Jizhong Zhou

Summary

Affiliation: University of Oklahoma
Country: USA

Publications

  1. ncbi Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions
    Bo Li
    School of Computing, Clemson University, Clemson, SC 29634, USA
    BMC Syst Biol 5:73. 2011
  2. ncbi Pellicle formation in Shewanella oneidensis
    Yili Liang
    School of Minerals Processing and Bioengineering, Central South University, Changsha, PR China
    BMC Microbiol 10:291. 2010
  3. ncbi Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site
    Jessica E Butler
    Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
    BMC Genomics 8:180. 2007
  4. ncbi Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1
    Weimin Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    BMC Genomics 7:76. 2006
  5. ncbi Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach
    Debora F Rodrigues
    Michigan State University, NASA Astrobiology Institute and Center for Microbial Ecology, East Lansing, MI 48824, USA
    BMC Genomics 9:547. 2008
  6. ncbi Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory
    Feng Luo
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    BMC Bioinformatics 8:299. 2007
  7. ncbi Spatial scaling of functional gene diversity across various microbial taxa
    Jizhong Zhou
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Proc Natl Acad Sci U S A 105:7768-73. 2008
  8. ncbi How sulphate-reducing microorganisms cope with stress: lessons from systems biology
    Jizhong Zhou
    Stephenson Research and Technology Center, 101 David L Boren Blvd, Institut for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    Nat Rev Microbiol 9:452-66. 2011
  9. ncbi Reproducibility and quantitation of amplicon sequencing-based detection
    Jizhong Zhou
    Department of Environmental Science and Engineering, Tsinghua University, Beijing, China
    ISME J 5:1303-13. 2011
  10. ncbi GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer
    Joy D Van Nostrand
    Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
    Environ Microbiol 11:2611-26. 2009

Detail Information

Publications100

  1. ncbi Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions
    Bo Li
    School of Computing, Clemson University, Clemson, SC 29634, USA
    BMC Syst Biol 5:73. 2011
    ..Synthetic lethal genetic interactions among proteins have been widely used to define functional relationships between proteins and pathways. However, the molecular mechanism of synthetic lethal genetic interactions is still unclear...
  2. ncbi Pellicle formation in Shewanella oneidensis
    Yili Liang
    School of Minerals Processing and Bioengineering, Central South University, Changsha, PR China
    BMC Microbiol 10:291. 2010
    ..The goal of this work was to understand basic requirements and mechanism of pellicle formation in S. oneidensis...
  3. ncbi Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site
    Jessica E Butler
    Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
    BMC Genomics 8:180. 2007
    ..Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known...
  4. ncbi Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1
    Weimin Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    BMC Genomics 7:76. 2006
    ....
  5. ncbi Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach
    Debora F Rodrigues
    Michigan State University, NASA Astrobiology Institute and Center for Microbial Ecology, East Lansing, MI 48824, USA
    BMC Genomics 9:547. 2008
    ..We used Exiguobacterium sibiricum strain 255-15, a psychrotrophic bacterium from 3 million year old Siberian permafrost that grows from -5 degrees C to 39 degrees C to study its thermal adaptation...
  6. ncbi Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory
    Feng Luo
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    BMC Bioinformatics 8:299. 2007
    ....
  7. ncbi Spatial scaling of functional gene diversity across various microbial taxa
    Jizhong Zhou
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Proc Natl Acad Sci U S A 105:7768-73. 2008
    ..0475-0.0959). However, the z values are several times lower than those commonly observed in plants and animals. These results suggest that the turnover in space of microorganisms may be, in general, lower than that of plants and animals...
  8. ncbi How sulphate-reducing microorganisms cope with stress: lessons from systems biology
    Jizhong Zhou
    Stephenson Research and Technology Center, 101 David L Boren Blvd, Institut for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    Nat Rev Microbiol 9:452-66. 2011
    ....
  9. ncbi Reproducibility and quantitation of amplicon sequencing-based detection
    Jizhong Zhou
    Department of Environmental Science and Engineering, Tsinghua University, Beijing, China
    ISME J 5:1303-13. 2011
    ..However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the β-diversity of microbial communities...
