BEEM Achievements
Publications
Zhuang, K., Yang. L., Cluett. W.R., and R. Mahadevan, Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design BMC Biotechnol 13:8 (2013)
Hong, Y., Nizami, A.-S., Bafrani, M.P., Saville, B.A., and H.L. MacLean, Impact of cellulase production on environmental and financial metrics for lignocellulosic ethanol Biofuel Bioprod Bior 7(3):303-313 (2013)
Alcaide, M., Tornes, J., Stogios, P.J., Xu, X., Gertler, C., Di Leo, R., Bargiela, R., Lafraya, A., Guazzaroni, M.E., Lopez-Cortes, N., Chernikova, T.N., Golyshina, O.V., Nechitaylo, T.Y., Plumeier, I., Pieper, D.H., Yakimov, M.M., Savchenko, A., Golyshin, P.N., and M. Ferrer, Single residues dictate the co-evolution of dual esterases: MCP hydrolases from the α/β hydrolase family Biochem J 454:157–166 (2013)
Kube, M., Chernikova, T.N., Al-Ramahi, Y., Beloqui, A., Lopez-Cortez, N., Guazzaroni, M.E., Heipieper HJ, Klages S, Kotsyurbenko OR, Langer, I., Nechitaylo, T.Y., Lünsdorf, H., Fernández, M., Juárez, S., Ciordia, S., Singer, A., Kagan, O., Egorova, O., Alain Petit, P., Stogios, P., Kim, Y., Tchigvintsev, A., Flick, R., Denaro, R., Genovese, M., Albar, J.P., Reva, O.N., Martínez-Gomariz, M., Tran, H., Ferrer, M., Savchenko, A., Yakunin, A.F., Yakimov, M.M., Golyshina, O.V., Reinhardt, R., and P.N. Golyshin, Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica Nat Commun 4:2156 (2013)
Tran, C., Characterization of hydrolytic dehalogenases: Substrate specificity and isotope fractionation M.Sc. Thesis, University of Toronto (2013)
Zheng, H., Beliavsky, A., Tchigvintsev, A., Brunzelle, J.S., Brown, G., Flick, R., Evdokimova, E., Wawrzak, Z., Mahadevan, R., Anderson, W.F., Savchenko, A., and A.F. Yakunin, Structure and activity of the NAD(P)+-dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium Proteins 81(6):1031-1041 (2013)
Tang, S., Gong, Y., and E.A. Edwards, Semi-automatic in silico gap closure enabled de novo assembly of two dehalobacter genomes from metagenomic data PLoS One 7(12):e52038 (2013)
Tang, S., Chan, W.W., Fletcher, K.E., Seifert, J., Liang, X., Loeffler, F.E., Edwards, E.A. and L. Adrian, Functional characterization of reductive dehalogenases using blue native polyacrylamide gel electrophoresis Appl Environ Microbiol 79(3):974-981 (2013)
Liang, X., Devine, C.E., Nelson, J.L., Sherwood Lollar, B., Zinder, S., and E.A. Edwards, Anaerobic conversion of monochlorobenzene and benzene to CH4 and CO2 in bioaugmented microcosms Environ Sci Technol 47(5):2378-2385 (2013)
Pourbafrani, M., McKechnie, J., MacLean, H.L., and B.A. Saville, Life cycle greenhouse gas impacts of ethanol, biomethane and limonene production from citrus waste Environ Res Letters 8(1):10 (2013)
Hug, L.A., Maphosa, F., Leys, D., Loeffler, F.E., Smidt, H., Edwards, E.A., and L. Adrian, Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases Philos Trans R Soc Lond B Biol Sci 368(1616):20120322 (2013)
Tang, S., and E.A. Edwards, Identification of Dehalobacter reductive dehalogenases that catalyse dechlorination of chloroform, 1,1,1- trichloroethane and 1,1-dichloroethane Philos T R Soc B 368(1616):20120318 (2013)
Beloglazova, N., Flick, R., Tchigvintsev, A., Brown, G., Popovic, A., Nocek, B., and A.F. Yakunin, Nuclease Activity of the Human SAMHD1 Protein Implicated in the Aicardi-Goutieres Syndrome and HIV-1 Restriction J Biol Chem 288(12):8101-8110 (2013)
