Recent Publications

November 2018

Banerjee A, Arnesen JA, Moser D, Motsa BB, Johnson SR, Hamberger B. “Engineering modular diterpene biosynthetic pathways in Physcomitrella patens.” Planta. (2018) Nov 23. doi: 10.1007/s00425-018-3053-0

Kamba PF, Dickson DA, White NA, Ekstrom JL, Koslowsky DJ, Hoogstraten CG. “The 27 kDa Trypanosoma brucei Pentatricopeptide Repeat Protein is a G-tract Specific RNA Binding Protein.” Sci Rep. (2018) Nov 19;8(1):16989. doi: 10.1038/s41598-018-34377-9

Chacón KN, Perkins J, Mathe Z, Alwan K, Ho EN, Ucisik MN, Merz KM, Blackburn NJ. “Trapping intermediates in metal transfer reactions of the CusCBAF export pump of Escherichia coli.” Commun Biol. (2018) Nov 14;1:192. doi: 10.1038/s42003-018-0181-9

Gaffney KA, Hong H. “The rhomboid protease GlpG has weak interaction energies in its active site hydrogen bond network.” J Gen Physiol. (2018) Nov 12;. doi: 10.1085/jgp.201812047

Aykul S, Martinez-Hackert E. “High-Throughput, Biosensor-Based Approach to Examine Bone Morphogenetic Protein (BMP)-Receptor Interactions.” Methods Mol Biol. (2019) Nov 10;1891:37-49. doi: 10.1007/978-1-4939-8904-1_5

Yu L, He J, Wang L, Yi H. “Inflammatory profiles revealed the dysregulation of cytokines in adult patients of HFMD.” Int J Infect Dis. (2018) Nov 10;. doi: 10.1016/j.ijid.2018.11.001

Sengupta A, Seitz A, Merz KM Jr. “Simulating the Chelate Effect.” J Am Chem Soc. (2018) Nov 6. doi: 10.1021/jacs.8b09371

Sommer M, Sutter M, Gupta S, Kirst H, Turmo A, Lechno-Yossef S, Burton RL, Saechao C, Sloan NB, Cheng X, Chan LG, Petzold CJ, Fuentes-Cabrera M, Ralston CY, Kerfeld CA. “Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells.” Plant Physiol. (2018) Nov 2;. doi: 10.1104/pp.18.01190

October 2018

Sharkey TD. “Discovery of the canonical Calvin-Benson cycle.” Photosynth Res. (2018) Oct 29. doi: 10.1007/s11120-018-0600-2

Li J, Tietz S, Cruz JA, Strand DD, Xu Y, Chen J, Kramer DM, Hu J. “Photometric screens identified Arabidopsis peroxisome proteins that impact photosynthesis under dynamic light conditions.” Plant J. (2018) Oct 23. doi: 10.1111/tpj.14134

Hagen A, Plegaria JS, Sloan N, Ferlez B, Aussignargues C, Kerfeld CA. “In vitro assembly of diverse bacterial microcompartment shell architectures.” Nano Lett. (2018) Oct 22. doi: 10.1021/acs.nanolett.8b02991

Guo Q, Yoshida Y, Major IT, Wang K, Sugimoto K, Kapali G, Havko NE, Benning C, Howe GA. “JAZ repressors of metabolic defense promote growth and reproductive fitness in Arabidopsis.” Proc Natl Acad Sci U S A. (2018) Oct 22. doi: 10.1073/pnas.1811828115

Dornbos P, Warren M, Crawford RB, Kaminski N, Threadgill DW, LaPres JJ. “Characterizing Serpinb2 as a modulator of TCDD-induced suppression of the B cell.” Chem Res Toxicol. (2018) Oct 19. doi: 10.1021/acs.chemrestox.8b00225

Kim Y, Kowiatek B, Opron K, Burton ZF. “Type-II tRNAs and Evolution of Translation Systems and the Genetic Code” Int. J. Mol. Sci. (2018) Oct 18;19(10):3275. doi: 10.3390/ijms19103275

