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Reference | Publication | Biosciences Division

BIO 2016 Publications

Howe, Adina; Ringus, Daina; Williams, Ryan; Choo, Zi-Ning; Greenwald, Stephanie ; Owens, Sarah; Coleman, Maureen; Meyer, Folker; Chang, EugeneDivergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in miceISME Journal(2016)

Sharma, Anukriti; Gilbert, Jack; Lal, Rup(Meta) genomic insights into the pathogenome of Cellulosimicrobium cellulansNature(2016)

Anderson, Lindsey; Koech, Phillip; Plymale, Andrew; Landorf, Elizabeth; Konopka, Allan; Collart, Frank; Lipton, Mary; Romine, Margaret; Wright, AaronLive cell discovery of microbial vitamin transport and enzyme-cofactor interactions by chemoproteomicsACS Chemical Biology(2016)

Adkins, Jaron; Jastrow, Julie; Morris, Geoffrey; Six, Johan; de Graaff, Marie-AnneEffects of switchgrass cultivars and intraspecific differences in root structure on soil carbon inputs and accumulationGeoderma(2016)

Manjasetty, Babu; Halavaty, Andrei; Luan, Chi-Hao; Osipiuk, Jerzy; Mulligan, Rory; Kwon, Keehwan; Anderson, Wayne; Joachimiak, AndrzejLoop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavityJournal of Structural Biology(2016)

Kamdar, Karishma; Khakpour, Samira; Chen, Jingyu; Leone, Vanessa; Brulc, Jennifer; Mangatu, Thomas; Antonopoulos, Dionysios; Chang, Eugene; Kahn, Stacy; Kirschner, Barbara; Young, Glenn; DePaolo, R. WilliamGenetic and metabolic signals during acute enteric bacterial infection alter the microbiota and drive progression to chronic inflammatory diseaseCell Host Microbe(2016)

Larsen, Peter; Sreedasyam, A; Trivedi, G; Desai, Shalaka; Dai, Yang; Cseke, Leland; Collart, FrankMulti-omics approach identifies molecular mechanisms of plant-fungus mycorrhizal interactionFrontiers in Plant Science(2016)

Tan, Kemin; Cao, Nan; Cheng, Bokun; Joachimiak, Andrzej; Tse-Dinh, Yuk-ChingInsights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein FoldJournal of Molecular Biology(2016)

Vandavasi, Venu Gopal; Weiss, Kevin; Cooper, Jonathan; Erskine, Peter; Tomanicek, Stephen; Ostermann, Andreas; Schrader, Tobias; Ginell, Stephan; Coates, LeightonExploring the Mechanism of β‑Lactam Ring Protonation in the Class A β‑lactamase Acylation Mechanism Using Neutron and X‑ray CrystallographyJournal of Medicinal Chemistry(2016)

Otani, Hiroshi; Stogios, Peter; Xu, Xiaohui; Nocek, Boguslaw; Li, Shu-Nan; Savchenko, Alexei; Eltis, LindsayThe activity of CouR, a MarR family transcriptional regulator, is modulated through a novel molecular mechanismNucleic Acids Research(2016)

Faries, Kaitlyn; Kressel, Lucas ; Dylla, Nicholas; Wander, Marc; Hanson, Deborah; Holten, Dewey; Laible, Philip; Kirmaier, ChristineOptimizing multi-step b-side charge separation in photosynthetic reaction centers from rhodobacter capsulatusBiochimica et Biophysica Acta. Bioenergetics(2016)

Latta, Drew; Kemner, Kenneth; Mishra, Bhoopesh; Boyanov, MaximEffects of calcium and phosphate on uranium(IV) oxidation: Comparison between nanoparticulate uraninite and amorphous U-IV-phosphateGeochimica et Cosmochimica Acta(2016)

Larsen, PeterMore of an Art than a Science: Using Microbial DNA Sequences to Compose MusicJournal of Microbiology and Biology Education(2016)

Huang, Lili; Khusnutdinova, Anna; Nocek, Boguslaw; Brown, Greg; Xu, Xiaohui; Cui, Hong; Petit, Pierre; Flick, Robert; Zallot, Remi; Balmant, Kelly; Ziemak, Michael; Shanklin, John; de Crecy-Lagard, Valerie; Fiehn, Oliver; Gregory, Jesse; Joachimiak, Andrzej; Savchenko, Alexei; Yakunin, Alexander; Hanson, Andrew D.A family of metal-dependent phosphatases implicated in metabolite damage-controlNature Chemical Biology(2016)

Huang, Pengxiang; Nedelcu, Daniel; Watanabe, Miyako; Jao, Cindy; Kim, Youngchang; Liu, Jing; Salic, AdrianCellular Cholesterol Directly Activates Smoothened in Hedgehog SignalingCell(2016)

Alkire, R.; Rotella, Frank; Duke, Norma; Otwinowski, Zbyszek; Borek, DominikaTaking a look at the calibration of a CCD detector with a fiber-optic taperJournal of Applied Crystallography(2016)

