{"id":150,"date":"2015-10-13T18:27:44","date_gmt":"2015-10-14T01:27:44","guid":{"rendered":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/?page_id=150"},"modified":"2021-12-29T10:56:26","modified_gmt":"2021-12-29T18:56:26","slug":"publications","status":"publish","type":"page","link":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

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<\/h4>\n

 <\/p>\n

Lab publications<\/span><\/strong><\/div>\n
\n

(* undergraduate, ** graduate students)<\/span><\/p>\n<\/div>\n

<\/div>\n
\n
<\/h5>\n<\/div>\n
\n
<\/span><\/div>\n<\/div>\n
2021<\/b><\/span><\/span><\/h5>\n
    \n
  1. \u00a0*<\/span>Johnson ZJ, *<\/span>Krutkin DD, Bohutskyi P, Kalyuzhnaya MG (2021)<\/span> Metals and methylotrophy: Via global gene expression studies. Methods Enzymol. 650:185-213. doi: 10.1016\/bs.mie.2021.01.046<\/a><\/span><\/li>\n
  2. \u00a0**<\/span>Afshin Y, **<\/span>Delherbe N, Kalyuzhnaya MG (2021)<\/span> Methylotenera. Bergey’s Manual of Systematics of Archaea and Bacteria (BMSAB).\u00a0<\/span><\/li>\n
  3. Xiong W, Kalyuzhanaya MG, Henard CA (2021)\u00a0Editorial:<\/i> Microbial C1 Metabolism and Biotechnology. Front Microbiol. 12. 2403. \u00a0https:\/\/doi.org\/10.3389\/fmicb.2021.744030<\/a><\/span><\/li>\n
  4. **<\/span>Hamilton R, Nizovtseva I, Chernuskin D, Kalyuzhnaya MG (in press<\/i>) <\/span>C1-proteins prospect for production of industrial proteins and protein-based materials from methane.\u00a0 In. Algal Biorefineries and the Circular Bioeconomy. Ed.\u00a0 Mehariya S, Bhatia S, and Karthikeyan OP.\u00a0 Taylor & Francis\/CRC.<\/span><\/li>\n
  5. \u00a0 **McNamara\u00a0JP,\u00a0**Delherbe N, Kalyuzhnaya MG (in press<\/i>)<\/span> Methylophilus.\u00a0Bergey’s Manual of Systematics of Archaea and Bacteria (BMSAB).<\/span><\/li>\n<\/ol>\n
    2020<\/b><\/span><\/span><\/h5>\n
      \n
    1. Ortega DR, Yang W, Subramanian P, Mann P, Kj\u00e6r A, Chen S, Watts KJ, Pirbadian S, **<\/span>Collins DA, Kooger R, Kalyuzhnaya MG, Ringgaard S, Briegel A, Jensen GJ (2020) Repurposing a chemosensory macromolecular machine. Nat Commun. 11(1):2041.<\/span> doi: 10.1038\/s41467-020-15736-5.<\/a><\/span><\/span><\/li>\n
    2. **<\/span>Nariya S, Kalyuzhnaya MG. (2020) Hemerythrins enhance aerobic respiration in <\/span><\/span>Methylomicrobium alcaliphilum<\/i><\/span> 20ZR, a methane-consuming bacterium. FEMS Microbiol Lett 1, 367(2):fnaa003.<\/span><\/span>\u00a0<\/a><\/span>doi: 10.1093\/femsle\/fnaa003.<\/a><\/span><\/span><\/li>\n
    3. Nguyen AD, Park JY, Hwang IY, **<\/span>Hamilton R, Kalyuzhnaya MG, Kim D, Lee EY. 2020.\u00a0 Genome-scale evaluation of core one-carbon metabolism in gammaproteobacterial methanotrophs grown on methane and methanol. Metab Eng. 57:1-12.<\/span> doi: 10.1016\/j.ymben.2019.10.004<\/a>.<\/span><\/span><\/li>\n
    4. \u00a0\u00a0Kalyuzhanaya MG, Kumaresan D, Heimann K, Caetano NS, Visvanathan C, Karthikeyan OP \u00a0(2020).\u00a0Editorial:<\/i>\u00a0<\/i>Methane: A Bioresource for Fuel and Biomolecules.\u00a0 Front. Environ. Sci.,9<\/span>.<\/span> \u00a0doi: 10.3389\/978-2-88963-562-7c<\/a><\/span>
      <\/span><\/span><\/li>\n<\/ol>\n
      2019<\/b><\/span><\/span><\/h5>\n
        \n
      1. Henard CA, Akberdin IR, Kalyuzhnaya MG, Guarnieri MT (2019) Muconic acid production from methane using rationally-engineered methanotrophic biocatalysts. Green Chem doi: 10.1039\/C9GC03722E.<\/a><\/span><\/span><\/li>\n
      2. Kalyuzhnaya MG, **<\/span>Collins DA, Chistoserdova L (2019) <\/span>Microbial Cycling of Methane. In: Schmidt, Thomas M. (ed.) Encyclopedia of Microbiology, 4th Edition. vol. 3, pp. 115- 124. UK: Elsevier.<\/span><\/li>\n
