Holman Lab

Publications

2010-2012

  1. Mason, O.U.; Hazen, T.C.; Borglin, S.; Chain, P.S.G.; Dubinsky, E.A.; Fortney, J.L.; Han, J.; Holman, H.-Y.N.; Hultman, J.; Lamendella, R.; Mackelprang, R.; Malfatti, S.; Tom, L.M.; Tringe, S.G.; Woyke, T.; Zhou, J.; Rubin, E.M.; Jansson, J.K. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISEM, DOI:10.1038/ismej.2012.59 link

  2. Chen, L., Holman, H.-Y.N., Hao, Z., Bechtel H.A., Martin M.C., Wu C., and Chu Steven. Synchrotron infrared measurements of protein phosphorylation in living single PC12 cells during neuronal differentiation. Analytical Chemistry,  84(9), 4118-4125, and in Chemical & Engineering News, 2012. link

  3. Choi S., Park I., Hao Z., Holman H.-Y.N., Pisano, A.P. Quantitative Studies of Long-term Stable, Top-down Fabricated Silicon Nanowire pH Sensors. Appl Phys A, published online, 2012.
  4. Cheng, YG, Holman, H.-Y.N., Lin, Z. Remediation of Chromium and Uranium Contamination by Microbial Activity. Elements, 8(2), 107-112, 2012.

  5. Bælum, J., Borglin, S., Chakraborty, R., Fortney, J.L., Lamendella, R., Mason, O.U., Auer, M., Zemla, M., Bill, M., Conrad, M.E., Malfatti, S.A., Tringe, S.G., Holman,H.-Y.N., T.C. Hazen, and Jansson, J.K. Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environmental Microbiology, accepted 2012.

  6. Holman, H.-Y.N. and F. G. Blankenbery. Mid-Infrared Reflectivity of Mouse Atheromas: A Case Study,  in Biomedical Applications of Synchrotron Infrared Microspectroscopy: A Practical Approach(RSC Analytical Spectroscopy Series), Royal Society of Chemistry, 351-366, 2011.
  7. Tsibakhashvili, N.Y., Kalabegishvili, T.L., Rcheulishvili, A.N., Gintury, E.N., Lomidze, L.G., Gvarjaladze, Rcheulishvili, O.A., H.-Y.N. Holman. Effect of Zn (II) on the reduction and accumulation of Cr(VI) by Arthrobacter species. J. Ind. Microbiol. Biotechnol. (published online), 2011.  
  8. Holman, H.-Y. N.,  Bechtel, H.A., Hao, Z., and M.C. Martin. Synchrotron IR Spectromicroscopy: Chemistry of Living Cells. Analytical Chemistry (Cover feature article), 82(21), 8757-8765, November 1, 2010.
  9. Hoi-Ying N. Holman, Zhao Hao, Michael C. Martin, Hans A. Bechtel, Infrared Spectromicroscopy: Probing Live Cellular Responses to Environmental Changes, Synchrotron Radiation News, 23, 12, 2010.
  10. Hazen, T.C., Dubinsky, E. A., DeSantis, T.Z., Andersen, G.L., Piceno, Y. M., Singh, N., Jansson, J.R., Probst, A., Borglin, S.E., Fortney, J.L., Stringfellow, W.T., Bill, M., Conrad, M.S., Tom, L.M., Chavarria, K.L., Alusi, T.R., Lamendella, R., Joyner, D.C., Spier, C., Auer, M., Zemla, M.L., Chakraborty, R., Sonnenthal, E.L.,  D'haeseleer, P.,   Holman, H.-Y. N.,  Osman, S., Lu, Z.,  Van Nostrand, J.D., Deng, Y., Zhou,  J., and Mason, O.U.  Deep-sea oil plume enriches psychrophilic oil-degrading bacteria, Science, 330(6001), 204-208, 2010.
  11. Holman, H.-Y.N. Synchrotron infrared spectromicroscopy for studying chemistry of microbial activity in geologic materials, in Synchrotron-Based Techniques in Soils and Sediments, (Editors: B. Singh and M. Gräfe), Developments in Soil Science, Vol. 34, 103-130, Elsevier, 2010.
  12. Lacayo, C.I., Malkin, A.J., Holman, H.-Y. N., Chen, L., Ding, S.-Y., Hwang, M.S., and M.P. Thelen. Imaging cell wall architecture in single Zinnia elegans tracheary elements, Plant Physiology, 154, 121-133, 2010.
  13. Asatiani, N., Abuladze, M., Kartvelishvili, T., Kulikova, N., Asanishvili, L., Holman, H.-Y.N., and N. Sapojnikova. Response of antioxidant defense system to chromium(CI)-induced cytotoxicity in human diploid cells, Biometals, 23:161-172, 2010.

