Noguera Research Group at UW-Madison

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Bioenergy-Related Publications

1.      Yilmaz L.S., W.S. Kontur, A.P. Sanders, U. Sohmen, T.J. Donohue, and D.R. Noguera. 2010. Electron Partitioning During Light- and Nutrient-Powered Hydrogen Production by Rhodobacter sphaeroides. BioEnergy Research, 3:55-66. 

2.      Cho Y.K., T.J. Donohue, I. Tejedor, M.A. Anderson, K.D. McMahon, and D.R. Noguera. 2008. Development of a Solar Powered Microbial Fuel Cell.  Journal of Applied Microbiology, 104:640-650.  

3.      Noguera D. R., G. A. Brusseau, B.E. Rittmann, and D. A. Stahl. 1998. A Unified Model Describing the Role of Hydrogen in the Growth of Desulfovibrio vulgaris under Different Environmental Conditions. Biotechnology and Bioengineering, 59:732-746.


FISH-Related Publications  

1.      Yilmaz L.S., Parnerkar S., and D.R. Noguera. 2010.  mathFISH, A Web Tool for the in silico Evaluation of Oligonucleotide Probes for Fluorescence in situ Hybridization Based on Thermodynamic Models.  Applied and Environmental Microbiology, Accepted.

2.      Yilmaz L.S., Kang, D.W., and D.R. Noguera. 2009. Fluorescence in situ hybridization (FISH) and probe design.  In:  Microbial Ecology of Activated Sludge, Robert Seviour and Per H Nielsen (Eds), IWA Publishing. 

3.      Hoshino T., L.S. Yilmaz, D.R. Noguera, H. Daims, and M. Wagner. 2008. Quantification of target molecules needed to by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH, Applied and Environmental Microbiology, 74(16):5068-5077. 

4.   Yilmaz L.S., L.I. Bergsven, and D.R. Noguera. 2008. Single mismatch stability predictors for fluorescence in situ hybridization.  Environmental Microbiology, 10(10):2872–2885.

5.      Yilmaz L.S., and D.R. Noguera. 2007.  Development of Thermodynamic Models for Simulating Probe Dissociation Profiles in Fluorescence in situ Hybridization.  Biotechnology and Bioengineering, 96(2):349-363.

6.      Yilmaz L.S., H. E. Okten, and D. R. Noguera.  2006.  Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides.  Applied and Environmental Microbiology, 72(1):733-744. [PDF] [Supplementary Material]

7.      Yilmaz L.S., and D. R. Noguera.  2004.  A mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization.  Applied and Environmental Microbiology, 70(12):7126-7139. [PDF] [Supplementary Material]

8.      Raskin L., L.K. Poulsen, D.R. Noguera, B.E. Rittmann, and D.A. Stahl.  1994.  Quantification of Methanogenic Groups in Anaerobic Biological Reactors using Oligonucleotide Probe Hybridizations. Applied and Environmental Microbiology, 60:1241-1248. [PDF]


Water Quality-Related Publications

1.      Noguera D.R., Yilmaz L.S., R.G. Goel, and G.W. Harrington. 2009. Identification of Heterotrophic Bacteria that Colonize Chloraminated Drinking Water Distribution Systems.  American Water Works Association Research Foundation.

2.      Fleming K.K, G.W. Harrington, and D.R. Noguera.  2008. Nitrification potential curve evaluation of full-scale drinking water distribution systems.  Journal AWWA, 100(10):92-103.

3.      Yang J., G. W. Harrington, and D. R. Noguera. 2008. Nitrification modeling in pilot-scale chloraminated drinking water distribution systems.  Journal of Environmental Engineering, 134(9):731-742

4.      Yang J., G. W. Harrington, D. R. Noguera, and K. K. Fleming. 2007. Risk analysis of nitrification occurrence in pilot scale chloraminated distribution systems. Journal of Water Supply: Research and Technology—AQUA, 56(5):293-311.

5.      Fleming K.K., Harrington G.W., and D. R. Noguera. 2005. Nitrification Potential Curves as a New Strategy for Nitrification Prevention.  Journal AWWA, 97(8):90-99.