Martínez-Martínez, M., Alcaide, M., Tchigvintsev, A., Reva, O., Polaina, J., Bargiela, R., Guazzaroni, M.E., Chicote A, Canet A, Valero F, Eguizabal, E.R., Guerrero, M.D., Yakunin, A.F., and M. Ferrer, Biochemical diversity of carboxyl esterases and lipases from Lake Arreo -- a metagenomic approach Appl Environ Microbiol 79(12):3553-3562 (2013)
Porter, M.S., and R.G. Beiko, SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles Bioinformatics 29(15):1858-1864 (2013)
Pourbafrani, M., McKechnie, J., MacLean, H.L., and B.A. Saville, Bioplastic products from citrus wastes Bioplastics Magazine 3:28-30 (2013)
Ho, H., Understanding a Methanogenic Benzene-degrading Culture using Metabolic Models Created from Metagenomic Sequences M.Sc. Thesis, University of Toronto (2013)
Loeffler, F.E., Yan, J., Ritalahti, K.M., Adrian, L., Edwards, E.A., Konstantinidis, K.T., Mueller, J.A., Fullerton, H., Zinder, S.H., and A.M. Spormann, Dehalococcoides mccartyi gen. nov., sp. nov., obligate organohalide-respiring anaerobic bacteria, relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidetes classis nov., within the phylum Chloroflexi Int J Syst Evol Microbiol doi:10.1099/ijs.0.034926-0 (2013)
Xu, Y.F., Létisse, F., Absalan, F., Lu, W., Kuznetsova, E., Brown, G., Caudy, A.A., Yakunin, A.F., Broach, J.R., and J.D. Rabinowitz, Nucleotide degradation and ribose salvage in yeast Mol Syst Biol 9:665 (2013)
Goacher, R.E., Tsai, A.Y.-L, and E.R. Master, Towards practical time-of-flight secondary ion mass spectrometry lignocellulolytic enzyme assays Biotechnol Biofuels 6(1):13 (2013)
Mahajan, S., Jeremic, D., Goacher, R.E., and E.R. Master, Mode of coniferous wood decay by the white rot fungus Phanerochaete carnosa as elucidated by FTIR and ToF-SIMS Appl Microbiol Biot DOI: 10.1007/s00253-011-3830-1 (2012)
Gonzalez, C.F., Tchigvintsev, A., Brown, G., Flick, R., Evdokimova, E., Xu, X., Osipiuk, J., Cuff, M., Lynch, S., Joachimiak, A., Savchenko, A., and A. Yakunin, Structure and activity of the Pseudomonas aeruginosa hotdog-fold thioesterases PA5202 and PA2801 Biochem. J. doi:10.1042/BJ20112032 (2012)
Goacher, R.E., Edwards, E.A., Yakunin, A.F., Mims, C.A., and E.R. Master, Application of ToF-SIMS for the Detection of Enzyme Activity on Solid Wood Substrates Anal Chem 84(10):4443-4451 (2012)
Zhuang, K., Ma, E., Lovley, D.R., and R. Mahadevan, The design of long-term effective uranium bioremediation strategy using a community metabolic model Biotechnol Bioeng doi: 10.1002/bit.24528 (2012) doi: 10.1002/bit.24528 (2012)
Lemak, S., Tchigvintsev, A., Petit, P., Flick, R., Singer, A.U., Brown, G., Evdokimova, E., Egorova, O., Gonzalez, C.F., Chernikova, T.N., Yakimov, M.M., Kube, M., Reinhardt, R., Golyshin, P.N., Savchenko, A., and A. Yakunin, Structure and activity of the cold-active and anion-activated carboxyl esterase OLEI01171 from the oil-degrading marine bacterium Oleispira antarctica Biochem J doi:10.1042/BJ20112113 (2012)
Wagner, D.D., Hug, L.A., Hatt, J.K., Spitsmiller, M.A., Padilla-Crespo, E., Ritalahti, K.M., Edwards, E.A., Konstantinidis, K.T., and F.E. Loeffler, Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae BMC Genomics 13:200 (2012)
Manchester, M. J., Hug, L.A., Zarek, M., Zila, A., and E.A. Edwards, Discovery of a trans-Dichloroethene Respiring Dehalogenimonas in the 1,1,2,2-Tetrachloroethane-Dechlorinating WBC-2 Consortium Appl Environ Micrbiol doi:10.1128/AEM.00384-12 (2012)
Hug, L.A., Beiko, R.G., Rowe, A.R., Richardson, R.E., and E.A. Edwards, Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community BMC Genomics 13:327 (2012)
Barlett, M., Zhuang, K., Mahadevan, R., and D. Lovley, Integrative analysis of Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation Biogeosciences 9:1033-1040 (2012)