  10. ncbi GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer
    Joy D Van Nostrand
    Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
    Environ Microbiol 11:2611-26. 2009
    ..This biostimulation approach may potentially offer an effective means for the bioremediation of U(VI)-contaminated sites...
  11. ncbi Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer
    Joy D Van Nostrand
    University of Oklahoma, 101 David L Boren Blvd, SRTC 2022, Norman, OK 73019, USA
    Appl Environ Microbiol 77:3860-9. 2011
    ....
  12. ncbi GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity
    Zhili He
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, 101 David L Boren Boulevard, Norman, OK 73019, USA
    ISME J 4:1167-79. 2010
    ..As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning...
  13. ncbi Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels
    Patricia J Waldron
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    Environ Sci Technol 43:3529-34. 2009
    ..This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination...
  14. ncbi Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities
    Yuting Liang
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Appl Environ Microbiol 76:1088-94. 2010
    ..The developed CORS provides a useful approach for microarray data normalization and comparison for studies of complex microbial communities...
  15. ncbi Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2
    Zhili He
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Ecol Lett 13:564-75. 2010
    ..This study provides insights into potential activity of microbial community and associated feedback responses of terrestrial ecosystems to eCO2...
  16. ncbi Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico
    Liyou Wu
    Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
    Appl Environ Microbiol 74:4516-29. 2008
    ....
  17. ncbi Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough
    Aifen Zhou
    Virtual Institute of Microbial Stress and Survival, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Environ Microbiol 12:2645-57. 2010
    ..In addition, a conceptual cellular model of D. vulgaris responses to H(2)O(2) stress was constructed to illustrate that this bacterium may employ a complicated molecular mechanism to defend against the H(2)O(2)-induced stresses...
  18. ncbi The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide
    Zhili He
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    ISME J 6:259-72. 2012
    ..This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure...
  19. ncbi Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community
    Christopher L Hemme
    Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
    ISME J 4:660-72. 2010
    ....
  20. ncbi Elevated carbon dioxide alters the structure of soil microbial communities
    Ye Deng
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, USA
    Appl Environ Microbiol 78:2991-5. 2012
    ..The results suggest that the soil microbial community composition and structure significantly altered under conditions of eCO(2), which was closely associated with soil and plant properties...
  21. ncbi Microbial functional gene diversity with a shift of subsurface redox conditions during In Situ uranium reduction
    Yuting Liang
    School of Environment, Tsinghua University, Beijing, China
    Appl Environ Microbiol 78:2966-72. 2012
    ..Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation...
  22. ncbi Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough
    Aifen Zhou
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, USA
    Appl Environ Microbiol 78:1168-77. 2012
    ..vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses...
  23. ncbi Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness
    Liyou Wu
    Department of Botany and Microbiology, Institute for Environmental Genomics, Stephenson Research and Technology Center, University of Oklahoma, Norman, OK 73019, USA
    ISME J 2:642-55. 2008
    ..These results suggest that CGA-based DNA-DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms...
  24. ncbi Probing regulon of ArcA in Shewanella oneidensis MR-1 by integrated genomic analyses
    Haichun Gao
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    BMC Genomics 9:42. 2008
    ..Shewanella oneidensis MR-1 contains a gene encoding a putative ArcA homolog with ~81% amino acid sequence identity to the E. coli ArcA protein but not a full-length arcB gene...
  25. ncbi Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation
    Meiying Xu
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
    ISME J 4:1060-70. 2010
    ....
  26. ncbi Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields
    Christopher L Hemme
    Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
    Appl Environ Microbiol 77:7998-8008. 2011
    ..The availability of whole-genome sequence and comparative genomic analyses will aid in engineering and optimizing Thermoanaerobacter strains for viable CBP strategies...
  27. ncbi Development of functional gene microarrays for microbial community analysis
    Zhili He
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Curr Opin Biotechnol 23:49-55. 2012
    ..In this review, we first summarize currently reported FGAs, and then focus on the FGA development. We will also discuss several key issues of FGA technology as well as challenges and directions in future FGA development...