      3. **Nariya S, \u00a0Kalyuzhna, MG 2019<\/span>. Diversity, Physiology, and Biotechnological Potential of Halo(alkali)philic Methane-Consuming Bacteria. In E.Y. Lee (Ed) Methanotrophs: Microbiology Fundamentals and Biotechnological Applications (Ed.\u00a0 E.Y. Lee). Springer Nature. 278 pp.<\/span><\/li>\n
      4. Kalyuzhnaya MG, **<\/span>Gomez OA, Murrell JC (2019)<\/span> The Methane-Oxidizing Bacteria (Methanotrophs). In: McGenity T. (Eds) Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes. Handbook of Hydrocarbon and Lipid Microbiology. Springer, Cham. <\/span>doi.org\/10.1007\/978-3-319-60053-6_10-1<\/a><\/li>\n<\/ol>\n
        2018<\/span><\/strong><\/h5>\n
          \n
        1. **<\/span>Collins D.A., Kalyuzhnaya M.G. 2018. Navigating methane metabolism: Enzymes, Compartments, and Networks. Methods Enzymol. 613:349-383. doi: 10.1016\/bs.mie.2018.10.010.<\/span><\/span><\/li>\n
        2. Henard, C., Franklin, T., Youhenna, B*<\/span>., But, S., Alexander, D.,\u00a0Kalyuzhnaya, M.G.,\u00a0Guarnieri, M. (2018)<\/span>.\u00a0Biogas Biocatalysis: Methanotrophic\u00a0Bacterial Cultivation, Metabolite\u00a0Profiling, and Bioconversion to Lactic\u00a0Acid. Frontiers in Microbiology<\/i>. doi:\u00a010.3389\/fmicb.2018.02610.<\/a><\/li>\n
        3. Akberdin, I., **<\/span>Collins, D., *<\/span>Hamilton, R., Oshchepkov, D., Shukla, A., Nicora, C.,\u00a0Nakayaku, E., Adkins, J., Kalyuzhanaya, M. (2018)<\/span>. Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum<\/em> 20ZR<\/em>.\u00a0Frontiers in Microbiology<\/i>.\u00a0doi:\u00a010.3389\/fmicb.2018.02735.<\/a><\/li>\n
        4. Akberdin, I. R., **<\/span>Thompson, M., *<\/span>Hamilton, R., Desai, N., Alexander, D., Henard, C. A., … & Kalyuzhnaya, M. G.<\/span> (2018). Methane utilization in Methylomicrobium <\/em>alcaliphilum 20Z R<\/em>: a systems approach.\u00a0Scientific Reports<\/i>,\u00a08<\/i>(1), 2512.\u00a0doi: 10.1038\/s41598-018-20574-z<\/a>.<\/li>\n
        5. Chistoserdova, L.\u00a0& Kalyuzhnaya, M. G.<\/span> (2018).\u00a0Current Trends in Methylotrophy.\u00a0\u00a0Trends in Microbiology<\/i>, doi:\u00a010.1016\/j.tim.2018.01.011<\/a>.<\/li>\n
        6. Akberdin, I. R., **<\/span>Thompson, M., & Kalyuzhnaya, M. G. (2018). Systems Biology and Metabolic Modeling of C1-Metabolism. In\u00a0Methane Biocatalysis: Paving the Way to Sustainability\u00a0\u00a0<\/em>(Eds: Kalyuzhnaya, M.G., Xing, X.H.) Springer International Publishing. 312pp.<\/span><\/em><\/span><\/em><\/a><\/span><\/span><\/li>\n
        7. Khmelenina V.N., Rozova O.N., Akberdin I. R., Kalyuzhnaya M. G. & Trotsenko Y. A. (2018). Pyrophosphate-Dependent Enzymes in Methanotrophs: New Findings and Views.<\/span> In\u00a0Methane Biocatalysis: Paving the Way to Sustainability<\/em><\/a>\u00a0(Eds: Kalyuzhnaya, M.G., Xing, X.H.) Springer International Publishing. 312pp.<\/span><\/span><\/span><\/li>\n
        8. *Hamilton, R., Becken U.,\u00a0& Kalyuzhnaya, M. G. <\/span>(2018). Growth of methanotrophic bacteria in chemostat mode in Eppendorf BioBlu 0.3f single-use vessels.\u00a0Eppendorf’s Application note,\u00a0362, <\/em>pdf file<\/a>.<\/li>\n<\/ol>\n
          2017<\/span><\/strong><\/h5>\n
            \n
          1. Osborne, K. A., Gray, N. D., Sherry, A., Leary, P., Mejeha, O., Bischoff, J., … & Talbot, H. M.<\/span> (2017). Methanotroph\u2010derived bacteriohopanepolyol (BHP) signatures as a function of temperature related growth, survival, cell death and preservation in the geological record.\u00a0Environmental Microbiology Reports<\/i>. doi:\u00a010.1111\/1758-2229.12570<\/a>.<\/li>\n