Ogrodzinski MP, Teoh ST, Yu L, Broadwater D, Ensink E, Lunt SY. “Measuring the Nutrient Metabolism of Adherent Cells in Culture.” Methods Mol Biol. (2018) Oct 13;1862:37-52. doi: 10.1007/978-1-4939-8769-6_3

Bramer D, Wei GW. “Blind prediction of protein B-factor and flexibility.” J Chem Phys. (2018) Oct 7;149(13):134107. doi: 10.1063/1.5048469

Fellner M, Hausinger RP, Hu J. “A structural perspective on the PP-loop ATP pyrophosphatase family.” Crit Rev Biochem Mol Biol. (2018) Oct 3;1-16. doi: 10.1080/10409238.2018.1516728

Pande K, Donatelli JJ, Malmerberg E, Foucar L, Poon BK, Sutter M, Botha S, Basu S, Bruce Doak R, Dörner K, Epp SW, Englert L, Fromme R, Hartmann E, Hartmann R, Hauser G, Hattne J, Hosseinizadeh A, Kassemeyer S, Lomb L, Montero SFC, Menzel A, Rolles D, Rudenko A, Seibert MM, Sierra RG, Schwander P, Ourmazd A, Fromme P, Sauter NK, Bogan M, Bozek J, Bostedt C, Schlichting I, Kerfeld CA, Zwart PH. “Free-electron laser data for multiple-particle fluctuation scattering analysis.” Sci Data. (2018) Oct 2;5:180201. doi: 10.1038/sdata.2018.201

September 2018

Dickson A. “Mapping the Ligand Binding Landscape.” Biophys J. (2018) Sep 29. doi: 10.1016/j.bpj.2018.09.021

Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC. “Niche partitioning of a pathogenic microbiome driven by chemical gradients.” Sci Adv. (2018) Sep;4(9):eaau1908. doi: 10.1126/sciadv.aau1908

Silva GFF, Silva EM, Correa JPO, Vicente MH, Jiang N, Notini MM, Junior AC, De Jesus FA, Castilho P, Carrera E, Lopes-Diaz I, Grotewold E, Peres LEP, Nogueira FTS. “Tomato floral induction and flower development are orchestrated by the interplay between gibberellin and two unrelated microRNA-controlled modules.” New Phytol. (2018) Sep 20. doi: 10.1111/nph.15492

Lienemann M, TerAvest MA, Pitkänen JP, Stuns I, Penttilä M, Ajo-Franklin CM, Jäntti J. “Towards patterned bioelectronics: facilitated immobilization of exoelectrogenic Escherichia coli with heterologous pili.” Microb Biotechnol. (2018) Sep 17. doi: 10.1111/1751-7915.13309

Fan M, Herburger K, Jensen JK, Zemelis-Durfee S, Brandizzi F, Fry SC, Wilkerson CG. “A Trihelix Family Transcription Factor is Associated with Key Genes in Mixed-linkage Glucan Accumulation.” Plant Physiol. (2018) Sep 17. doi: 10.1104/pp.18.00978

Toyota M, Spencer D, Sawai-Toyota S, Jiaqi W, Zhang T, Koo AJ, Howe GA, Gilroy S. “Glutamate triggers long-distance, calcium-based plant defense signaling.” Science. (2018) Sep 14;361(6407):1112-1115. doi: 10.1126/science.aat7744