2008-2009

  1. Choi, S., Park, I., Hao, Z., Holman, H.-Y.N., Pisano, A., and T. Zohdi. Ultra-Fast Self-Assembly of Micro-Scale Particles by Open-Channel Flow. Langmuir, 26(7):, 4661-4667, 2009.  
  2. Holman, H.-Y.N., Miles, R., Hao, Z., Wozei, E., Anderson, L.M., and H. Yang. Real-time Chemical Imaging of Bacterial Activity in Biofilms Using Open-Channel Microfluidics and Synchrotron FTIR Spectromicroscopy. Analytical Chemistry, 81(20), 8564-8570, 2009.
  3. Holman, H.-Y.N., Wozei, E., Lin, Z., Comolli, L.R., Ball, D.A., Borglin, S., Field M.W., Hazen, T.C. and K.H. Downing. Real-time molecular monitoring of chemical environment in obligated anaerobes during oxygen adaptive response. PNAS USA, 106(31), 12599-12640, 2009.
  4. Tsibakhashvili, N., Kalabegishvili, T., Rchenlishvili A. V., Murusidze, I., Rchenlishvili O.A., Kerkenjia, S.. Holman, H.-Y. N. Decomposition of Cr(V)-diols to Cr(III) complexes A. oxydans. Microbial Ecology, 57:360-366, 2009.
  5. Holman, H.-Y.N. Bjornstad, C., Rosenberg, C., Martin, M.C., McKinney, W.R., Blakely E.A., and  F.G.  Blankenberg, Mid-infrared reflectivity of Experimental Atheromas. J. of Biomedical Optics, 13, 2008.
  6. Tsibakhashvili, N., Kalabegishvili, T., Mosulishvili,L., Kirkesali, E., Kerkenjia, S.. Murusidze, I., Holman, H.-Y. N., Frontasyeva, M.V., and S.F. Gundorina. Biotechnology of Cr(VI) transformation into Cr(III) complexes. J. of Radioanalytical and Nuclear Chemistry, 278(3), 2008.