          2. Frindte, K., Kalyuzhnaya, M. G., Bringel, F., Dunfield, P. F., Jetten, M. S., Khmelenina, V. N., … & Semrau, J. D.<\/span> (2017). Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems.\u00a0Genome Announcements<\/i>,\u00a05<\/i>(33), e00526-17.\u00a0doi: 10.1128\/genomeA.00526-17<\/a>.<\/li>\n
          3. Demidenko, A., Akberdin, I. R., Allemann, M., Allen, E. E., & Kalyuzhanaya, M. G.<\/span> (2017). Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G (B1)<\/em>. Frontiers in Microbiology<\/i>, 7<\/i>, 2167. doi: <\/span>10.3389\/fmicb.2016.02167<\/a>.<\/li>\n
          4. **<\/span>Collins, D.A., Akberdin, I.R., & Kalyuzhnaya, M.G.\u00a0<\/span>(2016). Methylobacter<\/em>. Bergey’s Manual of Systematics of Archaea and Bacteria, 1-11. doi: 10.1002\/9781118960608.gbm01179.pub2<\/a>.<\/li>\n<\/ol>\n
            2016<\/span><\/strong><\/h5>\n
              \n
            1. Rush, D., Osborne, K. A., Birgel, D., Kappler, A., Hirayama, H., Peckmann, J., … Kalyuzhnaya, M., Sidgwick, F. R.&Talbot, H.M. (2016). The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems. PloS one<\/i>, 11<\/i>(11), e0165635. <\/span>doi:<\/span>10.1371\/journal.pone.0165635<\/a><\/span><\/li>\n
            2. Kalyuzhnaya, M.G.<\/span>\u00a0(2016). Methylomicrobium<\/em>. Bergey’s Manual of Systematics of Archaea and Bacteria, 1-10.\u00a0<\/span><\/span><\/li>\n
            3. Kalyuzhnaya, M.G.\u00a0(2016). Methylosarcina<\/em>.Bergey’s Manual of Systematics of Archaea and Bacteria, 1-7.\u00a0<\/span><\/span><\/li>\n
            4. Strong, P. J., Kalyuzhnaya, M., Silverman, J., & Clarke, W. P. A methanotroph-based biorefinery: Potential scenarios for generating multiple products from a single fermentation. Bioresource technology<\/i>, 215<\/i>, 314-323.\u00a0<\/span>doi:<\/span>\u00a010.1016\/j.biortech.2016.04.099<\/a><\/span><\/li>\n
            5. Henard, C.A., Smith, H., Dowe, N., Kalyuzhnaya, M.G.,\u00a0Pienkos, P.T., Guarnieri, M.T.<\/span> Bioconversion of methane to lactate by an obligate methanotrophic bacterium. Scientific Reports<\/i>,\u00a0<\/em> 6<\/i>, 21585.<\/span> doi:\u00a0<\/span>10.1038\/srep21585<\/a>.<\/li>\n
            6. Kalyuzhnaya M.G.<\/span> Methane biocatalysis: selecting the right microbe. In. Biotechnologies for biofuel production and optimization<\/em> (Ed. By C. Eckert and C.T.Trinh).<\/span><\/li>\n
            7. *<\/span>Flynn, J, Hirayama, H., Sakai, Y., Dunfield, P.F., Klotz, M.G., Knief, C., Op den Camp, H.J.M., … Kalyuzhnaya, M.G.<\/span> Draft genomes of gammaproteobacterial methanotrophs isolated from marine ecosystems. <\/span>Genome Announcements,<\/span>\u00a0<\/em> 4<\/i>(1), e01629-15<\/span>.\u00a0doi:\u00a0<\/span>10.1128\/genomeA.01629-15<\/a><\/li>\n<\/ol>\n
              2015<\/span><\/strong><\/h5>\n
                \n
              1. *<\/span>Hamilton, R., Kits, K. D., Ramonovskaya, V. A., Rozova, O. N., Yurimoto, H., Iguchi, H., … & Kalyuzhnaya, M. G<\/span>.<\/strong><\/span><\/span> (2015). Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems.\u00a0Genome Announcements<\/i>, 3<\/i>(3).\u00a0doi:\u00a010.1128\/genomeA.00515-15<\/a><\/li>\n
              2. de la Torre, A., *<\/span>Metivier, A., Chu, F., Laurens, L.M.L., Beck, D.A.C., Pienkos, P.T., Lidstrom, M.E. and Kalyuzhnaya, M.G.<\/span> (2015). Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in\u00a0Methylomicrobium buryatense<\/em>\u00a0strain 5G(B1). Microbial Cell<\/em> Factories<\/em>,\u00a014:188.\u00a0\u00a0doi: 10.1186\/s12934-015-0377-3<\/a><\/li>\n
              3. Kalyuzhnaya, M. G., Puri, A. W., & Lidstrom, M. E.<\/span> (2015). Metabolic engineering in methanotrophic bacteria. Metabolic Engineering<\/i>, 29<\/i>, 142-152.\u00a0doi:\u00a010.1016\/j.ymben.2015.03.01<\/a><\/li>\n