Pizzo L, Jensen M, Polyak A, Rosenfeld JA, Mannik K, Krishnan A, McCready E, Pichon O, Le Caignec C, Van Dijck A, Pope K, Voorhoeve E, Yoon J, Stankiewicz P, Cheung SW, Pazuchanics D, Huber E, Kumar V, Kember RL, Mari F, Curró A, Castiglia L, Galesi O, Avola E, Mattina T, Fichera M, Mandarà L, Vincent M, Nizon M, Mercier S, Bénéteau C, Blesson S, Martin-Coignard D, Mosca-Boidron AL, Caberg JH, Bucan M, Zeesman S, Nowaczyk MJM, Lefebvre M, Faivre L, Callier P, Skinner C, Keren B, Perrine C, Prontera P, Marle N, Renieri A, Reymond A, Kooy RF, Isidor B, Schwartz C, Romano C, Sistermans E, Amor DJ, Andrieux J, Girirajan S. “Rare variants in the genetic background modulate cognitive and developmental phenotypes in individuals carrying disease-associated variants.” Genet Med. (2018) Sep 7. doi: 10.1038/s41436-018-0266-3

Zheng Z, Pei J, Bansal N, Liu H, Song LF, Merz KM. “Generation of Pairwise Potentials Using Multi-Dimensional Data Mining.” J Chem Theory Comput. (2018) Sep 5. doi: 10.1021/acs.jctc.8b00516

Li M, Martinez S, Hausinger RP, Emerson JP. “Thermodynamics of iron(II) and substrate binding to the ethylene-forming enzyme.” Biochemistry. (2018) Sep 5. doi: 10.1021/acs.biochem.8b00730

Hoang Y, Kroos L. “Ultrasensitive response of developing Myxococcus xanthus to the addition of nutrient medium correlates with the level of MrpC.” J Bacteriol. (2018) Sep 4. doi: 10.1128/JB.00456-18

Herwaldt EJ, Rivett ED, White AJ, Hegg EL. “Cox15 interacts with the cytochrome bc1 dimer within respiratory supercomplexes as well as in the absence of cytochrome c oxidase.” J Biol Chem. (2018) Sep 4. doi: 10.1074/jbc.RA118.002496

Zhao R, Cang Z, Tong Y, Wei GW. “Protein pocket detection via convex hull surface evolution and associated Reeb graph.” Bioinformatics. (2018) Sep 1;34(17):i830-i837. doi: 10.1093/bioinformatics/bty598

August 2018

Righini S, Rodriguez EJ, Berosich C, Grotewold E, Casati P, Falcone Ferreyra ML. “Apigenin produced by maize flavone synthase I and II protects plants against UV-B-induced damage.” Plant Cell Environ. (2018) Aug 30. doi: 10.1111/pce.13428

Fellner M, Rankin JA, Desguin B, Hu J, Hausinger RP. “Analysis of the Active Site Cysteine Residue of the Sacrificial Sulfur Insertase LarE from Lactobacillus plantarum.” Biochemistry. (2018) Aug 29. doi: 10.1021/acs.biochem.8b00601

Woodard J, Srivastava KR, Rahamim G, Grupi A, Hogan S, Witalka DJ, Nawrocki G, Haas E, Feig M, Lapidus LJ. “Intramolecular Diffusion in α-Synuclein: It Depends on How You Measure It.” Biophys J. (2018) Aug 27. doi: 10.1016/j.bpj.2018.08.023

Song LF, Bansal N, Zheng Z, Merz KM Jr. “Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.” J Comput Aided Mol Des. (2018) Aug 24. doi: 10.1007/s10822-018-0153-7

Dixon T, Lotz SD, Dickson A. “Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge.” J Comput Aided Mol Des. (2018) Aug 23. doi: 10.1007/s10822-018-0149-3

Nguyen DD, Cang Z, Wu K, Wang M, Cao Y, Wei GW. “Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges.” J Comput Aided Mol Des. (2018) Aug 16. doi: 10.1007/s10822-018-0146-6

Galtier d'Auriac I, Quinn RA, Maughan H, Nothias LF, Little M, Kapono CA, Cobian A, Reyes BT, Green K, Quistad SD, Leray M, Smith JE, Dorrestein PC, Rohwer F, Deheyn DD, Hartmann AC. “Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism.” Proc Biol Sci. (2018) Aug 15;285:(1884). doi: 10.1098/rspb.2018.1307