6.      Regan J.M., G.W.  Harrington, H. Baribeau, R. De Leon, and D.R. Noguera. 2003.  Diversity of nitrifying bacteria in full-scale chloraminated distribution systems.  Water Research, 37(1):197-205.

7.      Harrington G. W., D. R. Noguera, C. C. Bone, A. I. Kandou, P. S. Oldenburg, J. M. Regan, and D. Van Hoven.  2003.  Ammonia Release from Chloramine Decay:  Implications for the Prevention and Control of Nitrification in Distribution Systems.  American Water Works Association Research Foundation, ISBN 1-58321-283-3.

8.      Harrington G.W., D.R. Noguera, A.I. Kandou, and D. J. VanHoven.  2002.  Pilot-Scale Evaluation of Nitrification Control Strategies.  Journal AWWA, 94(11):78-89.

Received the Publications Award from AWWA for the most notable contribution to the science of public water supply development through a paper published by the Association.

Received the Best Paper Award from the Engineering and Construction Division of AWWA.

9.      Oldenburg P. S., J. M. Regan, G. W. Harrington, and D. R. Noguera. 2002. Kinetics of Nitrosomonas europaea inactivation by chloramine.  Journal AWWA, 94(10):100-110.

10.  Regan J.M., G.W. Harrington, and D.R. Noguera.  2002.  Ammonia- and nitrite-oxidizing bacteria communities in a pilot-scale chloraminated drinking water distribution system.  Applied and Environmental Microbiology, 68(1):73-81.


Activated Sludge-Related Publications

1.      Flowers J.J., S. He, L.S. Yilmaz, D. R. Noguera, K.D. McMahon. 2009. Denitrification capabilities of two biological phosphorus removal sludges dominated by different “Candidatus Accumulibacter” clades.  Environmental Microbiology Reports, 1(6), 583–588.

2.      Park H.-D., and D.R. Noguera. 2008.  Nitrospira Community Composition in Nitrifying Reactors Operated with Two Different Dissolved Oxygen Levels.  Journal of Microbiology and Biotechnology, 18(8):1470-1474.

3.      Park H.-D., and D.R. Noguera. 2007.  Characterization of Two Ammonia-Oxidizing Bacteria Isolated from Reactors Operated with Low Dissolved Oxygen Concentrations.  Journal of Applied Microbiology, 102(5):1401-1417.

4.      Goel R.K., and D.R. Noguera. 2006. Evaluation of sludge yield and phosphorus removal in a Cannibal™ solids reduction system.  Journal of Environmental Engineering, 132(10):1331-1337.

5.      Perez-Feito R. and D.R. Noguera. 2006. Recovery of polyhydroxyalkanoate ( PHA ) from enhanced biological phosphorus removal (EBPR) treatment plants.  Water Environment Research, 78(7):770-775.

6.      Maixner F., D. R. Noguera, B. Anneser, K. Stoecker, G. Wegl, M. Wagner, and H. Daims.  2006. Nitrite concentration influences the population structure of Nitrospira-like bacteria.  Environmental Microbiology, 8(8):1487-1495.

7.      Park H.-D., Whang L.-M., Reusser S.R., and D. R. Noguera. 2006. Taking Advantage of Aerated-Anoxic Operation in a Full-Scale University of Cape Town (UCT) Process.  Water Environment Research, 78(6):637-642.

8.      Perez-Feito R., J. Peccia, and D. R. Noguera.  2006. Comparison between direct microscopy and flow cytometry for quantifiable RNA-based population analysis of activated sludge.  Water Environment Research, 78(2):181-188.

9.      Drnevich M.A. and D.R. Noguera. 2004.  Production of polyhydroxyalkanoate during treatment of low-phosphorus content wastewater.  Water Environment Research, 76(4):380-383.

10.  Park H.-D. and D. R. Noguera. 2004. Evaluating the Effect of Dissolved Oxygen on Ammonia-Oxidizing Bacterial Communities in Activated Sludge.  Water Research, 38(14-15):3275-3286.