              4. Smalley, N. E., Taipale, S., De Marco, P., Doronina, N. V., Kyrpides, N., Shapiro, N., … & Kalyuzhnaya, M. G.<\/span> (2015). Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of the new species Methyloversatilis discipulorum<\/em> sp. nov. IJSEM <\/i>\u00a0ijs-0.\u00a0doi: 10.1099\/ijs.0.000190<\/a><\/li>\n
              5. Good, N. M., Lamb, A., Beck, D. A., Martinez-Gomez, N. C., & Kalyuzhnaya, M. G.<\/span> (2015). C1-Pathways in Methyloversatilis universalis<\/em> FAM5: genome wide gene expression and mutagenesis studies. Microorganisms<\/i>, 3<\/i>(2), 175-197.\u00a0doi:\u00a010.3390\/microorganisms3020175<\/a><\/li>\n<\/ol>\n
                Other (2015)<\/strong><\/h6>\n
                  \n
                1. Sharp, C. E., Smirnova, A. V., Kalyuzhnaya, M. G., Bringel, F., Hirayama, H., Jetten, M. S., … & Dunfield, P. F.<\/span> (2015). Draft genome sequence of the moderately halophilic methanotroph Methylohalobius crimeensis<\/em>\u00a0strain 10Ki.\u00a0Genome Announcements<\/i>, 3<\/i>(3), e00644-15.\u00a0doi:\u00a010.1128\/genomeA.00644-15<\/a><\/li>\n
                2. Kalyuzhnaya, M. G., <\/span>Lamb, A. E., McTaggart, T. L., Oshkin, I. Y., Shapiro, N., Woyke, T., & Chistoserdova, L<\/span>.<\/span> (2015). Draft genome sequences of gammaproteobacterial methanotrophs isolated from Lake Washington sediment.Genome Announcements<\/i>, 3<\/i>(2), e00103-15.\u00a0doi:\u00a010.1128\/genomeA.00103-15<\/a><\/li>\n
                3. Dedysh, S. N., Naumoff, D. G., Vorobev, A. V., Kyrpides, N., Woyke, T., Shapiro, N., … & Dunfield, P. F.<\/span> (2015). Draft genome sequence of Methyloferula stellata<\/em> AR4, an obligate methanotroph possessing only a soluble methane monooxygenase. Genome Announcements<\/i>, 3<\/i>(2), e01555-14.\u00a0doi:\u00a010.1128\/genomeA.01555-14<\/a><\/li>\n
                4. McTaggart, T. L., Beck, D. A., Setboonsarng, U., Shapiro, N., Woyke, T., Lidstrom, M. E., … & Chistoserdova, L<\/span>.<\/span> (2015). Genomics of methylotrophy in gram-positive methylamine-utilizing bacteria. Microorganisms<\/i>, 3<\/i>(1), 94-112.\u00a0doi:10.3390\/microorganisms3010094<\/a><\/li>\n
                5. Beck, D. A., McTaggart, T. L., Setboonsarng, U., Vorobev, A., Goodwin, L., Shapiro, N., … & Chistoserdova, L. <\/span>(2015). Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates. Environmental Microbiology<\/i>, 17<\/i>(3), 547-554.\u00a0doi:\u00a010.1111\/1462-2920.12736<\/a><\/li>\n
                6. But, S. Y., Khmelenina, V. N., Reshetnikov, A. S., Mustakhimov, I. I., Kalyuzhnaya, M. G., & Trotsenko, Y. A. <\/span>(2015). Sucrose metabolism in halotolerant methanotroph Methylomicrobium alcaliphilum<\/em> 20Z. Archives of Microbiology<\/i>, 197<\/i>(3), 471-480.\u00a0doi:\u00a010. 1007\/ s00203-015-1080-9<\/a><\/span><\/span><\/li>\n<\/ol>\n
                  Other (selected)<\/strong><\/h6>\n
                    \n
                  1. Yang, S., Matsen, J.B., Konopka, M., Green-Saxena, A., Clubb, J., Sadilek, M., Orphan, V.J., Beck, D., & <\/span>Kalyuzhnaya, M.G<\/span>.<\/em> 2013. Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium<\/em> OB3b. Part II. Metabolomics and 13C-labeling study. Front. Microbiol<\/em>., \u00a0doi:\u00a010.3389\/fmicb.2013.00070<\/a>.<\/li>\n
                  2. Matsen, J.B., Yang, S., Stein, L.Y., Beck, D., & Kalyuzhnaya, M.G.<\/em><\/span> 2013. Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium<\/em> OB3b. Part I. Transcriptomic study. Front. Microbiol.<\/em>,\u00a0 doi: 10.3389\/fmicb.2013.00040<\/a>.<\/li>\n
