009).  PubMed
  • Taghavi S., Lesaulnier, C., Monchy, S., Wattiez, R., Mergeay, M., and van der Lelie D.
    Lead(II) resistance in Cupriavidus metallidurans CH34: Interplay between plasmid and chromosomally-located functions.
    Antonie van Leeuwenhoek, 2008 Oct 24. [Epub ahead of print] (2009).  PubMed
  • Weyens, N., Taghavi S., Barac, T., van der Lelie D., Boulet, J., Artois, T., Carleer, R., and Vangronsveld, J.
    Bacterial associated with oak and ash on a TCE-contaminated site: Characterization of isolates with potential to avoid evapotranspiration of TCE.
    Environ Sci Pollut Res Int. 2009 Apr 25. [Epub ahead of print]  PubMed
  • Weyens, N., van der Lelie D., Taghavi S., and Vangronsveld, J.
    Phytoremediation: Plant-endophyte partnerships take the challenge.
    Current Opinion in Biotechnology, 20(2):248-254 (April, 2009).  PubMed
  • Xiong, H., van der Lelie D., and Gang, O.
    Phase behavior of nanoparticles assembled by DNA linkers.
    Physical Review Letters, 102:015504-1 to -4 (January, 2009).  PubMed
  • Zhang, Y.-B., Monchy, S., Greenberg, B., Mergeay, M., Gang, O., Taghavi S., and van der Lelie D.
    ArsR arsenic-resistance regulatory protein from Cupriavidus metallidurans CH34.
    Antonie Van Leeuwenhoek. 2009 Feb 24. [Epub ahead of print].  PubMed
  • Adney W.S., van der Lelie D., Berry A.M. and Himmel M.E.
    Understanding the biomass decay community.
    Biomass Recalcitrance: Deconstructing the Plant Cell Wall for Bioenergy, M.E. Himmel, Editor, Chapter 15, pp. 454-479, Blackwell Publishing Ltd., Oxford, UK (2008). 
  • Geets J., Vangronsveld J., Diels L., Taghavi S. and van der Lelie D.
    Microbial activities, monitoring and application as part of a management strategy for heavy metal- contaminated soil and groundwater.
    Developments in Soil Science: Chemical Bioavailability in Terrestrial Environment, R. Naidu, Editor, Vol. 32, Chapter 21, pp. 519-556, Elsevier B.V., Amsterdam, The Netherlands (2008).
  • Kim K.-H., Jung E.J., Im H., van der Lelie D. and Kim E.E.
    Expression, purification, and crystallization and preliminary X-ray crystallographic analysis of CnrX from Cupriavidus metallidurans CH34.
    Journal of Microbiology and Biotechnology 18(1): 43-47 (2008).
  • Lesaulnier C., Papamichail D., McCorkle S., Ollivier B., Skiena S., Taghavi S., Zak D., van der Lelie D.
    Elevated Atmospheric CO2 Affects Soil Microbial Diversity Associated with Trembling Aspen.
    Environmental Microbiology, 10(4):926-941 (2008).  PubMed
  • Mastretta C., Taghavi S., van der Lelie D., Mengoni A., Galardi F., Gonnelli C., Barac T., Boulet J., Weyens N. and Vangronsveld J.
    Endophytic bacteria from seeds of Nicotiana tabacum can reduce cadmium phytotoxicity.
    International Journal of Phytoremediation (in press). 
  • Moreels D., Crosson G., Garafola C., Monteleone D., Taghavi S., Fitts J.P., and van der Lelie D.
    Mibrobial community dynamics in uranium contaminated subsurface sediments under biostimulated conditions with high nitrate and nickel pressure.
    Environmental Science and Pollution Research, 15(6):481-491 (2008).  PubMed
  • Nykypanchuk D., Maye M.M., van der Lelie D. and Gang O.
    DNA-guided crystallization of colloidal nanoparticles.