  28. ncbi Assimilatory nitrate utilization by bacteria on the West Florida Shelf as determined by stable isotope probing and functional microarray analysis
    Boris Wawrik
    Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    FEMS Microbiol Ecol 79:400-11. 2012
    ..e. nirS, nirK, narG, nosZ, napA, and nrfA was detected. These data directly implicate several bacterial populations in nitrate uptake, but suggest a more complex pattern for N flow than traditionally implied...
  29. ncbi Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation
    Zhili He
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    Appl Environ Microbiol 76:1574-86. 2010
    ..A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of D. vulgaris adaptation to elevated NaCl levels...
  30. ncbi The tricarboxylic acid cycle in Shewanella oneidensis is independent of Fur and RyhB control
    Yunfeng Yang
    Department of Environmental Science and Engineering, Tsinghua University, Beijing 100084, China
    BMC Microbiol 10:264. 2010
    ..This down-regulation is mediated by a Fur-regulated small regulatory RNA named RyhB. It is unclear in the γ-proteobacterium S. oneidensis whether TCA is also regulated by Fur and RyhB...
  31. ncbi Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis
    Zhili He
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Appl Environ Microbiol 74:2957-66. 2008
    ..This study provides general guidance for users to select appropriate SNR thresholds for different samples under different hybridization conditions...
  32. ncbi Design and analysis of mismatch probes for long oligonucleotide microarrays
    Ye Deng
    Institute for Environmental Genomics, Department of Botany and Microbiology, The University of Oklahoma, Norman, OK 73019, USA
    BMC Genomics 9:491. 2008
    ..One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes...
  33. ncbi Generation and validation of a Shewanella oneidensis MR-1 clone set for protein expression and phage display
    Haichun Gao
    Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
    PLoS ONE 3:e2983. 2008
    ..g., mass spectrometry-based proteomic analysis), and facilitates a wide variety of integrated studies, including protein expression, purification, and functional analyses of proteins both in vivo and in vitro...
  34. ncbi Microarray-based evaluation of whole-community genome DNA amplification methods
    Jian Wang
    State Key Joint Laboratory of Environmental Stimulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
    Appl Environ Microbiol 77:4241-5. 2011
    ..For pure-culture DNA, REPLI-g and Templiphi showed less bias than Bst. For community DNA, REPLI-g showed the least bias and highest number of genes, while Bst had the highest success rate and was suitable for low-quality DNA...
  35. ncbi Applications of functional gene microarrays for profiling microbial communities
    Zhili He
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Curr Opin Biotechnol 23:460-6. 2012
    ..We also discuss challenges and future directions of FGA applications...
  36. ncbi Molecular ecological network analyses
    Ye Deng
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    BMC Bioinformatics 13:113. 2012
    ....
  37. ncbi Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume
    Zhenmei Lu
    College of Life Sciences, Zhejiang University, Hangzhou, China
    ISME J 6:451-60. 2012
    ..Together, these results suggest that the indigenous marine microbial communities could have a significant role in biodegradation of oil spills in deep-sea environments...
  38. ncbi Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes
    Yuguang Zhang
    Institute of Forestry Ecology, Environment and Protection, Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
    FEMS Microbiol Lett 266:144-51. 2007
    ..cluster analysis demonstrated that primitive forest soil was clustered more closely to soil from the spruce plantation established in 1960s...
  39. ncbi GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
    Zhili He
    Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
    ISME J 1:67-77. 2007
    ..It is particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions...
  40. ncbi Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands
    Kai Xue
    Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
    Appl Environ Microbiol 79:1284-92. 2013
    ....
  41. ncbi Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil
    Yuting Liang
    Department of Environmental Science and Engineering, Tsinghua University, Beijing, China
    Chemosphere 75:193-9. 2009
    ..These changes demonstrate the feasibility of an integrated ozonation and biodegradation treatment to remove recalcitrant soil contaminants...