Loeffler, F.E., Ritalahti, K.M., and S.H. Zinder, Dehalococcoides and Reductive Dechlorination of Chlorinated Solvents SERDP ESTCP Environmental Remediation Technology 5:39-88 (2012)
Hug, L.A., Edwards, E.A., Vrionis, H., and D.W. Major, Research Needs for Bioaugmentation SERDP ESTCP Environmental Remediation Technology 5:333-361 (2012)
Parks, D., Georeferenced trees and the phylogenetic similarity of biological communities Ph.D. Thesis, Dalhousie University (2012)
Porter, M.S., Evaluating a microbial community through feature matching and graph topology M.C.Sc. Thesis, Dalhousie University (2012)
Li, Y.X., Adaptation of a dechlorinating culture, KB-1, to acidic environments M.A.Sc. Thesis, University of Toronto (2012)
Wei, K., Substrates and substrate interactions in anaerobic dechlorinating cultures M.A.Sc. Thesis, University of Toronto (2012)
Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., and D. R. Lovley, Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME Journal 5:305-316 (2011)
Makarova, K.S., Haft, D.H., Barrangou, R., Brouns, S.J.J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F.J.M., Wolf, Y.I., Yakunin, A.F., van der Oost, J., and Eugene V. Koonin, Evolution and classification of CRISPR-Cas systems Nat Rev Microbiol doi:10.1038/nrmicro2577 (2011)
McKechnie, J., Zhang, Y., Ogino, A., Saville, B., Sleep, S., Turner, M., Pontius, R., and H.L. MacLean, Impacts of co-location, co- production, and process energy source on life cycle energy use and greenhouse gas emissions of lignocellulosic ethanol BioFPR 5(3):279-292 (2011)
Tchigvintsev, A., Singer, A.U., Flick, R., Petit, P., Brown, G., Evdokimova, E., Savchenko, A., and A.F. Yakunin, Structure and activity of the Saccharomyces cerevisiae deoxyuridine triphosphate pyrophosphatase DUT1, an essential housekeeping enzyme Biochem J 437:243-253 (2011)
Fletcher, K.E., Costanza, J., Cruz-Garcia, C., Ramaswamy, N.S., Pennell, P.D., and F.E. Loeffler, Effects of Elevated Temperature on Dehalococcoides Dechlorination Performance and DNA and RNA Biomarker Abundance Environ Sci Technol 45(2):712-718 (2011)
Zhuang, K., Vemuri, G.N., and R. Mahadevan, Economics of membrane occupancy and respiro-fermentation Mol Sys Biol Vol 7 Article 500 doi:10.1038/msb.2011.34 (2011)
Clasquin, M.F., Melamud, E., Singer, A., Gooding, J.R., Xu, X., Aiping, D., Cui, H., Campagna, S.R., Savchenko, A., Yakunin, A.F., Rabinowitz, J.D., and A. A. Caudy, Riboneogenesis in yeast Cell 145(6):969-980 (2011)
Zila, A., A molecular study of field bioaugmentation using the KB-1(c) mixed microbial consortium: the application of real-time PCR in analyzing population dynamics M.Eng. Thesis, University of Toronto (2011)
Hug, L.A., Salehi, M., Nuin, P., Tillier, E.R., and E.A. Edwards, Design and Verification of a Pangenome Microarray Oligonucleotide Probe Set for Dehalococcoides spp. Appl Environ Microbiol 77(15):5361-5369 (2011)
Tchigvintsev, A., Singer, A., Brown, G., Flick, R., Evdokimova, E., Tan, K., Gonzalez, C.F., Savchenko, A., and A.F. Yakunin, Biochemical and structural studies of the uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed a NAD+-dependent L-serine dehydrogenase J Biol Chem doi: 10.1074/jbc.M111.294561 (2011)
Sanscartier, D., MacLean, H.L., and B. Saville, Electricity Production from Anaerobic Digestion of Household Organic Waste in Ontario: Techno-Economic and GHG Emission Analyses Environ Sci Technol 46(2):1233-1242 (2011)