    Nature (cover), 451:549-552 (2008).  PubMed
  • Panessa-Warren B.J., Warren J.B., Maye M.M., van der Lelie D., Gang O., Wong S.S., Ghebrehiwet B., Tortora G.T. and Misewich J.A.
    Human epithelial cell processing of carbon and gold nanoparticles.
    Int. J. Nanotechnology, 5(1):55-91 (2008).
  • Taghavi S., Lesaulnier C., Monchy S., Wattier R., Mergeay M. and van der Lelie D.
    Lead(II) resistance in Cupriavidus metallidurans CH34: Interplay between plasmid and chromosomally-located functions.
    Antonie Van Leeuwenhoek. 2008 Oct 24. [Epub ahead of print]  PubMed
  • Vanhulle S., Trovaslet M., Enaud E.,Lucas M., Taghavi S., van der Lelie D., Van Aken B., Foret M., Onderwater R., Wesenberg D., Agathos S.N., Schneider Y.-J. and Corbisier A.-M.
    Decolourisation, cytotoxicity and genotoxicity reduction during a combined ozonation/fungal treatment of dye contaminated wastewater.
    Env. Sci. Technol., 42(2):584-589 (2008).  PubMed
  • Xiong H., van der Lelie D., and Gang O.
    DNA linker mediated crystallization of nanocolloids.
    Journal of American Chemical Society, 130(8):2442-2443 (2008).  PubMed
  • Peng R. Chen, Erik C. Wasinger, Jing Zhao, Daniel van der Lelie, Lin X. Chen, and Chuan He.
    The Mechanism of the Selective Lead(II) Recognition by the PbrR691 Protein: Insights from the Spectroscopic Investigations.
    J. Am. Chem. Soc., 129(41):12350-12351 (2007).  PubMed  Full Text
  • Mathew M. Maye, Dmytro Nykypanchuk, Daniel van der Lelie, and Oleg Gang (2007).
    DNA based control of interparticle interactions for regulated micro- and nano-particle assembly.
    SMALL, 3(10):1678-1682.  PubMed  Full Text
  • Monchy S., Benotmane M.A., Janssen P., Vallaeys T., Taghavi S., van der Lelie D., Mergeay M.
    Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialised in the maximal viable response to heavy metals.
    J. Bacteriol., 189:7417-7425 (2007).  PubMed
  • Nykypanchuk D., Maye M.M., van der Lelie D. and Gang O.
    A DNA based approach for interparticle interaction control.
    Langmuir, 23:6305-6314 (2007). PubMed
  • Zhang Y.-B., Kanungo M., Ho A.J., Freimuth P., van der Lelie D., Chen M., Khamis S., Datta S., Johnson A.T.C., Panessa-Warren B., Misewich J.A. and Wong S.S.
    Functionalized carbon nanotubes for detection of viral proteins.
    Nanoletters, 7(10):3086-3091; DOI: 10.1021/nl071572l (2007).  PubMed
  • De la Iglesia R., Castro D., Ginocchio R., van der Lelie D. and González B.
    Factors influencing the composition of bacterial communities found at abandoned copper-tailings dumps.
    J. Appl Microbiol, 100:537-544 (2006).   PubMed
  • Geets J., Borremans B., Diels L., Springael D., Vangronsveld J., van der Lelie D. and Vanbroekhoven K.
    DsrB gene-based DGGE for community and diversity surveys of sulfate- reducing bacteria.
    J. Microbiol. Methods, 66:194-205 (2006).
  • Mastretta C., Barac T., Vangronsveld J., Newman L., Taghavi S. and van der Lelie D.
    Endophytic bacteria and their potential application to improve the phytoremediation of contaminated environments.
    Biotechnology and Genetic Engineering Reviews, Vol. 23: 175-207 (2006).
  • Maye M.M., Nykypanchuk D., van der Lelie D. and Gang O.
    A simple method for kinetic control of DNA-induced nanoparticle assembly.