Chen, Ji-Yun; Liu, Liang; Cao, Chun-Ling; Li, Mei-Jun; Tan, Kemin; Yang, Xiaohan; Yun, CaihongStructure and function of human Naa60 (NatF), a Golgi-localized bi-functional acetyltransferase Scientific Reports(2016)

Dong, Yiran; Sanford, Robert; Boyanov, Maxim; Kemner, Kenneth; Flynn, Theodore; O'Loughlin, Edward; Chang, Yun-juan; Locke, Randall; Weber, Joseph; Egan, Sheila; Mackie, Roderick; Cann, Isaac; Fouke, BruceOrenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep SubsurfaceApplied and Environmental Microbiology(2016)

Houghton, J.; Foustoukos, D.; Flynn, T.; Vetriani, C.; Bradley, A.; Fike, D.Thiosulfate oxidation by Thiomicrospira thermophila: metabolic flexibility in response to ambient geochemistryEnvironmental Microbiology(2016)

Weglarz-Tomczak, Ewelina; Berlicki, Lukasz; Pawelczak, Malgorzata; Nocek, Boguslaw; Joachimiak, Andrzej; Mucha, ArturA structural insight into the P1eS1 binding mode of diaminoethylphosphonic and phosphinic acids, selective inhibitors of alanine aminopeptidasesEuropean Journal of Medicinal Chemistry(2016)

Wang, Weijun; Yan, Ruoyu; Nocek, Boguslaw; Vuong, Thu; Di Leo, Rosa; Xu, Xiaohui; Cui, Hong; Gatenholm, Paul; Toriz, Guillermo; Tenkanen, Maija; Savchenko, Alexei; Master, EmmaBiochemical and Structural Characterization of a Five-domain GH115 -Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T*□SJournal of Biological Chemistry (2016)

Rudolf, Jeffey; Dong, Liao-Bin; Cao, Hongnan; Hatzos - Skintges, Catherine; Osipiuk, Jerzy; Endres, Michael; Chang, Chin-Yuan; Ma, Ming; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George; Shen, BenStructure of the ent-Copalyl Diphosphate Synthase PtmT2 from Streptomyces platensis CB00739, a Bacterial Type II Diterpene SynthaseJournal of the American Chemical Society (2016)

Sung, Nuri; Lee, Jungsoon; Kim, Ji-Hyun; Chang, Changsoo; Tsai, Francis; Lee, Sukyeong2.4 A˚ resolution crystal structure of human TRAP1NM, the Hsp90 paralog in the mitochondrial matrixActa Crystallographica. Section D (2016)

Kim, Youngchang; Joachimiak, Grazyna; Bigelow, Lance; Babnigg, Gyorgy; Joachimiak, AndrzejHow Aromatic Compounds Block DNA Binding of HcaR Catabolite RegulatorJournal of Biological Chemistry(2016)

Dong, Yiran; Sanford, Robert; Boyanov, Maxim; Kemner, Kenneth; Flynn, Theodore; O'Loughlin, Edward; Locke, Randall; Weber, Joseph; Egan, Sheila; Fouke, BruceTepidibacillus decaturensis sp. nov.: a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from a depth of 1.7 km in the Illinois Basin, USAInternational Journal of Systematic and Evolutionary Microbiology(2016)

Jha, Ramesh; Kern, Teresa; Kim, Youngchang; Tesar, Christine; Jedrzejczak, Robert; Joachimiak, Andrzej; Strauss, Charlie EA microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factorNucleic Acids Research(2016)

Wu, Dalei; Su, Xiaoyu; Potluri, Nalini; Kim, Youngchang; Rastinejad, FraydoonNPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factorseLife(2016)

Dylla, Nicholas; Faries, Kaitlyn; Wyllie, Ryan; Swenson, Angela; Hanson, Deborah; Holten, Dewey; Kirmaier, Christine; Laible, PhilipSpecies differences in unlocking b-side electron transfer in bacterial reaction centersFEBS Letters(2016)

Morris, Geoffrey; Hu, Zhenbin; Grabowski, Paul; Borevitz, Justin; de Graaff, Marie-Anne; Miller, R.; Jastrow, JulieGenotypic diversity effects on biomass production in native perennial bioenergy cropping systemsGlobal Change Biology. Bioenergy(2016)

Boyanov, Maxim; Latta, Drew; Scherer, Michelle; O'Loughlin, Edward; Kemner, KennethSurface area effects on the reduction of U(VI) in the presence of synthetic montmorilloniteChemical Geology(2016)

Dantas, Joana M; Simões, Telma; Morgado, Leonor; Caciones, Clara; Fernandes, Ana ; Silva, Marta; Bruix, Marta; Pokkuluri, P. Raj; Salgueiro, CarlosUnveiling the Structural Basis That Regulates the Energy Transduction Properties within a Family of Triheme Cytochromes from Geobacter sulfurreducensJournal of Physical Chemistry B(2016)