White NA, Sumita M, Marquez VE, Hoogstraten CG. “Coupling Between Conformational Dynamics and Catalytic Function at the Active Site of the Lead-Dependent Ribozyme.” RNA. (2018) Aug 15. doi: 10.1261/rna.067579.118

Shen X, Kou Q, Guo R, Yang Z, Chen D, Liu X, Hong H, Sun L. “Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry.” Anal Chem. (2018) Aug 13. doi: 10.1021/acs.analchem.8b02725

Zhang Q, van Wijk R, Zarza X, Shahbaz M, van Hooren M, Guardia A, Scuffi D, García-Mata C, Van den Ende W, Hoffmann-Benning S, Haring MA, Laxalt AM, Munnik T. “Knock-Down of Arabidopsis PLC5 Reduces Primary Root Growth and Secondary Root Formation While Overexpression Improves Drought Tolerance and Causes Stunted Root Hair Growth.” Plant Cell Physiol. (2018) Aug 9;. doi: 10.1093/pcp/pcy120

July 2018

Mejia-Guerra MK, Li W, Doseff AI, Grotewold E. “Genome-Wide TSS Identification in Maize.” Methods Mol Biol. (2018) Jul 25;1830:239-256. doi: 10.1007/978-1-4939-8657-6_14

Basson MD, Wang Q, Chaturvedi LS, More S, Vomhof-DeKrey EE, Al-Marsoummi S, Sun K, Kuhn LA, Kovalenko P, Kiupel M. “Schlafen 12 Interaction with SerpinB12 and Deubiquitylases Drives Human Enterocyte Differentiation.” Cell Physiol Biochem. (2018) Jul 25;48(3):1274-1290. doi: 10.1159/000492019

Hagen A, Sutter M, Sloan N, Kerfeld CA. “Programmed loading and rapid purification of engineered bacterial microcompartment shells.” Nat Commun. (2018) Jul 23;9(1):2881. doi: 10.1038/s41467-018-05162-z

Song G, Hsu PY, Walley JW. “Assessment and refinement of sample preparation methods for deep and quantitative plant proteome profiling.” Proteomics. (2018) Jul 23;e1800220. doi: 10.1002/pmic.201800220

Feroz H, Ferlez B, Lefoulon C, Ren T, Baker CS, Gajewski JP, Lugar DJ, Gaudana SB, Butler PJ, Hühn J, Lamping M, Parak WJ, Hibberd JM, Kerfeld CA, Smirnoff N, Blatt MR, Golbeck JH, Kumar M. “Light-Driven Chloride Transport Kinetics of Halorhodopsin.” Biophys J. (2018) Jul 17;115(2):353-360. doi: 10.1016/j.bpj.2018.06.009

Deng X, Kuo MH. “Tripartite Chromatin Localization of Budding Yeast Shugoshin Involves Higher-Ordered Architecture of Mitotic Chromosomes.” G3 (Bethesda). (2018) Jul 12. doi: 10.1534/g3.118.200522

Hausinger RP, Desguin B, Fellner M, Rankin JA, Hu J. “Nickel-pincer nucleotide cofactor.” Curr Opin Chem Biol. (2018) Jul 9;47:18-23. doi: 10.1016/j.cbpa.2018.06.019

Kim Y, Benning N, Pham K, Baghdadi N, Caruso G, Colligan M, Grayson A, Hurley A, Ignatoski N, Mcclure S, Mckaig K, Neag E, Showers C, Tangalos A, Vanells J, Padmanabhan K, Burton ZF. “Homology threading to generate RNA polymerase structures.” Protein Expr Purif. (2018) Jul;147:13-16. doi: 10.1016/j.pep.2018.02.002

June 2018

Zeng X, Uyar A, Sui D, Donyapour N, Wu D, Dickson A, Hu J. “Structural Insights into Lethal Contractural Syndrome Type 3 (LCCS3) Caused by a Missense Mutation of PIP5Kγ.” Biochem J. (2018) Jun 29;. doi: 10.1042/BCJ20180326

