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Reference | Publication | Biosciences Division

BIO 2018 Publications

Konar, Arkaprabha; Sechrist, Riley; Song, Yin; Policht, Veronica; Laible, Philip; Bocian, David; Holten, Dewey; Kirmaier, Christine; Ogilvie, Jennifer Electronic Interactions in the Bacterial Reaction Center Revealed by Two-Color 2D Electronic Spectroscopy The Journal of Physical Chemistry Letters (2018)

Yu, Qiang; Boyanov, Maxim; Liu, Jinling ; Kemner, Kenneth; Fein, Jeremy Adsorption of selenite onto Bacillus subtilis: the overlooked role of cell envelope sulfhydryl sites in the microbial conversion of Se(IV) Environmental Science and Technology (2018)

Yu, Qiang; Boyanov, Maxim; Liu, Jinling ; Kemner, Kenneth; Fein, Jeremy Adsorption of selenite onto Bacillus subtilis: the overlooked role of cell envelope sulfhydryl sites in the microbial conversion of Se(IV) Environmental Science and Technology (2018)

Ho, Thao; Groer, Maureen; Kane, Bradley; Yee, Alyson; Torres, Benjamin; Gilbert, Jack; Maheshwari, Akhil Dichotomous development of the gut microbiome in preterm infants Microbiome (2018)

Andrews, M. Grace; Jacobson, Andrew; Osburn, Magdalena; Flynn, Theodore Dissolved carbon dynamics in meltwaters from the Russell Glacier, Greenland Ice Sheet Journal of Geophysical Research: Biogeosciences (2018)

Ma, Bin ; Zhao, Kun; Lv, Xiaofei; Su, Weiqin; Dai, Zhongmin; Gilbert, Jack; Brookes, Philip; Faust, Karoline; Xu, Jiangming Genetic correlation network prediction of forest soil microbial functional organization ISME Journal (2018)

Fan, Kunkun; Weisenhorn, Pamela; Gilbert, Jack; Chu, Haiyan Wheat rhizosphere harbors a less complex and more stable microbial co-occurence pattern than bulk soil Soil Biology & Biochemistry (2018)

Hajighasemi, Mahbod; Tchigvintsev, Anatoly; Nocek, Boguslaw; Flick, Robert; Popovic, Ana; Hai, Tran; khusnutdinova, Anna; Brown, Greg; Xu, Xiaohui; Cui, Hong; Anstett, Julia; Joachimiak, Andrzej; Yakunin, Alexander Screening and Characterization of Novel Polyesterases from Environmental Metagenomes with High Hydrolytic Activity against Synthetic Polyesters Environmental Science and Technology (2018)

Ahmed, Ishfaq; Roy, Badal; Raach, Rita-Marie; Owens, Sarah; Xia, Lijun; Anant, Shrikant; Sampath, Venkatesh; Umar, Shahid Enteric infection coupled with chronic Notch pathway inhibition alters colonic mucus composition leading to dysbiosis, barrier disruption and colitis PLOS ONE (2018)

Nocek, Boguslaw; Khusnutdinova, Anna; Ruszkowski, Milosz; Flick, Robert; Burda, Malgorzata; Batyrova, Khorcheska; Brown, Greg; Mucha, Artur; Joachimiak, Andrzej; Berlicki, Lukasz; Yakuninb, Alexander Structural insights into substrate selectivity and activity of bacterial polyphosphate kinases ACS Catalysis (2018)

Kim, Youngchang; Chhor, Gekleng; Tsai, Ching-Sung; Winans, James; Jedrzejczak, Robert; Joachimiak, Andrzej; Winans, Stephen Crystal Structure of the Ligand-Binding Domain of a LysR-type Transcriptional Regulator: Transcriptional Activation via a Rotary Switch Molecular Microbiology (2018)

Noirot-Gros, Marie-Francoise; Shinde, Shalaka; Larsen, Peter; Zerbs, Sarah; Korajczyk, Peter; Kemner, Kenneth; Noirot, Philippe Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation Frontiers in microbiology (2018)