  42. ncbi Field and laboratory studies on the bioconversion of coal to methane in the San Juan Basin
    Boris Wawrik
    Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    FEMS Microbiol Ecol 81:26-42. 2012
    ..These data suggest that coal methanogenesis is unlikely to be limited by methanogen biomass, but rather the activation and degradation of coal constituents...
  43. ncbi Development of highly fluorescent silica nanoparticles chemically doped with organic dye for sensitive DNA microarray detection
    Aihua Liu
    Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Anal Bioanal Chem 401:2003-11. 2011
    ..1 pM, enhancing microarray hybridization sensitivity over tenfold. This promising technology may be potentially applied to other binding events such as specific interactions between proteins...
  44. ncbi Shifts of functional gene representation in wheat rhizosphere microbial communities under elevated ozone
    Xinyu Li
    State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
    ISME J 7:660-71. 2013
    ..This study provides new insight into our understanding of the influence of eO(3) and wheat cultivars on soil microbial communities...
  45. ncbi Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination
    Jinbo Xiong
    State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
    PLoS ONE 7:e50507. 2012
    ..This study provides new insights about the heterogeneity of microbial community metabolic potential and future biodiversity preservation for arsenic bioremediation management...
  46. ncbi Use of functional gene arrays for elucidating in situ biodegradation
    Joy D Van Nostrand
    Institute for Environmental Genomics, University of Oklahoma Norman, OK, USA Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
    Front Microbiol 3:339. 2012
    ..This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation...
  47. ncbi Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production
    Christopher L Hemme
    Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA
    J Bacteriol 192:6494-6. 2010
    ..The sequenced strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial systems biology...
  48. ncbi Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins
    Haichun Gao
    Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    J Bacteriol 188:4560-9. 2006
    ..Mutational analyses confirmed that the small cold shock proteins, So1648 and So2787, are involved in the cold shock response of S. oneidensis. The analyses also indicated that So1648 may function only at very low temperatures...
  49. ncbi Metal reduction and iron biomineralization by a psychrotolerant Fe(III)-reducing bacterium, Shewanella sp. strain PV-4
    Yul Roh
    Institute for Environmental Genomics, and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
    Appl Environ Microbiol 72:3236-44. 2006
    ..The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation...
  50. ncbi Use of microarrays with different probe sizes for monitoring gene expression
    Zhili He
    Environmental Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6038, USA
    Appl Environ Microbiol 71:5154-62. 2005
    ..The results demonstrated that 70-mer oligonucleotides can provide the performance most comparable to the performance obtained with PCR-generated probes...
  51. ncbi Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation
    Xingyuan Li
    PerkinElmer Life and Analytical Sciences, 549 Albany Street, Boston, MA 02118, USA
    Nucleic Acids Res 33:6114-23. 2005
    ..The program was used to design probes for both whole-genome and highly homologous sequence data. CommOligo and CommOligo_PE are freely available to academic users upon request...
  52. ncbi Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris
    Yasuhiro Oda
    Department of Microbiology, University of Washington, Seattle, 98195-7242, USA
    J Bacteriol 187:7784-94. 2005
    ....
  53. ncbi Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction
    Rizlan Bencheikh-Latmani
    Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093 0202, USA
    Appl Environ Microbiol 71:7453-60. 2005
    ..This study sheds light on the multifaceted response of MR-1 to U(VI) and Cr(VI) under anaerobic conditions and suggests that the same electron transport pathway can be used for more than one electron acceptor...
  54. ncbi Impacts on microbial communities and cultivable isolates from groundwater contaminated with high levels of nitric acid-uranium waste
    Matthew W Fields
    Department of Microbiology, Miami University, Pearson Hall, Room 32, Oxford, OH 45056, USA
    FEMS Microbiol Ecol 53:417-28. 2005
    ....
  55. ncbi Improving solubility of Shewanella oneidensis MR-1 and Clostridium thermocellum JW-20 proteins expressed into Esherichia coli
    Irina Kataeva
    Southeast Collaboratory for Structural Genomics, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
    J Proteome Res 4:1942-51. 2005
    ..A suggestion has been made that the Wilkinson-Harrison model is not applicable to C. thermocellum proteins because it did not account for the peculiarities of protein sequences from thermophiles...