Haslun JA, Ostrom NE, Hegg EL, Ostrom PH. “Estimation of Isotope Variation of N2O during Denitrification by Pseudomonas aureofaciens and Pseudomonas chlororaphis: Implications for N2O Source Apportionment.” Biogeosciences. (2018) Jun 27. 15:3873-3882. doi: 10.5194/bg-15-3873-2018

Brooks LRK, Mias GI. “Streptococcus pneumoniae's Virulence and Host Immunity: Aging, Diagnostics, and Prevention.” Frontiers in Immunology (2018) Jun 22; doi: 10.3389/fimmu.2018.01366

Yuan Z, Li G, Hegg EL. “Enhancement of sugar recovery and ethanol production from wheat straw through alkaline pre-extraction followed by steam pretreatment.” Bioresour Technol. (2018) Jun 21;266:194-202. doi: 10.1016/j.biortech.2018.06.065

Li M, Henderson KL, Martinez S, Hausinger RP, Emerson JP. “The Irving-Williams series and the 2-His-1-carboxylate facial triad: a thermodynamic study of Mn2+, Fe2+, and Co2+ binding to taurine/α-ketoglutarate dioxygenase (TauD).” J Biol Inorg Chem. (2018) Jun 19;. doi: 10.1007/s00775-018-1574-4

Chanoca A, Burkel B, Grotewold E, Eliceiri KW, Otegui MS. “Imaging Vacuolar Anthocyanins with Fluorescence Lifetime Microscopy (FLIM).” Methods Mol Biol. (2018) Jun 19;1789:131-141. doi: 10.1007/978-1-4939-7856-4_10

Hurlock AK, Wang K, Takeuchi T, Horn PJ, Benning C. “In Vivo Lipid "Tag and Track" Approach Shows Acyl Editing of Plastid Lipids and Chloroplast Import of Phosphatidylglycerol Precursors in Arabidopsis thaliana.” Plant J. (2018) Jun 19;. doi: 10.1111/tpj.13999

Hackenberg C, Hakanpää J, Cai F, Antonyuk S, Eigner C, Meissner S, Laitaoja M, Jänis J, Kerfeld CA, Dittmann E, Lamzin VS. “Structural and functional insights into the unique CBS-CP12 fusion protein family in cyanobacteria.” Proc Natl Acad Sci U S A. (2018) Jun 18;. doi: 10.1073/pnas.1806668115

Midic U, Vincent KA, Wang K, Lokken A, Severance AL, Ralston A, Knott JG, Latham KE. “Novel key roles for Structural maintenance of chromosome flexible domain containing 1 (Smchd1) during preimplantation mouse development.” Mol Reprod Dev. (2018) Jun 13; doi: 10.1002/mrd.23001

Severin GB, Ramliden MS, Hawver LA, Wang K, Pell ME, Kieninger AK, Khataokar A, O'Hara BJ, Behrmann LV, Neiditch MB, Benning C, Waters CM, Ng WL. “Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae.” Proc Natl Acad Sci U S A. (2018) Jun 11. doi: 10.1073/pnas.1801233115

Desguin B, Fellner M, Riant O, Hu J, Hausinger R, Hols P, Soumillion P. “Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.” J Biol Chem. (2018) Jun 10. doi: 10.1074/jbc.RA118.003741

May 2018

Agostoni M, Logan-Jackson AR, Heinz ER, Severin GB, Bruger EL, Waters CM, Montgomery BL. “Homeostasis of Second Messenger Cyclic-di-AMP Is Critical for Cyanobacterial Fitness and Acclimation to Abiotic Stress.” Front Microbiol. (2018) May 29;9:1121. doi: 10.3389/fmicb.2018.01121

Teoh ST, Ogrodzinski MP, Ross C, Hunter KW, Lunt SY. “Sialic Acid Metabolism: A Key Player in Breast Cancer Metastasis Revealed by Metabolomics.” Front Oncol. (2018) May 28;8:174. doi: 10.3389/fonc.2018.00174