11.  Chaparro S.K. and D.R. Noguera. 2003.  Controlling biosolids phosphorus content in enhanced biological phosphorus removal reactors.  Water Environmental Research, 73(3):254-262.

Received the Harrison Prescott Eddy Medal from the Water Environment Federation for Outstanding Contribution to Wastewater Principles/Processes Research

12.  Zilles J.L., J. Peccia, and D. R. Noguera. 2002.  Microbiology of Enhanced Biological Phosphorus Removal in Aerated-Anoxic Orbal Processes.  Water Environment Research, 74(5):428-436.

13.  Hung C.-H., J. Peccia, J.L. Zilles, and D.R. Noguera. 2002.  Physical enrichment of polyphosphate-accumulating organisms in activated sludge.  Water Environment Research, 74(4):354-361.

14.  Zilles J.L., J. Peccia, M-W. Kim, C-H. Hung, and D.R. Noguera. 2002.  Involvement of Rhodocyclus-related organisms in phosphorus removal in full-scale wastewater treatment plants.  Applied and Environmental Microbiology.  68(6):2763-2769.

15.  Zilles J.L., C.-H. Hung, and D.R. Noguera. 2002.  Presence of Rhodocyclus in a full-scale wastewater treatment plant and their participation in enhanced biological phosphorus removal.  Water Science and Technology. 46(1-2):123-128.

16.  Park H.-D., J. M. Regan, and D.R. Noguera. 2002.  Molecular analysis of nitrifying bacterial populations in aerated-anoxic processes.  Water Science and Technology. 46(1-2):273-280.

17.  Wagner M., D.R. Noguera, S. Juretschko, G. Rath, H-P. Koops, and K-H. Schleifer. 1998. Combining Fluorescent in Situ Hybridization (FISH) with Cultivation and Mathematical Modeling to Study Population Structure and Function of Ammonia-Oxidizing Bacteria in Activated Sludge. Water Science and Technology, 37:441-449.


Biofilm and Biofouling-Related Publications

1.      Perez-Roa R.E., M.A. Anderson, D. Rittschof, C.G. Hunt, and D.R. Noguera. 2009. Inhibition of Barnacle Biofouling by Electrochemical Reactive Oxygen Species ( ROS ) Generation. Biofouling, 25(6):563-571.

2.      Perez-Roa R.E., M.A. Anderson, D. Rittschof, B. Orihuela, D. Wendt, G.L. Kowalke, and D.R. Noguera. 2008. Inhibition of barnacle (Amphibalanus amphitrite) cyprid settlement by means of localized, pulsed electric fields. Biofouling, 24(3):177-184.

3.      Perez-Roa R.E., D.T. Tompkins, M. Paulose, C. A. Grimes, M.A. Anderson, and D. R. Noguera.  2006. Effects of Localized, Low-Voltage Pulsed Electric Fields on the Development and Inhibition of Pseudomonas aeruginosa Biofilms.  Biofouling, 22(6):383-390.

4.      Wanner O., Eberl, H., E. Morgenroth, D. R. Noguera, C. Picioreanu, B. Rittmann, M. van Loosdrecht. 2005.  Mathematical Modeling of Biofilms, Scientific and Technical Report No. 18, IWA publishing, ISBN 1-84339-087-6.

5.      Pizarro G.E., J. Teixeira, M. Sepulveda, and D. R. Noguera. 2005. Bitwise implementation of a two-dimensional cellular automata biofilm model.  Journal of Computing in Civil Engineering, 39(3):258-268.

6.      Noguera, D.R., Pizarro, G.E., and Regan, J.M. 2004. Modeling Biofilms, pp. 222-249. In: Microbial Biofilms, M.  Ghannoum, G. A. O'Toole, eds., ASM Press, Washington D.C.

7.      Noguera D.R. and E. Morgenroth. 2004.  Introduction to the IWA Task Group on Biofilm Modeling.  Water Science and Technology, 49(11-12):131-136.