                  3. Konopka, M., Strovas, T. J., Ojala, D.S., Chistoserdova, L., Lidstrom, M.E., & Kalyuzhnaya, M.G<\/em>.<\/span> 2011. Respiration response imaging for real time detection of microbial function at the single cell level.Appl. Environ. Microbiol.,<\/em> 77 (1): 67-72.\u00a0doi:\u00a010.1128\/AEM.01166-10<\/a>.<\/li>\n
                  4. Ojala, D.S., Beck, D.A.C. & Kalyuzhnaya, M. G<\/em>.<\/em> <\/span>2011. Genetic systems for moderately halo(alkali)philic bacteria of the genus Methylomicrobium. Methods Enzymol.,<\/em> 495: 99-118.<\/li>\n
                  5. Latypova, E., Y.S. Wang, T. Wang, M. Hackett, H. Schafer, & Kalyuzhnaya, M. G<\/em>.<\/span> 2010. Genetics of the glutamate-mediated methylamine utilization pathway in the facultative methylotrophic beta-proteobacterium Methyloversatilis universalis<\/em> FAM5. Mol.Microbiol.,<\/em> 75(2): 426-439.\u00a0doi: \u00a010.1111\/j.1365-2958.2009.06989.x<\/a><\/li>\n
                  6. Kalyuzhnaya, M.G<\/em>.<\/em>, Lapidus, A., Ivanova, N., Copeland, A.C., McHardy, A.C., Szeto, E. Salamov, A., Grigoriev, I.V., Suciu, D., Levine, S.R., Markowitz, V.M., Rigoutsos, I., Tringe, S.G., Bruce, D.C., Richardson, P.M., Lidstrom, M.E., & L. Chistoserdova.<\/span> 2008. High-resolution metagenomics targets specific functional types in complex microbial communities. Nature Biotech.<\/em>\u00a0, 26: 1029 – 1034.\u00a0doi:\u00a010.1038\/nbt.1488<\/a>.<\/li>\n
                  7. Kalyuzhnaya, M.G<\/span><\/em>., Beck, D.A.C., Suciu, D., Pozhitkov, A., M.E. Lidstrom & L. Chistoserdova<\/span>. 2009. Functioning in situ<\/em>: gene expression in Methylotenera mobilis<\/em> in its native environment as assessed through transcriptomics. The ISME Journal.<\/em> 4: 388\u2013398.\u00a0doi:\u00a010.1038\/ismej.2009.117.<\/a><\/li>\n
                  8. Kalyuzhnaya, M.G<\/em>., Lidstrom, M.E. & L. Chistoserdova.<\/span> 2008. Real-time detection of actively metabolizing microbes via redox sensing as applied to methylotroph populations in Lake Washington. The ISME J.<\/em>, 2: 696-706.\u00a0doi:\u00a010.1038\/ismej.2008.32<\/a>.<\/li>\n<\/ol>\n

                    [\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

                      Lab publications (* undergraduate, ** graduate students) 2021 \u00a0*Johnson ZJ, *Krutkin DD, Bohutskyi P, Kalyuzhnaya MG (2021) Metals and methylotrophy: Via global gene expression studies. Methods Enzymol. 650:185-213. doi: 10.1016\/bs.mie.2021.01.046 \u00a0**Afshin Y, **Delherbe N, Kalyuzhnaya MG (2021) Methylotenera. Bergey’s Manual of Systematics of Archaea and Bacteria (BMSAB).\u00a0 Xiong W, Kalyuzhanaya MG, Henard CA (2021)\u00a0Editorial: […]<\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"

                    <\/h4>\r\n

                    Lab publications<\/h4>\r\n(* undergaduate student)\r\n

                    2018<\/span><\/h6>\r\n
                      \r\n \t
                    1. Akberdin, I. R., Thompson, M., Hamilton, R., Desai, N., Alexander, D., Henard, C. A., ... & Kalyuzhnaya, M. G.<\/span> (2018). Methane utilization in Methylomicrobium <\/em>alcaliphilum 20Z R<\/em>: a systems approach.\u00a0Scientific Reports<\/i>,\u00a08<\/i>(1), 2512.\u00a0doi: 10.1038\/s41598-018-20574-z<\/a>.<\/li>\r\n \t
                    2. Chistoserdova, L.\u00a0& Kalyuzhnaya, M. G.<\/span> (2018).\u00a0Current Trends in Methylotrophy.\u00a0\u00a0Trends in Microbiology<\/i>, doi:\u00a010.1016\/j.tim.2018.01.011<\/a>.<\/li>\r\n \t
                    3. Akberdin, I. R., Thompson, M., & Kalyuzhnaya, M. G. (2018).\u00a0 Book Chapter 7: \"Systems Biology and Metabolic Modeling of C1-Metabolism.\" in\u00a0Methane Biocatalysis: Paving the Way to Sustainability<\/em>, Editors: Kalyuzhnaya, Marina G., Xing, Xin-Hui, Springer Publishing.<\/span><\/span><\/li>\r\n<\/ol>\r\n