Wong AK, Krishnan A, Troyanskaya OG. “GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.” Nucleic Acids Res. (2018) May 25. doi: 10.1093/nar/gky408

JasiĹ„ski M, Feig M, Trylska J. “Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.” J Chem Theory Comput. (2018) May 23. doi: 10.1021/acs.jctc.8b00291

Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC. “Best practices for analysing microbiomes.” Nat Rev Microbiol. (2018) May 23. doi: 10.1038/s41579-018-0029-9

Buehl CJ, Kuo MH. “Critical roles of Shugoshin and histones as tension sensors during mitosis.” Curr Genet. (2018) May 23. doi: 10.1007/s00294-018-0846-4

Bhalla A, Fasahati P, Particka CA, Assad AE, Stoklosa RJ, Bansal N, Semaan R, Saffron CM, Hodge DB, Hegg EL. “Integrated experimental and technoeconomic evaluation of two-stage Cu-catalyzed alkaline-oxidative pretreatment of hybrid poplar.” Biotechnol Biofuels. (2018) May 17. 11:143. doi: 10.1186/s13068-018-1124-x

Rangan AV, McGrouther CC, Kelsoe J, Schork N, Stahl E, Zhu Q, Krishnan A, Yao V, Troyanskaya O, Bilaloglu S, Raghavan P, Bergen S, Jureus A, Landen M. “A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.” PLoS Comput Biol. (2018) May 14;14(5):e1006105. doi: 10.1371/journal.pcbi.1006105

Attanayake G, Walter T, Walker KD. “Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase Define its Mutase and Lyase Activities.” Biochemistry. (2018) May 14. doi: 10.1021/acs.biochem.8b00269

Nault R, Doskey CM, Fader KA, Rockwell CE, Zacharewski TR. “Comparison of hepatic NRF2 and AHR binding in 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treated mice demonstrates NRF2-independent PKM2 induction.” Mol Pharmacol. (2018) May 11. doi: 10.1124/mol.118.112144

Liu MJ, Sugimoto K, Uygun S, Panchy N, Campbell MS, Yandell M, Howe GA, Shiu SH. “Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato.” Plant Cell. (2018) May 9. doi: 10.1105/tpc.18.00194

Pak D, Kim Y, Burton ZF. “Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code.” Transcription. (2018) May 4;1-36. doi: 10.1080/21541264.2018.1467718

Ye Y, Bian W, Fu F, Hu J, Liu H. “Selenoprotein S inhibits inflammation-induced vascular smooth muscle cell calcification.” J Biol Inorg Chem. (2018) May 2. doi: 10.1007/s00775-018-1563-7

April 2018

Herr CQ, Hausinger RP. “Amazing Diversity in Biochemical Roles of Fe(II)/2-Oxoglutarate Oxygenases.” Trends Biochem Sci. (2018) Apr 27. doi: 10.1016/j.tibs.2018.04.002

Salim V, Jones AD, DellaPenna D. “Camptotheca acuminata 10-hydroxycamptothecin O-methyltransferase: an alkaloid biosynthetic enzyme coopted from flavonoid metabolism.” Plant J. (2018) Apr 22. doi: 10.1111/tpj.13936

Dutagaci B, Heo L, Feig M. “Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations.” Proteins. (2018) Apr 20. doi: 10.1002/prot.25508

Frum T, Ralston A. “AttrActin' Attention to Early Mouse Development.” Cell. (2018) Apr 19;173(3):544-545. doi: 10.1016/j.cell.2018.03.078

Wang K, Guo Q, Froehlich JE, Hersh HL, Zienkiewicz A, Howe GA, Benning C. “Two Abscisic Acid Responsive Plastid Lipase Genes Involved in Jasmonic Acid Biosynthesis in Arabidopsis thaliana.” Plant Cell. (2018) Apr 17. doi: 10.1105/tpc.18.00250