2006-2007

  1. Yang, C., Cheng, Y., Ma, X., Zhu, Y., Holman, H.-Y.N., Zhang, L., and C. Wang. Surface mediated chromate-resistant mechanism of Enterobacter cloacae bacteria investigated by atomic force microscopy. Langmuir, 23(8), 4480-4485, 2007.
  2. Holman, H-Y. N., and M.C. Martin. Synchrotron radiation infrared spectromicroscopy: a non-invasive molecular probe for biogeochemical processes. Advances in Agronomy, 90: 79-127, 2006.
  3. R. Codd, P. Lay, N. Tsibakhashvili, T. Kalabegishvili, I. Murusidze, H.-Y. N. Holman. Chromium(V) complexes generated in Arthrobacter oxydans  by simulation analysis of EPR spectra.  J. Inorg. Biochem. 100, 1827-1833, 2006.
  4. Lin, Z., Zhu, Y., Kalabegishvili T.L., Tsibakhashvili, N.Y., and H.-Y. N. Holman. Effect of chromate action on morphology of basalt-inhabiting bacteria. Materials Science and Engineering C. 26:610-612, 2006.
  5. Woods, K.N., Lee, S.A., Holman, H.-Y. N., and J. Wiedemann. “The effect of solvent dynamics on the low frequency collective motions of DNA in solution and unoriented films”, J. Chemical Physics, 124:224706-1 – 224706-8, 2006.
  6. Mukhopadhyay A., He Z., Alm E.J., Arkin A.P., Baidoo E.E., Borglin S.C., Chen W., Hazen T.C., He Q.,  Holman H.-Y. N., Huang K., Huang R., Joyner D.C., Katz N., Keller M., Oeller P., Redding A., Sun J., Wall J., Wei1 J., Yen H.-C., Zhou J., and J. D. Keasling. Salt stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics approach. J. of Bacteriology, 188(11): 4068-4018, 2006. 
  7. Tsibakhashvili N.Y., Frontasyeva M.V., Kirkesali E.I., Aksenova N.G., Kalabegishvili, T.L., Murusidze I.G., Mosulishvili, L.M., H.-Y. N. Holman. Epithermal Neutron Activation Analysis of Cr(VI)-Reducer Basalt-Inhabiting Bacteria. Analytical Chemistry, 78(18), 6285-6290, 2006.
  8. Kalabegishvili, T.L., Tsibakhashvili, N.Y., Murusidze, G., Pataraya, D.T., Gurielidze, M.A., and H.-Y.N. Holman. Formation of Cr(V) and Cr(III) in Arthrobacter oxydans Exposed to High Concentratins of Cr(VI). in Modern Multidisciplinary Applied Microbiology: Exploiting Microbes and Their Interactions, A. Mendez-Vilas (edt.), 516-520, Wiley Online Library.
  9. Wozei E., Hermanowicz S. W., and H-Y. N. Holman. Developing a biosensor for estrogens in water samples: Study of the real-time response of live cells of the estrogen-sensitive yeast strain RMY/ER-ERE using fluorescence microscopy. Biosensors & Bioelectronics. 21(8): 1654-1658, 2006.
  10. Monaselidze J., Abuladze M., Asatiani N., Kiziria E., Barbakadze S., Majagaladze G., Iobadze M., Tabatadze L., Holman H.-Y. N., and N. Sapojnikova. Characterization of chromium-induced apoptosis in cultured mammalian cells: A differential scanning calorimetry study. Thermochimica Acta. 441:8-15, 2006.