  56. ncbi Cellular response of Shewanella oneidensis to strontium stress
    Steven D Brown
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Appl Environ Microbiol 72:890-900. 2006
    ....
  57. ncbi Microbial diversity and heterogeneity in sandy subsurface soils
    Jizhong Zhou
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Appl Environ Microbiol 70:1723-34. 2004
    ..Finally, the overall diversity of the subsurface samples was much lower than that of the corresponding surface soil samples...
  58. ncbi Effects of a strong static magnetic field on bacterium Shewanella oneidensis: an assessment by using whole genome microarray
    Weimin Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
    Bioelectromagnetics 26:558-63. 2005
    ..Among these genes, 21 were upregulated while other 44 were downregulated, compared with control...
  59. ncbi Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1
    Karuna Chourey
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Appl Environ Microbiol 72:6331-44. 2006
    ....
  60. ncbi Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Proc Natl Acad Sci U S A 102:2099-104. 2005
    ..We propose that this integrative approach offers a valuable means to undertake the enormous challenge of characterizing the rapidly growing number of hypothetical proteins with each newly sequenced genome...
  61. ncbi Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis
    Xiu Feng Wan
    Environmental Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, TN 37831 6038, USA
    J Bacteriol 186:8385-400. 2004
    ....
  62. ncbi Global transcriptome analysis of the heat shock response of Shewanella oneidensis
    Haichun Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    J Bacteriol 186:7796-803. 2004
    ..Finally, a putative regulatory site with high conservation to the Escherichia coli sigma32-binding consensus sequence was identified upstream of a number of heat-inducible genes...
  63. ncbi Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress
    Dorothea K Thompson
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Appl Environ Microbiol 68:881-92. 2002
    ..These results suggest a possible regulatory role of S. oneidensis MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems...
  64. ncbi Microbial genomics--challenges and opportunities: the 9th International Conference on Microbial Genomes
    Jizhong Zhou
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    J Bacteriol 184:4327-33. 2002
  65. ncbi Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications
    Liyou Wu
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Environ Sci Technol 38:6775-82. 2004
    ..The results suggest that CGA hybridization has potential as a specific, sensitive, and quantitative tool for detection and identification of microorganisms in environmental samples...
  66. ncbi Empirical establishment of oligonucleotide probe design criteria
    Zhili He
    Environmental Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6038, USA
    Appl Environ Microbiol 71:3753-60. 2005
    ....
  67. ncbi PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis
    Dong Xu
    Protein Informatics Group, Life Sciences Division Environmental Sciences Division, Oak Ridge, TN 37831, USA
    Bioinformatics 18:1432-7. 2002
    ..The PCR amplification results indicate that this method is very efficient and reliable for designing specific probes for microarray analysis...
  68. ncbi Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough
    Kelly S Bender
    Department of Biochemistry, 117 Schweitzer Hall, Columbia, MO 65211, USA
    Appl Environ Microbiol 73:5389-400. 2007
    ..Both the physiological and transcriptional data implicate a global regulatory role for Fur in the sulfate-reducing bacterium D. vulgaris...
  69. ncbi Response of Desulfovibrio vulgaris to alkaline stress
    Sergey Stolyar
    University of Washington, Department of Civil and Environmental Engineering, 616 NE North Lake Place, Box 355014, Seattle, WA 98195 2700, USA
    J Bacteriol 189:8944-52. 2007
    ....
  70. ncbi Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough
    Sean M Caffrey
    Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
    J Bacteriol 189:6159-67. 2007
    ..In contrast, growth with 5% hydrogen is associated with a low intracellular hydrogen concentration, requiring the lower activity, higher affinity [NiFeSe] hydrogenase...
  71. ncbi Molecular diversity of 16S rRNA and gyrB genes in copper mines
    Huaqun Yin
    School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, China
    Arch Microbiol 189:101-10. 2008
    ..Moreover, our results also indicated that gyrB sequence analysis may be very useful for differentiating very closely related species in the study of microbial communities...