Herrou, Julien; Czyz, Daniel; Fiebig, Aretha; Willett, Jonathan; Kim, Youngchang; Wu, Ruiying; Babnigg, Gyorgy; Crosson, Sean Molecular control of gene expression by Brucella BaaR, an IclR-type transcriptional repressor Journal of Biological Chemistry (2018)

Larsen, Peter; Zerbs, Sarah; Laible, Philip; Collart, Frank; Korajczyk, Peter; Dai, Yang; Noirot, Philippe Modeling the Pseudomonas Sulfur Regulome as Quantification, Storage, and Communication of Information mSystems (2018)

Cardona, Cesar; Lax, Simon; Larsen, Peter; Stephens, Brent; Hampton-Marcell, Jarrad; Edwardson, Christian ; Henry, Chris; VanBonn, Bill; Gilbert, Jack Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics mSystems (2018)

Luong, Truc; Tirgar, Reyhaneh; Reardon-Robinson, Melissa; Joachimiak, Andrzej; Osipiuk, Jerzy; Ton-That, Hung Structural Basis of a Thiol-Disulfide Oxidoreductase in the Hedgehog-Forming Actinobacterium Corynebacterium matruchotii Journal of Bacteriology (2018)

Gilbert, Jack; Jansson, Janet; Knight, Robert Earth Microbiome Project and Global Systems Biology mSystems (2018)

Liu, Yu; Holmstrom, Erik; Yu, Ping; Tan, Kemin; Zuo, Xiaobing; Nesbitt, David; Sousa, Rui; Stagno, Jason R. ; Wang, Yun-Xing Incorporation of Isotopic, Fluorescent, and Heavy-atom-modified Nucleotides into RNAs by Position-selective Labeling of RNA Nature Protocols (2018)

Johnson, Dana; Beddows, Patricia; Flynn, Theodore; Osburn, Magdalena Microbial Diversity and Biomarker Analysis of Modern Freshwater Microbialites from Laguna Bacalar, Mexico Geobiology (2018)

García García, Tránsito; Ventroux, Magali; Derouiche, Abderahmane ; Bidnenko, Vladimir; Correia Santos, Sara; Henri, Celine; Mijakovic, Ivan; Noirot-Gros, Marie-Francoise; Poncet, Sandrine Phosphorylation of the Bacillus subtilis Replication Controller YabA Plays a Role in Regulation of Sporulation and Biofilm Formation Frontiers in microbiology (2018)

McDonald, Daniel ; Hyde, Embrietta R; Debelius, Justine; Morton, James; Gonzalez, Antonio; Ackermann, Gail; Askenov, Alexander; Behsaz, Bahar; Chen, Yingfeng; Gilbert, Jack American Gut: an Open Platform for Citizen Science Microbiome Research mSystems (2018)

Seyler, Lauren; McGuinness, Lora; Gilbert, Jack; Biddle, Jennifer ; Gong, Donglai; Kerkhof, Lee Discerning autotrophy, mixotrophy and heterotrophy in marine TACK archaea from the North Atlantic FEMS Microbiology Reviews (2018)

Kryshafovych, Andriy; Albrecht, Reinhard; Basle, Arnaud; Bule, Pedro; Caputo, Alessandro; Carvalho, Ana Luisa; Chao, Kinlin; Diskin, Ron; Fidelis, Krzysztof; Fontes, Carlos; Fredslund, Folmer; Gilbert, Harry ; Goulding, Celia; Hartmann, Marcus D.; Hayes, Christopher; Herzberg, Osnat; Hill, Johan; Joachimiak, Andrzej; Kohring, Gert-Wieland; Koning, Roman; Leggio, Leila Lo; Mangiagalli, Marco; Michalska, Karolina; Moult, John; Najmudin, Shabir; Nardini, Marco; Nardone, Valentina; Ndeh, Didier; Nguyen, Thanh; Pintacuda, Guido; Postel, Sandra; van Raaij, Mark; Roversi, Pierto; Shimon, Amir; Singh, Abhimanyu; Sundberg, Eric; Tars, Kaspars; Zitmann, Nicole; Schwede, Torsten Target Highlights from the First Post-PSI CASP Experiment (CASP12, May-August 2016) Proteins: Structure, Function, and Bioinformatics (2018)