                      2017<\/span><\/h6>\r\n
                        \r\n \t
                      1. Osborne, K. A., Gray, N. D., Sherry, A., Leary, P., Mejeha, O., Bischoff, J., ... & Talbot, H. M.<\/span> (2017). Methanotroph\u2010derived bacteriohopanepolyol (BHP) signatures as a function of temperature related growth, survival, cell death and preservation in the geological record.\u00a0Environmental Microbiology Reports<\/i>. doi:\u00a010.1111\/1758-2229.12570<\/a>.<\/li>\r\n \t
                      2. Frindte, K., Kalyuzhnaya, M. G., Bringel, F., Dunfield, P. F., Jetten, M. S., Khmelenina, V. N., ... & Semrau, J. D.<\/span> (2017). Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems.\u00a0Genome Announcements<\/i>,\u00a05<\/i>(33), e00526-17.\u00a0doi: 10.1128\/genomeA.00526-17<\/a>.<\/li>\r\n \t
                      3. Demidenko, A., Akberdin, I. R., Allemann, M., Allen, E. E., & Kalyuzhanaya, M. G.<\/span> (2017). Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G (B1)<\/em>. Frontiers in Microbiology<\/i>, 7<\/i>, 2167. doi: <\/span>10.3389\/fmicb.2016.02167<\/a>.<\/li>\r\n \t
                      4. Collins, D.A., Akberdin, I.R., & Kalyuzhnaya, M.G.\u00a0<\/span>(2016). Methylobacter<\/em>. Bergey's Manual of Systematics of Archaea and Bacteria, 1-11. doi: 10.1002\/9781118960608.gbm01179.pub2<\/a>.<\/li>\r\n<\/ol>\r\n
                        2016<\/span><\/h6>\r\n
                          \r\n \t
                        1. Rush, D., Osborne, K. A., Birgel, D., Kappler, A., Hirayama, H., Peckmann, J., ... Kalyuzhnaya, M., Sidgwick, F. R.&Talbot, H.M. (2016). The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems. PloS one<\/i>, 11<\/i>(11), e0165635. doi:<\/span>10.1371\/journal.pone.0165635<\/a><\/span><\/li>\r\n \t
                        2. Kalyuzhnaya, M.G.<\/span>\u00a0(2016). Methylomicrobium<\/em>. Bergey's Manual of Systematics of Archaea and Bacteria, 1-10.\u00a0<\/span><\/li>\r\n \t
                        3. Kalyuzhnaya, M.G.\u00a0(2016). Methylosarcina<\/em>.Bergey's Manual of Systematics of Archaea and Bacteria, 1-7.\u00a0<\/span><\/span><\/li>\r\n \t
                        4. Strong, P. J., Kalyuzhnaya, M., Silverman, J., & Clarke, W. P. A methanotroph-based biorefinery: Potential scenarios for generating multiple products from a single fermentation. Bioresource technology<\/i>, 215<\/i>, 314-323.\u00a0doi:<\/span>\u00a010.1016\/j.biortech.2016.04.099<\/a><\/span><\/li>\r\n \t
                        5. Henard, C.A., Smith, H., Dowe, N., Kalyuzhnaya, M.G.,\u00a0Pienkos, P.T., Guarnieri, M.T.<\/span> Bioconversion of methane to lactate by an obligate methanotrophic bacterium. Scientific Reports<\/i>,\u00a0<\/em> 6<\/i>, 21585. doi:\u00a0<\/span>10.1038\/srep21585<\/a>.<\/li>\r\n \t
                        6. Kalyuzhnaya M.G.<\/span> Methane biocatalysis: selecting the right microbe. In. Biotechnologies for biofuel production and optimization<\/em> (Ed. By C. Eckert and C.T.Trinh).<\/span><\/li>\r\n \t
                        7. Flynn, J*, Hirayama, H., Sakai, Y., Dunfield, P.F., Klotz, M.G., Knief, C., Op den Camp, H.J.M., ... Kalyuzhnaya, M.G.<\/span> Draft genomes of gammaproteobacterial methanotrophs isolated from marine ecosystems. Genome Announcements,\u00a0<\/em> 4<\/i>(1), e01629-15.\u00a0doi:\u00a0<\/span>10.1128\/genomeA.01629-15<\/a><\/li>\r\n<\/ol>\r\n
                          2015<\/span><\/h6>\r\n
                            \r\n \t
                          1. Hamilton, R.*, Kits, K. D., Ramonovskaya, V. A., Rozova, O. N., Yurimoto, H., Iguchi, H., ... & Kalyuzhnaya, M. G<\/span>.<\/strong><\/span><\/span> (2015). Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems.\u00a0Genome Announcements<\/i>, 3<\/i>(3).\u00a0doi:\u00a010.1128\/genomeA.00515-15<\/a><\/li>\r\n \t