  72. ncbi Transcriptome of a Nitrosomonas europaea mutant with a disrupted nitrite reductase gene (nirK)
    Catherine Mee-Hie Cho
    Department of Environmental Sciences, Geology 2207, University of California, Riverside, CA 92521, USA
    Appl Environ Microbiol 72:4450-4. 2006
    ..Relationships of differentially regulated genes to the nirK mutant phenotype are discussed...
  73. ncbi Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs)
    Mary Beth Leigh
    Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
    ISME J 1:134-48. 2007
    ....
  74. ncbi Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect
    Etienne Yergeau
    Center for Terrestrial Ecology, Netherlands Institute for Ecology NIOO KNAW, Heteren, The Netherlands
    ISME J 1:163-79. 2007
    ....
  75. ncbi Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach
    Aindrila Mukhopadhyay
    Virtual Institute of Microbial Stress and Survival, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    J Bacteriol 188:4068-78. 2006
    ..vulgaris responded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response in D. vulgaris that can be compared to those in other microorganisms...
  76. ncbi Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response
    Yunfeng Yang
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    BMC Genomics 9:S11. 2008
    ..In many bacterial species, coordinate regulation of iron homeostasis depends on the protein product of a Fur gene. Fur also plays roles in virulence, acid tolerance, redox-stress responses, flagella chemotaxis and metabolic pathways...
  77. ncbi Transcriptional response of Desulfovibrio vulgaris Hildenborough to oxidative stress mimicking environmental conditions
    Patricia M Pereira
    Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Lisbon, Portugal
    Arch Microbiol 189:451-61. 2008
    ..vulgaris as a consequence of oxidative damage to their metal clusters...
  78. ncbi Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean
    Haichun Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
    Int J Syst Evol Microbiol 56:1911-6. 2006
    ..nov. is proposed. The type strain is PV-4(T) (=ATCC BAA-1088(T)=DSM 17748(T))...
  79. ncbi Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference
    Yunfeng Yang
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    BMC Genomics 9:S5. 2008
    ..Conflicting results have been reported with regard to the reliability of microarray results using this method. To explain it, we hypothesize that data processing is a critical element that impacts the data quality...
  80. ncbi Unravelling microbial communities with DNA-microarrays: challenges and future directions
    Michael Wagner
    Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, A 1090, Wien, Austria
    Microb Ecol 53:498-506. 2007
    ..Finally, we outline scenarios for an innovative combination of microarrays with other molecular tools for structure-function analysis of complex microbial communities...
  81. ncbi Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems
    Huaqun Yin
    School of Minerals Processing and Bioengineering, Central South University Changsha, Hunan, 410083 China
    J Microbiol Methods 70:165-78. 2007
    ....
  82. ncbi Diversity of functional genes for methanotrophs in sediments associated with gas hydrates and hydrocarbon seeps in the Gulf of Mexico
    Tingfen Yan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
    FEMS Microbiol Ecol 57:251-9. 2006
    ....
  83. ncbi Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels
    Erick Cardenas
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Appl Environ Microbiol 74:3718-29. 2008
    ..Spatial differences in community structure within the treatment zone were likely related to the hydraulic pathway and to electron donor metabolism during biostimulation...
  84. ncbi Microarrays for bacterial detection and microbial community analysis
    Jizhong Zhou
    Environmental Sciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831 6038, USA
    Curr Opin Microbiol 6:288-94. 2003
    ..However, more rigorous and systematic assessment and development are needed to realize the full potential of microarrays for microbial detection and community analysis...
  85. ncbi Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants
    Orianna Bretschger
    Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, USA
    Appl Environ Microbiol 73:7003-12. 2007
    ..Overall, these data suggest a very complex picture of electron transfer to solid and soluble substrates by S. oneidensis MR-1...
  86. ncbi A computational study of Shewanella oneidensis MR-1: structural prediction and functional inference of hypothetical proteins
    Christal Yost
    The Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6480, USA
    OMICS 7:177-91. 2003
    ..This method, which uses a suite of computational tools that are freely available to academic users, can be used to annotate hypothetical proteins in general...