Gdor, Itay; Wang, Xiaolei; Daddysman, Matthew ; Yifat, Yuval; Wilton, Rosemarie; Hereld, Mark; Noirot-Gros, Marie-Francoise; Scherer, Norbert Particle tracking by repetitive phase-shift interferometric super resoluation microscopy Optics Letters (2018)

Chacko, Shibin; Boshoff, Helena; Singh, Vinayak; Ferraris, Davide; Gollapalli, Deviprasad; Zhang, Minjia; Lawson, Ann; Pepi, Michael; Joachimiak, Andrzej; Rizzi, Menico; Mizrahi, Valerie; Cuny, Gregory; Hedstrom, Lizbeth Expanding Benzoxazole-Based Inosine 5′-Monophosphate Dehydrogenase (IMPDH) Inhibitor Structure−Activity As Potential Antituberculosis Agents Journal of Medicinal Chemistry (2018)

Chang, Chin-Yuan; Lohman, Jeremy; Huang, Tingting; Michalska, Karolina; Bigelow, Lance; Rudolf, Jeffey; Jedrzejczak, Robert; Yan, Xiaohui; Ma, Ming; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George; Shen, Ben Structural Insights into the Free-Standing Condensation Enzyme SgcC5 Catalyzing Ester-Bond Formation in the Biosynthesis of the Enediyne Antitumor Antibiotic C‑1027 Biochemistry (2018)

Chang, Chungyu; Amer, Brendan; Osipiuk, Jerzy; McConnell, Scott; Huang, I-Hsiu; Hsieh, Van; Fu, Janine; Nguyen, Hong; Muroski, John; Flores, Erika ; Ogorzalek Loo, Rachel; Loo, Joseph; Putkey, John; Joachimiak, Andrzej; Das, Asis; Clubb, Robert; Ton-That, Hung In vitro reconstitution of sortase-catalyzed pilus polymerization reveals structural elements involved in pilin cross-linking Proceedings of the National Academy of Sciences of the United States of America (2018)

Rehman Kayani, Masood ur; Doyle, Shawn M.; Wang, Guanqun; Sangwan, Naseer; Gilbert, Jack; Christner, Brent; Zhu, Ting Metagenomic analysis of basal ice from an Alaskan glacier Microbiome (2018)

Huang, Pengxiang; Zhang, Sanduo; Wierbowski, Bradley; Kim, Youngchang; Nedelcu, Daniel; Aravena, Laura; Liu, Jing; Kruse, Andrew; Salic, Adrian The structural basis of Smoothened activation in Hedgehog signaling Cell (2018)

McConnell, Scott; Amer, Brendan; Muroski, John; Fu, Janine; Chang, Chungyu; Ogorzalek Loo, Rachel; Loo, Joseph; Osipiuk, Jerzy; Ton-That, Hung; Clubb, Robert Protein Labeling via a Specific Lysine-Isopeptide Bond Using the Pilin Polymerizing Sortase from Corynebacterium diphtheriae. Journal of the American Chemical Society (2018)

Wang, Nan; Rudolf, Jeffey; Dong, Liao-Bin; Osipiuk, Jerzy; Hatzos - Skintges, Catherine; Endres, Michael; Chang, Chin-Yuan; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George; Shen, Ben Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme. Nature Chemical Biology (2018)

van den Bosch, Tjis; Tan, Kemin; Joachimiak, Andrzej; Welte, Cornelia Functional Profiling and Crystal Structures of Isothiocyanate Hydrolases Found in Gut-Associated and Plant-Pathogenic Bacteria Applied and Environmental Microbiology (2018)

Kwon, Man Jae; O'Loughlin, Edward; Ham, Baknoon; Hwang, Yunho; Shim, Moojoon; Lee, Soonjae Application of an in-situ soil sampler for assessing subsurface biogeochemical dynamics in a diesel-contaminated coastal site during soil flushing operations Journal of Environmental Management (2018)

Abramoff, Rose; Xu, Xiaofeng; Hartman, Melanie; O'Brien, Sarah; Feng, Wenting; Davidson, Eric; Finzi, Adrien; Moorhead, Daryl; Schimel, Josh; Torn, Margaret; Mayes, Melanie The Millennial model: in search of measurable pools and transformations for modeling soil carbon in the new century Biogeochemistry (2018)