8.      Morgenroth E., H.J Eberl, M.C.M. van Loosdrecht, D.R. Noguera, G.E. Pizarro, C. Picioreanu, B.E. Rittmann, A.O. Schwartz, O. Wanner.  2004.  Comparing biofilm models for a single species biofilm system. Water Science and Technology, 49(11-12):145-154.

9.      Eberl, H.J., M.C.M. van Loosdrecht, E. Morgenroth, D.R. Noguera, C. Picioreanu, B.E. Rittmann, A.O. Schwarz, and O. Wanner.  2004. Modelling A Spatially Heterogeneous Biofilm And The Bulk Fluid: Selected Results From Benchmark Problem 2 (BM2). Water Science and Technology, 49(11-12):155-162.

10.  Noguera D.R. and C. Picioreanu. 2004.  Results from the multi-species benchmark problem 3 (BM3) using two-dimensional models.  Water Science and Technology, 49(11-12):169-176.

11.  Regan J.M., P.S. Oldenburg, H.D. Park, G.W. Harrington, and D.R. Noguera. 2003.  Simultaneous Determination of Bacterial Viability and Identity in Biofilms using Ethidium Monoazide and Fluorescent In Situ Hybridization.  Water Science and Technology, 47(5):123-128.

12.  Pizarro G., D. Griffeath, and D. R. Noguera.  2001. Quantitative Cellular Automaton Model for Biofilms.  Journal of Environmental Engineering, 127(9):782-789.

13.  Noguera D.R., G. E. Pizarro and L.W. Clapp. 2000. Mathematical modeling of trichloroethylene (TCE) degradation in membrane-attached biofilms. Water Science and Technology, 41(4-5):239–244.

14.  Noguera D.R., S. Okabe, and C. Picioreanu. 1999.  Biofilm Modeling: Present Status and Future Directions.  Water Science and Technology, 39:273-278.

15.  Noguera D. R., G. E. Pizarro, D. A. Stahl, and B. E. Rittmann. 1999. Simulation of Multispecies Biofilm Development in Three Dimensions. Water Science and Technology, 39:123-130.

16.  Clapp, L. W., J. M. Regan, F. Ali, J. D. Newman, J. K. Park, and D. R. Noguera. 1999. Activity, Structure, and Stratification of Membrane-Attached Methanotrophic Biofilms Cometabolically Degrading Trichloroethylene. Water Science and Technology, 39:153-161.

17.  Wirtel S.A. , D.R. Noguera, D.T. Kampmeier, M.S. Heath, and B.E. Rittmann.  1992.  Explaining Widely Varying Biofilm-Process Performance with Normalized-Loading Curves. Water Environment Research, 64:706-711.

18.  Heath M.S., S.A. Wirtel, B.E. Rittmann, and D.R. Noguera.  1991.  Closure for Simplified Design of Biofilm Processes Using Normalized Loading Curves. Research Journal Water Pollution Control Federation. 63:91-92.

Bioremediation and Other-Related Publications

1.      Pak, J. W., K. L. Knoke, D.R. Noguera, B. G. Fox, G. H. Chambliss.  2000.  Transformation of 2,4,6-trinitrotoluene ( TNT ) by purified xenobiotic reductase B from Pseudomonas fluorescens I-C.  Applied and Environmental Microbiology, 66(11):4742-4750.

2.      Noguera D.R. and D.L. Freedman.  1997.  Characterization of Products from the Biotransformation of 2,4-Dinitrotoluene by Denitrifying Enrichment Cultures.  Water Environment Research, 69:260-268.

3.      Freedman D.L., C.R. Smith, and D.R. Noguera.  1997.  Dichloromethane Biodegradation under Nitrate-Reducing Conditions.  Water Environment Research, 69:115-122.

4.      Noguera D.R. and Freedman D.L. 1996.  Reduction and Acetylation of 2,4-Dinitrotoluene by a Pseudomonas aeruginosa Strain.  Applied and Environmental Microbiology, 62:2257-2263.

5.      Noguera D.R., N. Araki, and B.E. Rittmann.  1994.  Soluble Microbial Products ( SMP ) in Anaerobic Chemostats. Biotechnology and Bioengineering. 44:1040-1047.


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