    J. Am. Chem. Soc., 128(43):14020-4021 (2006).  PubMed Full Text
  • Monchy S., Benotmane M.A., Wattiez R., van Aelst S., Auquier V., Borremans B., Mergeay M., Taghavi S., van der Lelie D. and Vallaeys T.
    Transcriptonic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34.
    Microbiology, 152:1765-1776 (2006).   PubMed
  • Moore F.P., Barac T., Borremans B., Oeyen L., Vangronsveld J., van der Lelie D., Campbell C.D. and Moore E.R.B.
    Endophytic bacterial diversity in poplar trees growing on a BTEX-contaminated site: the characterization of isolates with potential to enhance phytoremediation.
    Systematic and Applied Microbiology, 29:539–556 (2006).  PubMed
  • van der Lelie D., Lesaulnier C., McCorkle S., Geets J., Taghavi S. and Dunn J.
    Use of Single-Point Genome Signature Tags as a universal tagging method for microbial genome surveys.
    Appl. Environ. Microbiol., 72:2092-2101 (2006).   PubMed   Full Text
  • Chen P., Greenberg B., Taghavi S., Romano C., van der Lelie D. and He C.
    An exceptionally selective lead(II)-regulatory protein from ralstonia metallidurans: Development of a fluorescent lead(II) probe.
    Angew Chem Int Ed Engl, 44:2715-2719 (2005).   PubMed
  • Geets J., Borremans B., Vangronsveld J., Diels L. and van der Lelie D.
    Molecular monitoring of SRB community structure and dynamics in batch experiments to examine the applicability of in situ precipitation of heavy metals for groundwater remediation.
    J Soil Sediments, 5:149-163 (2005).
  • Geets J., Vanbroekhoven K., Borremans B., Vangronsveld J., Diels L. and van der Lelie D.
    Column Experiments to Assess the Effects of Electron Donors on the Efficiency of in situ Precipitation of Zn, Cd, Co and Ni in Contaminated Groundwater Applying the Biological Sulfate Removal Technology.
    Environ Sci & Pollut Res, 13(6):362-378 (2005).  PubMed ESPR Online First
  • Nachtegaal M., Marcus M.A., Sonke J.E., Vangronsveld J., Livi K., van der Lelie D. and Sparks D.L.
    Effects of in situ Remediation on the Speciation and Bioavailability of Zinc in a Smelter Contaminated Soil.
    Geochimica et Cosmochimica Acta, 69:4649-4664 (2005).
  • Taghavi S., Barac T., Greenberg B., Borremans B., Vangronsveld J. and van der Lelie D.
    Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene.
    Appl Environ Microbiol., 71:8500-8505 (2005).   PubMed   Full Text
  • van der Lelie D., Barac T., Taghavi S. and Vangronsveld J.
    New uses of endophytic bacteria to improve phytoremediation.
    Trends Biotechnology, 23:8-9 (2005).
  • Van Ooteghem S.A., Jones A., van der Lelie D., Dong B. and D. Mahajan.
    H(2) production and carbon utilization by Thermotoga neapolitana under anaerobic and microaerobic growth conditions.
    Biotechnology Letters, 26:1223-1232 (2004).   PubMed
  • Barac T.,Taghavi S., Borremans B., Provoost A., Loeyen, Colpaert J.V., Vangronsveld J. and van der Lelie D.
    Engineered endophytic bacteria improve phytoremediation of water-soluble volatile organic pollutants.
    Nature Biotechnol, 22:583-588 (2004).   PubMed   Full Text
    See also:
        BNL Press Release of March 11, 2004
        Scientific American, Science News, April 12, 2004, 'Plants
        Dispatched to Decontaminate Soil'
        Larger version of Nature Cover
  • Germaine K., Keogh E., Borremans B., van der Lelie D., Barac T, Oeyen, Vangronsveld J., Porteous-Moore F., Moore E., Campbell C., Ryan D. and Dowling D.
    Colonisation of Poplar trees by gfp expressing bacterial endophytes.
    FEMS Microbiology Ecology, 48:109-118 (2004).