Nocek, Boguslaw; Riedl, Cory; Starus, Anna; Heath, Tahirah; Bienvenue, David; Osipiuk, Jerzy; Jedrzejczak, Robert; Joachimiak, Andrzej; Becker, Daniel; Holz, Richard Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism Biochemistry (2018)

Wilton, Rosemarie; Ahrendt, Angela; Shinde, Shalaka; Sholto-Douglas, Deirdre; Johnson, Jessica; Brennan, Melissa; Kemner, Kenneth A New Suite of Plasmid Vectors for Fluorescence-Based Imaging of Root Colonizing Pseudomonads Frontiers in Plant Science (2018)

Schwartz, Michael; Wang, Haipeng; Pan, Jessica; Clark, Wesley; Cui, Steven ; Eckwahl, Matthew; Pan, David; Parisien, Marc; Owens, Sarah; Cheng, Brian ; Martinez, Kristina ; Xu, Jinbo; Chang, Eugene; Pan, Tao; Eren, A. Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis Nature Communications (2018)

Cao, Nan; Tan, Kemin; Annamalai, Thirunavukkarasu; Joachimiak, Andrzej; Tse-Dinh, Yuk-Ching Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site Nucleic Acids Research (2018)

Dantas, Joana; Ferreira, Marisa; Catarino, Teresa; Kokhan, Oleksandr; Pokkuluri, P. Raj; Salgueiro, Carlos Molecular interactions between Geobacter sulfurreducens triheme cytochromes and the redox active analog for humic substances Biochimica et Biophysica Acta. Bioenergetics (2018)

Michalska, Karolina; Nhan, Dinh Quan; Willett, Julia; Stols, Lucy; Eschenfeldt, William; Jones, Allison; Nguyen, Josephine; Koskiniemi, Sanna; Low, David; Goulding, Celia; Joachimiak, Andrzej; Hayes, Christopher Functional plasticity of antibacterial EndoU toxins Molecular Microbiology (2018)

Tan, Kemin; Tesar, Christine; Wilton, Rosemarie; Jedrzejczak, Robert; Joachimiak, Andrzej The Interaction of Anti-diabetic α-Glucosidase Inhibitors and Gut Bacteria α-Glucosidase Protein Science (2018)

Niedringhaus, Andrew; Policht, Veronica; Sechrist, Riley; Konar, Arkaprabha; Laible, Philip; Bocian, David; Holten, Dewey; Kirmaier, Christine; Ogilvie, Jennifer Primary processes in the bacterial reaction center probed by two-dimensional electronic spectroscopy Proceedings of the National Academy of Sciences of the United States of America (2018)

Yan, Sen; Boyanov, Maxim; Mishra, Bhoopesh; Kemner, Kenneth; O'Loughlin, Edward U(VI) Reduction by Biogenic and Abiotic Hydroxycarbonate Green Rusts: Impacts on U(IV) speciation and stability over time Environmental Science and Technology (2018)

Michalska, Martyna; Gambacorta, Francesca; Divan, Ralu ; Aranson, Igor; Sokolov, Andrey; Noirot, Philippe; Laible, Philip Tuning antimicrobial properties of biomimetic nanopatterned surfaces Nanoscale (2018)

Valleau, Dylan; Quaile, Andrew; Cui, Hong; Xu, Xiaohui; Evdokimova, Elena; Chang, Changsoo; Cuff, Marianne; Urbanus, Malene; Houliston, Scott; Arrowsmith, Cheryl; Ensminger, Alexander; Savchenko, Alexei Discovery of Ubiquitin Deamidases in the Pathogenic Arsenal of Legionella pneumophila. Cell Reports (2018)

Gao, Jianzhao; Wu, Zhonghua; Hu, Gang; Wang, Kui; Song, Jiangning; Joachimiak, Andrzej; Kurgan, Lukasz Survey of predictors of propensity for protein production and crystallization with application to predict resolution of crystal structures Current Protein and Peptide Science (2018)