2005 and Earlier

  1. Stroo H.F., Nakles D.V., Kreitinger J. P.,  Lohehr R.C.,  Hawthorn, S.B., Luthy, R.G., Holman H.-Y. N., and A. Lapierre. Improving Risk Assessments for Manufactured Gas Plant Soils by Measuring PAH Availability. Integrated Environmental Assessment and Management. 1( 3): 259–266,  2005. 
  2. Asatiani N.V., Abuladze MK., Kartvelishvili T.M., Bakradze N.G., Sapojnikova N.A., Tsibakhashvili N.Y., Tabatadze L.V., Lejava L.V. Asanishvili L.L., Holman H.Y. Effect of Chromium(VI) action on Arthrobacter oxydans. [Article] Current Microbiology. 49(5):321-326, 2004.
  3. Tsibakhashvili N.Y., Mosulishvili L.M., Kalabegishvili T.L., Kirkesali E.I., Frontasyeva M.V., Pomyakushina E.V., Pavlov S.S., Holman H.-Y.N. ENAA studies of chromium uptake by Arthrobacter oxydans. Journal of Radioanalytical & Nuclear Chemistry. 259(3):527-531, 2004.
  4. Asatiani N., Sapojnikova N., Abuladze M., Kartvelishvili T.L., Kulikov, N., Kiziria E., Namchevadz, E., and H.-Y. N. Holman. “Effects of Cr(VI) long-term and low-dose action on mammalian antioxidant enzymes: An in vitro study”. J. Inorganic Biochemistry, 98, 490-496, 2004.
  5. Kartvelishvili T, Abuladze M, Asatiani N, Akhvlediani J, Kiziria E, Asanishvili L, Lejava L, Holman H.-Y.N., Sapojnikova N. Estimation of the cellular antioxidant response to chromium action using ESR method. ScientificWorldJournal. Sep 2;4:785-794, 2004.
  6. Kartvelishvili T, Abuladze M, Asatiani N, Akhvlediani J, Asanishvili L, Holman H.-Y.N., Sapojnikova N. Antioxidant capacity of cultured mammalian cells estimated by ESR method. ScientificWorldJournal. Jun 29;4:490-499, 2004.
  7. Tsibakhashvili, N.Y., Mosulishvili, N.A., Kalabegishvili, T.L., Kirkesali, T.I., Frontasyeva, M.V., Pomyakushina, E.V., Pavlov, S.S., and H.-Y. N. Holman. “Epithermal neutron activation analysis (ENAA) studies of chromium uptake by Arthrobacter oxydans”. Journal of Radioanalytical and Nuclear Chemistry, 259 (1/2), 2004.
  8. Holman, H.-Y. N., Martin, M.C. and W.R. McKinney. "Tracking chemical changes in a live cell: Biomedical Applications of SR-FTIR Spectromicroscopy", in Special issue: First International Conference on Biomedical Spectroscopy: From Molecules to men”, Spectroscopy - An International Journal, 17(2-3), 139-160. 2003.
  9. Holman, H.-Y. N., Martin, M.C. and W. R. McKinney "Synchrotron-Based FTIR Spectromicroscopy: Cytotoxicity Considerations" J. Biological Physics 29, 275-286, 2003.
  10. Kalabegishvili, T.L, Tsibakhashvili, N.Y. and H.-Y. N. Holman. “Electron spin resonance study of chromium(V) formation and decomposition by basalt-inhabiting bacteria”. Environmental Science & Technology, 37, 4678-4684, 2003.
  11. Bakradze, N., Sokhadze, V., Abuladze, M., Asatiani, N., Sapojnikova, N., Kartvelishvili, T.L., Tsibakhashvili, N.Y., Namchevadze, E., Tabatadze, L., Lejava, L., and H.-Y.N. Holman. “A Calorimetric Characterization of Cr(VI)-reducing Arthrobacter oxydans at different phases of the cell growth cycle”. TheScientificWorldJournal, 3, 432-442, 2003.
  12. Holman, H.-Y. N., Bjornstad, K.A., McNamara, M.P., Martin, M.C., McKinney, W.R., and E.A. Blakely. “Synchrotron Infrared Spectromicroscopy as a Novel Bioanalytical Microprobe for Individual Living Cells: Cytotoxicity Considerations”. Selected as an important article of Frontier Research and published by Virtual Journal of Biological Physics Research at http://www.vjbio.org.  8(1), 2002. 
  13. Holman, H.-Y. N., Bjornstad, K.A., McNamara, M.P., Martin, M.C., McKinney, W.R., and E.A. Blakely. “Synchrotron Infrared Spectromicroscopy as a Novel Bioanalytical Microprobe for Individual Living Cells: Cytotoxicity Considerations”. J. of Biomedical Optics, 7(3), 417-424, 2002.
  14. Holman, H.-Y. N., Nieman, K., Sorensen, D.L., Miller, C.D., Martin, M.C.; Borch, T., McKinney, W.R., and R.C. Sims. “Catalysis of PAH Biodegradation by Humic Acid Shown in Synchrotron Infrared Studies”. Environmental Science & Technology, 36(6): 1276-1280, 2002.
  15. Holman, H.-Y. N., Bjornstad, K.A., McNamara, M.P., Martin, M.C., McKinney, W.R., and E.A. Blakely. “Synchrotron Infrared Spectromicroscopy as a Novel Bioanalytical Microprobe for Individual Living Cells: Cytotoxicity Considerations”. J. of Biomedical Optics, 7(3), 417-424, 2002.