Grostern, A., Duhamel, M., Dworatzek, S., and E. A. Edwards, Chloroform respiration to dichloromethane by a Dehalobacter population. Environ Microbiol 12:1053-1060 (2010)
Chan, W. Y., Wong, M., Guthrie, J., Savchenko, A. V., Yakunin, A. F., Pai, E. F., and E. A. Edwards, Sequence- and activity-based screening of microbial genomes for novel dehalogenases. Microbial Biotechnology (2010)
Chan, W. W. M., Characterization of reductive dehalogenases in a chlorinated ethene-degrading bioaugmentation culture Master's Thesis, University of Toronto (2010)
Islam, M.A., Edwards, E.A., and R. Mahadevan, Characterizing the metabolism of Dehalococcoides with a constraint-based model PLoS Comput Biol 6(8) e1000887. doi:10.1371/journal.pcbi.1000887 (2010)
Goacher, Robyn E., Jeremic, Dragica, and Emma R. Master, Expanding the library of secondary ions that distinguish lignin and polysaccharides in time-of-flight secondary ion mass spectrometry analysis of wood Anal Chem 83(3):804-812 (2010)
Slater, F.R., Johnson, C.R., Blackall, L.L., Beiko, R.G. and P.L. Bond, Monitoring associations between clade-level variation, overall community structure and ecosystem function in enhanced biological phosphorus removal (EBPR) systems using terminal-restriction fragment length polymorphism (T-RFLP) Water Research Volume 44(17):4908-4923 (2010)
Salimi, F., Zhuang, K. and R. Mahadevan, Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing Biotechnology Journal 5(7):726–738 (2010)
Waung, D., Optimizing enzymatic preparations of mechanical pulp through the characterization of new laccases and non-productive interactions between enzymes and lignin University of Toronto Master's thesis (2010)
Yang, M.I., Edwards, E.A., and D.G. Allen, Anaerobic treatability and biogas production potential of selected in-mill streams Water Science and Technology 62(10):2427-2434 (2010)
Babu, M., Beloglazova, N., Flick, R., Graham, C., Skarina, T., Nocek, B., Gagarinova, A., Pogoutse, O., Brown, G., Binkowski, A., Phanse, S., Joachimiak, A., Koonin, EV., Savchenko, A., Emili, A., Greenblatt, J., Edwards, A.M. and AF Yakunin, A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair Molecular Microbiology 79(2):484–502 (2010)
Ritalahti, K.M, Hatt, J.K., Petrovskis, E., and F.E. Loeffler, Groundwater sampling for nucleic acid biomarkers Handbook of Hydrocarbon and Lipid Microbiology Part 31, 3407-3418, DOI: 10.1007/978-3-540-77587-4_265 (2010)
Ritalahti, K.M., Cruz-Garcia, C., Padilla-Crespo, E., Hatt, J.K., and F.E. Loeffler, RNA Extraction and cDNA Analysis for Quantitative Assessment of Biomarker Transcripts in Groundwater Handbook of Hydrocarbon and Lipid Microbiology Part 32, 3671-3685, DOI: 10.1007/978-3-540-77587-4_289 (2010)
Grostern, A., Chan, W. W. M., and E. A. Edwards, 1,1,1-trichloroethane and 1,1-dichloroethane reductive dechlorination kinetics and co-contaminant effects in a Dehalobacter-containing mixed culture. Environ Sci Technol 43:6799-6807 (2009)
Grostern, A., and E. A. Edwards, Characterization of a Dehalobacter coculture that dechlorinates 1,2-dichloroethane to ethene and identification of the putative reductive dehalogenase gene. Appl Environ Microbiol 5:2684-2693 (2009)
McMurdie, P. J., Behrens, S. F., Mueller, J. A., Goeke, J., Ritalahti, K. M., Wagner, R., Goltsman, E., Lapidus, A., Holmes, S., Loeffler, F. E., and A. M. Spormann, Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genetics 5:e1000714 1-10 (2009)
Waller, A. S., Molecular investigation of chloroethene reductive dehalogentation by the mixed microbial community KB1 University of Toronto Ph.D. thesis (2009)