                          2. de la Torre, A., Metivier, A.*, Chu, F., Laurens, L.M.L., Beck, D.A.C., Pienkos, P.T., Lidstrom, M.E. and Kalyuzhnaya, M.G.<\/span> (2015). Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in\u00a0Methylomicrobium buryatense<\/em>\u00a0strain 5G(B1). Microbial Cell<\/em> Factories<\/em>,\u00a014:188.\u00a0\u00a0doi: 10.1186\/s12934-015-0377-3<\/a><\/li>\r\n \t
                          3. Kalyuzhnaya, M. G., Puri, A. W., & Lidstrom, M. E.<\/span> (2015). Metabolic engineering in methanotrophic bacteria. Metabolic Engineering<\/i>, 29<\/i>, 142-152.\u00a0doi:\u00a010.1016\/j.ymben.2015.03.01<\/a><\/li>\r\n \t
                          4. Smalley, N. E., Taipale, S., De Marco, P., Doronina, N. V., Kyrpides, N., Shapiro, N., ... & Kalyuzhnaya, M. G.<\/span> (2015). Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of the new species Methyloversatilis discipulorum<\/em> sp. nov. IJSEM <\/i>\u00a0ijs-0.\u00a0doi: 10.1099\/ijs.0.000190<\/a><\/li>\r\n \t
                          5. Good, N. M., Lamb, A., Beck, D. A., Martinez-Gomez, N. C., & Kalyuzhnaya, M. G.<\/span> (2015). C1-Pathways in Methyloversatilis universalis<\/em> FAM5: genome wide gene expression and mutagenesis studies. Microorganisms<\/i>, 3<\/i>(2), 175-197.\u00a0doi:\u00a010.3390\/microorganisms3020175<\/a><\/li>\r\n<\/ol>\r\nOther (2015)\r\n
                              \r\n \t
                            1. Sharp, C. E., Smirnova, A. V., Kalyuzhnaya, M. G., Bringel, F., Hirayama, H., Jetten, M. S., ... & Dunfield, P. F.<\/span> (2015). Draft genome sequence of the moderately halophilic methanotroph Methylohalobius crimeensis<\/em>\u00a0strain 10Ki.\u00a0Genome Announcements<\/i>, 3<\/i>(3), e00644-15.\u00a0doi:\u00a010.1128\/genomeA.00644-15<\/a><\/li>\r\n \t
                            2. Kalyuzhnaya, M. G., <\/span>Lamb, A. E., McTaggart, T. L., Oshkin, I. Y., Shapiro, N., Woyke, T., & Chistoserdova, L<\/span>.<\/span> (2015). Draft genome sequences of gammaproteobacterial methanotrophs isolated from Lake Washington sediment.Genome Announcements<\/i>, 3<\/i>(2), e00103-15.\u00a0doi:\u00a010.1128\/genomeA.00103-15<\/a><\/li>\r\n \t
                            3. Dedysh, S. N., Naumoff, D. G., Vorobev, A. V., Kyrpides, N., Woyke, T., Shapiro, N., ... & Dunfield, P. F.<\/span> (2015). Draft genome sequence of Methyloferula stellata<\/em> AR4, an obligate methanotroph possessing only a soluble methane monooxygenase. Genome Announcements<\/i>, 3<\/i>(2), e01555-14.\u00a0doi:\u00a010.1128\/genomeA.01555-14<\/a><\/li>\r\n \t
                            4. McTaggart, T. L., Beck, D. A., Setboonsarng, U., Shapiro, N., Woyke, T., Lidstrom, M. E., ... & Chistoserdova, L<\/span>.<\/span> (2015). Genomics of methylotrophy in gram-positive methylamine-utilizing bacteria. Microorganisms<\/i>, 3<\/i>(1), 94-112.\u00a0doi:10.3390\/microorganisms3010094<\/a><\/li>\r\n \t
                            5. Beck, D. A., McTaggart, T. L., Setboonsarng, U., Vorobev, A., Goodwin, L., Shapiro, N., ... & Chistoserdova, L. <\/span>(2015). Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates. Environmental Microbiology<\/i>, 17<\/i>(3), 547-554.\u00a0doi:\u00a010.1111\/1462-2920.12736<\/a><\/li>\r\n \t
                            6. But, S. Y., Khmelenina, V. N., Reshetnikov, A. S., Mustakhimov, I. I., Kalyuzhnaya, M. G., & Trotsenko, Y. A. <\/span>(2015). Sucrose metabolism in halotolerant methanotroph Methylomicrobium alcaliphilum<\/em> 20Z. Archives of Microbiology<\/i>, 197<\/i>(3), 471-480.\u00a0doi:\u00a010. 1007\/ s00203-015-1080-9<\/a><\/span><\/span><\/li>\r\n<\/ol>\r\nOther (selected)\r\n