  16. Tsibakhashvili,  N.Y., Asatiani, N.V., Abuladze, M.K., Birkaya, B.G., Sapojnikova, N.A., Mosulishvili, L.M., and H.-Y. N. Holman. “Capillary Electrophoresis of Cr(VI) Reducer Arthrobacter oxydans”. Biomedical Chromatography, 16(5): 327-331, 2002.
  17. Bhupathiraju, V. K., Krauter, P., Holman, H-Y. N., Conrad, M. E., Daley, P. F., Templeton, A. S., Hunt, J. R., Hernandez, M., and L. Alvarez-Cohen. "Assessment of in-situ bioremediation at a refinery waste-contaminated site and an aviation gasoline contaminated site". Biodegradation, 13(2):79-90, 2002.
  18. Abuladze, M.K., Asatiani, N.V., Bakradze, N.  G., Kartvelishvili, T.M., Holman, H.-Y. N., Kalabegishvili,  T.L., Mosulishvili, L.M., Rcheulishvili, A.N., Sapojnikova, N.A., and N. Y. Tsibakhashvili. “Effect of Chromium Action on the Protein Composition of A. oxydans" Fresenius of Environmental Bulletin, 11(9A): 562-567, 2002.
  19. Tsibakhashvili N.Y., Mosulishvili, L.M., Kalabegishvili, T.L., Pataraya, D.T., Gurielidze, M.A., and G.S. Nadareishvili, and H.-Y. N. Holman. “Chromate-Resistant and –Reducing Microorganisms in Georgia Basalts: Their Distribution and Characterization”. Fresenius of Environmental Bulletin, 11(10), 352-361, 2002.
  20. Holman, H.-Y. N., Goth-Goldstein, R., Martin, M.C., Russell, M.L., and W.R. McKinney. "Low-dose responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin in single living human cells measured by synchrotron infrared spectromicroscopy,” Environ. Sci. & Tech., 34 (12), 2513-2517, 2000.
  21. Holman, H.-Y. N., Martin, M.C., Blakely, E.A., Bjornstad, K., and W.R. McKinney. "Infrared spectroscopic characteristics of cell cycle and cell death probed by synchrotron-based FTIR spectromicroscopy,” Biopolymers: Biospectroscopy, 57[6], 329-335, 2000.
  22. Holman, H.-Y. N., Goth-Goldstein, R., Blakely, E.A., Bjornstad, K., Martin, M.C., and W.R. McKinney. "Individual Human Cell Responses to Low Doses of Chemicals Studied by Synchrotron Infrared Spectromicroscopy", in Biomedical Spectroscopy: Vibrational Spectroscopy and Other Novel Techniques, SPIE Vol. 3918, 57-63, 2000.
  23. Geller, J.T., Holman, H.-Y. N., Su, G., Conrad, M.E., Pruess, K., and J.C. Hunter-Cevera. “Flow dynamics and potential for biodegradation of organic contaminants in fractured rock vadose zones,” J. Contaminant Hydrology, 43(1), 63-90, 2000.
  24. Holman, H.-Y. N., Perry, D.L., Martin, M.C., Geraldine Lamble, W.R. McKinney, and J.C. Hunter-Cevera. “Real-time Characterization of Biogeochemical Reduction of Cr(VI) on Basalt Surfaces by SR-FTIR Imaging,” Geomicrobiology J., 16(4), 307-323. 1999.
  25. Holman, H.-Y. N., Tsang, Y.W., and W.R. Holman. Mineralization of sparsely water-soluble polycyclic aromatic hydrocarbons in a water table fluctuation zone. Environ. Sci. Technol., 33,1819-1824, 1999.
  26. Zhang, M., Holman, H.-Y. N., Ferrari, M., and J.C. Hunter-Cevera. “Synchrotron infrared microspectroscopy for assessment of mutagenicity of metal implants,” Biomedical Materials - Drug Delivery, Implants and Tissue Engineering, MRS Symp. Series, 163-169, 1999.  
  27. Holman, H.-Y. N., Perry, D.L., and J.C. Hunter-Cevera. Surface-enhanced infrared absorption-reflectance (SEIRA) microspectroscopy – a chemical/biological probe for bacteria localization in geologic materials. J. Microbiol. Methods, 34/1, 59-71, 1998.
  28. Holman, H.-Y. N., Perry, D.L., Martin, M.C., and W.R. McKinney. Applications of synchrotron infrared microspectroscopy to the study of inorganic-organic interactions at the bacterial-mineral interface, Application of Synchrotron Radiation Techniques to Materials Sciences, MRS Symp. Series, 17-24, 1998.
  29. Holman, H.-Y. N., and I. Javandel. Evaluation of transient dissolution of slightly water-soluble compounds from a light nonaqueous phase liquid pool, Water Resources Research, 32, 915-923, 1996.
  30. Holman, H.-Y. N., and Y.W. Tsang. Effects of soil moisture on biodegradation of petroleum hydrocarbons. In:  In situ aeration: air sparging, bioventing and related remediation processes, Battelle Press, Richland. 323-332, 1995.
  31. Javandel, I., Falta, R.W., and H.-Y.N. Holman. Recent developments in transport and fate of non-aqueous phase liquids in the subsurface environment, Iran. J. of Sci. and Technol., 14, 269, 1990.
  32. Narasimhan, T.N., Tsang, Y.W., and H.-Y. N. Holman. On the potential importance of transient air flow in advective radon entry into buildings. Geophysical Research Letters, 1990.