  • Vassilev A., Schwitzguébel J.-P., Thewys T, van der Lelie D. and Vangronsveld J.
    The use of plants for remediation of metal contaminated soils.
    The Scientific World Journal, 4:9-34 (2004).   PubMed
  • Renella G., Mench M., van der Lelie D., Pietramellara G., Ascher J., Ceccherini M.T., Landi L. and Nannipieri P.
    Hydrolase activity, microbial biomass and community structure in long-term Cd-contaminated soils.
    Soil Biol Biochem, 36:443-451 (2004).
  • Adriaensen K., van der Lelie D., Van Laere A., Vangronsveld J.S. and Colpaert J.V.
    Zinc adapted fungus protects pines from zinc stress.
    New Phytologist, 161:549-555 (2004).
  • Snellinx Z., Taghavi S., Vangronsveld J. and van der Lelie D.
    Microbial consortia that degrade 2,4-DNT by interspecies metabolism: isolation and characterisation.
    Biodegradation, 14:19-29 (2003).   PubMed
  • Mergeay M., Monchy S., Vallaeys T., Auquier V., Benotmane A., Bertin P., Dunn J., Taghavi S., van der Lelie D. and Wattiez R.
    Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a tentative catalogue of metal-responsive genes.
    FEMS Microb Rev, 27(2-3):385-410 (2003).   PubMed
  • Geebelen W., Adriano D.C., van der Lelie D., Mench M., Carleer R., Clijsters H. and Vangronsveld J.
    Selected bioavailability assays to test the efficacy of amendment-induced immobilization of lead in soils.
    Plant Soil, 249:217-228 (2003).
  • Dunn J.J., McCorkle S.R., Praissman L.A., Hind G., van der Lelie D., Bahou W.F., Guatenko D.V. and Krause M.K.
    Genomic signature tags (GSTs): A system for profiling genomic DNA.
    Genome Res, 11:1756-1765 (2002).   PubMed
  • Lodewyckx C., Vangronsveld J., Porteous F., Moore E.R.B., Taghavi S. and van der Lelie D.
    Endophytic bacteria and their potential applications.
    Critical Rev Plant Sci, 21:583-606 (2002).
  • Schwitzguebel J.P., van der Lelie D., Glass D.J., Vangronsveld J. and Baker A.
    Phytoremediation: European and American Trends, Successes, Obstacles and Needs.
    J Soil Sediments, 2:91-99 (2002).
  • Lodewyckx C., Mergeay M., Vangronsveld J., Clijsters H. and van der Lelie D.
    Isolation, characterization and identification of bacteria associated with the zinc hyperaccumulator Thlaspi caerulescens subsp. calaminaria.
    Int J Phytoremediation, 4:101-115 (2002).   PubMed
  • Snellinx Z., Nepovím A., Taghavi S., Vangronsveld J., Vanek T. and van der Lelie D.
    Biological remediation of explosives and related nitroaromatic compounds.
    Environ Sci Pollut Res Int, 9:48-61 (2002).   PubMed
  • Taghavi S., Delanghe H., Lodewyckx C., Mergeay M. and van der Lelie D.
    Nickel-resistance-based minitransposons: new tools for genetic manipulation of environmental bacteria.
    Appl Environ Microbiol, 67:1015-1019 (2001).   PubMed   Full Text
  • Lodewyckx C., Taghavi S., Mergeay M., Vangronsveld J., Clijsters H. and van der Lelie D.
    The effect of recombinant heavy metal resistant endophytic bacteria in heavy metal uptake by their host plant.
    Int J Phytoremediation, 3:173-187 (2001).
  • Tibazarwa C., Corbisier P., Mench M., Bossus A., Solda P., Mergeay M., Wyns L. and van der Lelie D.
    A microbial biosensor to predict bioavailable nickel in soil and its transfer to plants.
    Environ Pollut, 113:19-26 (2001).   PubMed
  • Borremans B., Hobman J.L., Provoost A., Brown N.L. and van der Lelie D.