                                \r\n \t
                              1. Yang, S., Matsen, J.B., Konopka, M., Green-Saxena, A., Clubb, J., Sadilek, M., Orphan, V.J., Beck, D., & <\/span>Kalyuzhnaya, M.G<\/span>.<\/em> 2013. Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium<\/em> OB3b. Part II. Metabolomics and 13C-labeling study. Front. Microbiol<\/em>., \u00a0doi:\u00a010.3389\/fmicb.2013.00070<\/a>.<\/li>\r\n \t
                              2. Matsen, J.B., Yang, S., Stein, L.Y., Beck, D., & Kalyuzhnaya, M.G.<\/em><\/span> 2013. Global molecular analyses of methane metabolism in methanotrophic Alphaproteobacterium, Methylosinus trichosporium<\/em> OB3b. Part I. Transcriptomic study. Front. Microbiol.<\/em>,\u00a0 doi: 10.3389\/fmicb.2013.00040<\/a>.<\/li>\r\n \t
                              3. Konopka, M., Strovas, T. J., Ojala, D.S., Chistoserdova, L., Lidstrom, M.E., & Kalyuzhnaya, M.G<\/em>.<\/span> 2011. Respiration response imaging for real time detection of microbial function at the single cell level.Appl. Environ. Microbiol.,<\/em> 77 (1): 67-72.\u00a0doi:\u00a010.1128\/AEM.01166-10<\/a>.<\/li>\r\n \t
                              4. Ojala, D.S., Beck, D.A.C. & Kalyuzhnaya, M. G<\/em>.<\/em> <\/span>2011. Genetic systems for moderately halo(alkali)philic bacteria of the genus Methylomicrobium. Methods Enzymol.,<\/em> 495: 99-118.<\/li>\r\n \t
                              5. Latypova, E., Y.S. Wang, T. Wang, M. Hackett, H. Schafer, & Kalyuzhnaya, M. G<\/em>.<\/span> 2010. Genetics of the glutamate-mediated methylamine utilization pathway in the facultative methylotrophic beta-proteobacterium Methyloversatilis universalis<\/em> FAM5. Mol.Microbiol.,<\/em> 75(2): 426-439.\u00a0doi: \u00a010.1111\/j.1365-2958.2009.06989.x<\/a><\/li>\r\n \t
                              6. Kalyuzhnaya, M.G<\/em>.<\/em>, Lapidus, A., Ivanova, N., Copeland, A.C., McHardy, A.C., Szeto, E. Salamov, A., Grigoriev, I.V., Suciu, D., Levine, S.R., Markowitz, V.M., Rigoutsos, I., Tringe, S.G., Bruce, D.C., Richardson, P.M., Lidstrom, M.E., & L. Chistoserdova.<\/span> 2008. High-resolution metagenomics targets specific functional types in complex microbial communities. Nature Biotech.<\/em>\u00a0, 26: 1029 - 1034.\u00a0doi:\u00a010.1038\/nbt.1488<\/a>.<\/li>\r\n \t
                              7. Kalyuzhnaya, M.G<\/span><\/em>., Beck, D.A.C., Suciu, D., Pozhitkov, A., M.E. Lidstrom & L. Chistoserdova<\/span>. 2009. Functioning in situ<\/em>: gene expression in Methylotenera mobilis<\/em> in its native environment as assessed through transcriptomics. The ISME Journal.<\/em> 4: 388\u2013398.\u00a0doi:\u00a010.1038\/ismej.2009.117.<\/a><\/li>\r\n \t
                              8. Kalyuzhnaya, M.G<\/em>., Lidstrom, M.E. & L. Chistoserdova.<\/span> 2008. Real-time detection of actively metabolizing microbes via redox sensing as applied to methylotroph populations in Lake Washington. The ISME J.<\/em>, 2: 696-706.\u00a0doi:\u00a010.1038\/ismej.2008.32<\/a>.<\/li>\r\n<\/ol>","_et_gb_content_width":"","footnotes":""},"class_list":["post-150","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/150","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/comments?post=150"}],"version-history":[{"count":87,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/150\/revisions"}],"predecessor-version":[{"id":1323,"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/pages\/150\/revisions\/1323"}],"wp:attachment":[{"href":"https:\/\/sci.sdsu.edu\/kalyuzhlab\/wp-json\/wp\/v2\/media?parent=150"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}