  87. ncbi Microarray transcription profiling of a Shewanella oneidensis etrA mutant
    Alex S Beliaev
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6038, USA
    J Bacteriol 184:4612-6. 2002
    ..This is the first microarray study indicating a possible involvement of EtrA in the regulation of gene expression in S. oneidensis MR-1...
  88. ncbi Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH
    Adam B Leaphart
    Environmental Sciences Division, Oak Ridge National Laboratory, Tennessee 37831, USA
    J Bacteriol 188:1633-42. 2006
    ..oneidensis modulates multiple transporters, cell envelope components, and pathways of amino acid consumption and central intermediary metabolism as part of its transcriptome response to changing external pH conditions...
  89. ncbi Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification
    Liyou Wu
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6038, USA
    Appl Environ Microbiol 72:4931-41. 2006
    ....
  90. ncbi Transcriptome analysis applied to survival of Shewanella oneidensis MR-1 exposed to ionizing radiation
    Xiaoyun Qiu
    Center for Microbial Ecology, PSSB 540, Michigan State University, East Lansing, MI 48824, USA
    J Bacteriol 188:1199-204. 2006
    ..Instead, a combination of oxidative stress, protein damage, and prophage-mediated cell lysis during irradiation and recovery might underlie this organism's great sensitivity to IR...
  91. ncbi Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications
    Jost Liebich
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Appl Environ Microbiol 72:1688-91. 2006
    ....
  92. ncbi A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery
    Xiaohu Wang
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
    Nucleic Acids Res 36:4863-71. 2008
    ....
  93. ncbi AggA is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of Shewanella oneidensis MR-1
    Wim De Windt
    Laboratory of Microbial Ecology and Technology LabMET, Ghent University, Coupure Links 653, B 9000 Gent, Belgium
    Microbiology 152:721-9. 2006
    ..By complementing this mutation with the vector pCM62, expressing the aggA gene, this effect could be nullified and biofilm formation was restored to at least the level of the MR-1 wild-type...
  94. ncbi Transcript profiles of Nitrosomonas europaea during growth and upon deprivation of ammonia and carbonate
    Xueming Wei
    Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    FEMS Microbiol Lett 257:76-83. 2006
    ..Compared to heterotrophic bacteria, N. europaea downregulates a greater proportion of its genes and fewer genes appear to be associated with the adaptation to starvation...
  95. ncbi Microarray-based analysis of microbial community RNAs by whole-community RNA amplification
    Haichun Gao
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
    Appl Environ Microbiol 73:563-71. 2007
    ..This is one of the first demonstrations that microarray-based technology can be used to successfully detect the activities of microbial communities from real environmental samples in a high-throughput fashion...
  96. ncbi Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB, and UVA radiation
    Xiaoyun Qiu
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    J Bacteriol 187:3556-64. 2005
    ..Our data suggested that activation of prophages appears the major lethal factor in MR-1 following UVC or UVB irradiation, whereas oxidative damage contributes greatly to the high UVA sensitivity in MR-1...
  97. ncbi Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions
    Yongqing Liu
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    J Bacteriol 187:2501-7. 2005
    ..The data also suggested an important role for metabolic adjustment in salt stress adaptation in S. oneidensis...
  98. ncbi Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays
    Sung-Keun Rhee
    Environmental Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6038, USA
    Appl Environ Microbiol 70:4303-17. 2004
    ....
  99. ncbi A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles
    Feng Luo
    Department of Computer Science, University of Texas at Dallas, Richardson, TX 75252, USA
    Bioinformatics 20:2605-17. 2004
    ..Furthermore, the biological functionality enrichment in the clusters is considerably high and the hierarchical structure of the clusters is more reasonable. AVAILABILITY: DGSOT is available upon request from the authors...
  100. ncbi Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples
    Sonia M Tiquia
    Oak Ridge National Laboratory, Oak Ridge, TN, USA
    Biotechniques 36:664-70, 672, 674-5. 2004
    ..These results suggest that the 50-mer oligonucleotide array can be used as a specific and quantitative parallel tool for the detection of microbial populations in environmental samples...