    Cloning and functional analysis of the pbr lead resistance determinant of Ralstonia metallidurans CH34.
    J Bacteriol, 183:5651-5658 (2001).   PubMed   Full Text
  • van der Lelie D., Schwitzguebel J.P., Glass D.J., Vangronsveld J. and Baker A.
    Assessing phytoremediation's progress in the United States and Europe.
    Environ Sci Technol, 35:446A-452A (2001).   PubMed
  • Kärenlampi S., Schat H., Vangronsveld J., Verkleij J., van der Lelie D., Mergeay M. and Tervahauta A.
    Genetic engineering in the improvement of plants for phytoremediation of metal polluted soils.
    Environ Pollution, 107:225-231 (2000).
  • Tibazarwa C., Wuertz S., Mergeay M., Wyns L. and van der Lelie D.
    Regulation of the cnr cobalt and nickel resistance determinant of Ralstonia eutropha (Alcaligenes eutrophus) CH34.
    J Bacteriol, 182:1399-1409 (2000).   PubMed   Full Text
  • Garg R.P., Yindeeyoungyeon W., Gilis A., Denny T.P., van der Lelie D. and Schell M.A.
    Evidence that Ralstonia eutropha (Alcaligenes eutrophus) contains a functional homolog of the Ralstonia solanacearum Phc cell density sensing system.
    Mol Microbiol, 38:359-367 (2000).   PubMed
  • Kamnev A.A. and van der Lelie D.
    Chemical and biological parameters as tools to evaluate and improve heavy metal phytoremediation.
    Biosci Rep, 20:239-258 (2000).   PubMed
  • Corbisier P., van der Lelie D., Bierkens J., Vangronsveld J., Mench M. and Diels L.
    Integrated approach to quantify bioavailable concentrations of heavy metals in polluted soils.
    Contaminated Soil, 2:1029-1039 (2000).
  • Verschaeve L., Van Gompel J., Thilemans L., Regniers L., Vanparys P. and van der Lelie D.
    VITOTOX bacterial genotoxicity and toxicity test for the rapid screening of chemicals.
    Environ Mol Mutagen, 33:240-248 (1999).   PubMed
  • Corbisier P., van der Lelie D., Borremans B., Provoost A., de Lorenzo V., Brown N.L., Lloyd J.R., Hobman J.L., Csöregi E., Johansson G. and Mattiasson B.
    Whole cell- and protein-based biosensors for the detection of bioavailable heavy metals in environmental samples.
    Analytica Chem Acta, 387:235-244 (1999).
  • van der Lelie D., Corbisier P., Diels L., Gilis A., Lodewyckx C., Mergeay M., Taghavi S., Spelmans N. and Vangronsveld J.
    The role of bacteria in the phytoremediation of heavy metals.
    In: Phytoremediation of Contaminated Soil and Water, (N Terry and G Bañuelos eds), Lewis Publishers, CRC Press LLC, Boca Raton, London, New York, Washington DC, pp 265-281 (1999).
  • Hassan M.T., van der Lelie D., Springael D., Römling U., Ahmed N. and Mergeay M.
    Identification of a gene cluster, czr, involved in cadmium and zinc resistance in Pseudomonas aeruginosa.
    Gene, 238:417-425 (1999).   PubMed
  • Gilis A., Corbisier P., Baeyens W., Taghavi S., Mergeay M. and van der Lelie D.
    Effect of the siderophore alcaligin E on the bioavailability of Cd to Alcaligenes eutrophus CH34.
    J Ind Microbiol Biotechnol, 20:61-68 (1998).   PubMed
  • van der Lelie D.
    Biological interactions: the role of soil bacteria in the bioremediation of heavy metal-polluted soils.
    In: Metal-contaminated Soils. In situ Inactivation and Phytorestoration, (J Vangronsveld and SD Cunningham eds), Springer-Verlag Berlin Heidelberg New York pp 31-50 (1998).


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