Metcalf, Jessica; Xu, Zhenjiang; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embrietta R; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg; Ackermann, Gail; Thompson, Luke; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew ; Petrosino, Joseph; Reed, Sasha; Gilbert, Jack; Lynne, Aaron; Bucheli, Sibyl; Carter, David; Knight, RobertMicrobial community assembly and metabolic function during mammalian corpse decompositionScience(2016)

Huang, Tingting; Chang, Chin-Yuan; Lohman, Jeremy; Rudolf, Jeffey; Kim, Youngchang; Chang, Changsoo; Yang, Dong; Ma, Ming; Yan, Xiaohui; Crnovcic, Ivana; Bigelow, Lance; Clancy, Shonda; Bingman, Craig; Yennamalli, Ragothaman; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George; Shen, BenCrystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027The Journal of Antibiotics(2016)

Sung, Nuri; Lee, Jungsoon; Kim, Ji-Hyun; Chang, Changsoo; Joachimiak, Andrzej; Lee, Sukyeong; Tsai, FrancisMitochondrial Hsp90 is a ligand-activated molecular chaperone coupling ATP binding to dimer closure through a coiled-coil intermediate.Proceedings of the National Academy of Sciences of the United States of America(2016)

Denner, Darcy; Sangwan, Naseer; Becker, Julia; Hogarth, D.; Oldham, Justin; Castillo, Jamee; Sperling, Anne; Solway, Julian; Naureckas, Edward; Gilbert, Jack; White, StevenCorticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways.Journal of Allergy and Clinical Immunology(2016)

Verduzco-Castro, Ernesto; Michalska, Karolina; Endres, Michael; Juarez-Vazquez, Ana; Noda-Garcia, Lianet; Chang, Changsoo; Henry, Christopher; Babnigg, Gyorgy; Joachimiak, Andrzej; Barona-Gomez, FranciscoCo-occurrence of Analogous Enzymes Determines Evolution of a Novel (βα)8-Isomerase Sub-family After Non-conserved Mutations in Flexible LoopBiochemical Journal(2016)

O'Brien, Sarah; Gibbons, Sean; Owens, Sarah; Hampton-Marcell, Jarrad; Johnston, Eric; Jastrow, Julie; Gilbert, Jack; Meyer, Folker; Antonopoulos, DionysiosSpatial scale drives patterns in soil bacterial diversityEnvironmental Microbiology(2016)

Urbanus, Marlene; Quaile, Andrew; Stogios, Peter; Morar, Mariya; Rao, Chitong; Di Leo, Rosa; Evdokimova, Elena; Lam, Mandy; Oatway, Christina; Cuff, Marianne; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; Taipale, Mikko; Savchenko, Alexei; Ensminger, AlexanderDiverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophilaMolecular Systems Biology(2016)

Sachleben, Joseph; Adhikari, Aashish; Gawlak, Grzegorz; Hoey, Robert; Liu, Gaohua; Joachimiak, Andrzej; Montelione, Gaetano; Sosnick, Tobin; Koide, ShoheiAromatic claw: A new fold with high aromatic content that evades structural predictionProtein Science(2016)

Kwon, Man Jae; O'Loughlin, Edward; Boyanov, Maxim; Brulc, Jennifer; Johnston, Eric; Kemner, Kenneth; Antonopoulos, DionysiosImpact of organic carbon electron donors on microbial community development under iron- and sulfate-reducing conditionsPLOS ONE(2016)

Vineis, Joseph; Ringus, Daina; Morrison, Hilary; Delmont, Tom; Dalal, Sushila; Raffals, Laura; Antonopoulos, Dionysios; Rubin, David; Eren, A.; Chang, Eugene; Sogin, MitchellPatient-specific Bacteroides genome variants in pouchitismBio(2016)

Chang, Chin-Yuan; Lohman, Jeremy; Cao, Hongnan; Tan, Kemin; Rudolf, Jeffey; Ma, Ming; Xu, Weijun; Bingman, Craig; Yennamalli, Ragothaman; Bigelow, Lance; Babnigg, Gyorgy; Yan, Xiaohui; Joachimiak, Andrzej; Phillips, George; Shen, BenCrystal Structures of SgcE6 and SgcC, the Two-Component Monooxygenase That Catalyzes Hydroxylation of a Carrier ProteinTethered Substrate during the Biosynthesis of the Enediyne Antitumor Antibiotic C‑1027 in Streptomyces globisporusBiochemistry(2016)

Herrou, Julien; Czyz, Daniel; Willette, Jonathan; Kim, Hye-Sook; Chhor, Gekleng; Babnigg, Gyorgy; Kim, Youngchang; Crosson, SeanWrpA Is an Atypical Flavodoxin Family Protein under Regulatory Control of the Brucella abortus General Stress Response SystemJournal of Bacteriology(2016)