Fader KA, Nault R, Raehtz S, McCabe LR, Zacharewski TR. “2,3,7,8-Tetrachlorodibenzo-p-dioxin dose-dependently increases bone mass and decreases marrow adiposity in juvenile mice.” Toxicol Appl Pharmacol. (2018) Apr 16. doi: 10.1016/j.taap.2018.04.013

Ouma WZ, Pogacar K, Grotewold E. “Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties.” PLoS Comput Biol. (2018) Apr;14(4):e1006098. doi: 10.1371/journal.pcbi.1006098

Duhl KL, Tefft NM, TerAvest MA. “Shewanella oneidensis MR-1 utilizes both sodium- and proton-pumping NADH dehydrogenases during aerobic growth.” Appl Environ Microbiol. (2018) Apr 13. doi: 10.1128/AEM.00415-18

Schwarz EM, Tietz S, Froehlich JE. “Photosystem I-LHCII megacomplexes respond to high light and aging in plants.” Photosynth Res. (2018) Apr;136(1):107-124. doi: 10.1007/s11120-017-0447-y

Xu H, Lybrand D, Bennewitz S, Tissier A, Last RL, Pichersky E. “Production of trans-chrysanthemic acid, the monoterpene acid moiety of natural pyrethrin insecticides, in tomato fruit.” Metab Eng. (2018) Apr 9. doi: 10.1016/j.ymben.2018.04.004

Wu K, Zhao Z, Wang R, Wei GW. “TopP-S: Persistent homology-based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility.” J Comput Chem. (2018) Apr 6. doi: 10.1002/jcc.25213

Hiser C, Liu J, Ferguson-Miller S. “The K-path entrance in cytochrome c oxidase is defined by mutation of E101 and controlled by an adjacent ligand binding domain.” Biochim Biophys Acta. (2018) Apr 4. doi: 10.1016/j.bbabio.2018.03.017

Im H, Rao V, Sridhar K, Bentley J, Mishra T, Chen R, Hall J, Graber A, Zhang Y, Li X, Mias GI, Snyder MP, Greenberg PL. “Distinct transcriptomic and exomic abnormalities within myelodysplastic syndrome marrow cells.” Leuk Lymphoma. (2018) Apr 4;1-11. doi: 10.1080/10428194.2018.1452210

Eschweiler JD, Farrugia MA, Dixit SM, Hausinger RP, Ruotolo BT. “A Structural Model of the Urease Activation Complex Derived from Ion Mobility-Mass Spectrometry and Integrative Modeling.” Structure. (2018) Apr 3;26(4):599-606.e3. doi: 10.1016/j.str.2018.03.001

Bansal N, Zheng Z, Song LF, Pei J, Merz KM. “The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation.” J Am Chem Soc. (2018) Apr 2. doi: 10.1021/jacs.8b00743

Raschka S, More SK, Devadoss D, Zeng B, Kuhn LA, Basson MD. “Identification of potential small-molecule protein-protein inhibitors of cancer metastasis by 3D epitope-based computational screening.” J Physiol Pharmacol. (2018) Apr;69:(2). doi: 10.26402/jpp.2018.2.11

March 2018

Mias, G. “Mathematica for Bioinformatics.” Springer (2018) March ISBN: 978-3-319-72377-8

Raschka S, Scott AM, Huertas M, Li W, Kuhn LA. “Automated Inference of Chemical Discriminants of Biological Activity.” Methods Mol Biol. (2018) March 29;1762:307-338. doi: 10.1007/978-1-4939-7756-7_16

Guo Q, Major IT, Howe GA. “Resolution of growth-defense conflict: mechanistic insights from jasmonate signaling.” Curr Opin Plant Biol. (2018) Mar 16;44:72-81. doi: 10.1016/j.pbi.2018.02.009

Banerjee A, Hamberger B. “P450s controlling metabolic bifurcations in plant terpene specialized metabolism.” Phytochem Rev. (2018) 17(1):81-111. doi: 10.1007/s11101-017-9530-4

Heskes AM, Sundram TCM, Boughton BA, Jensen NB, Hansen NL, Crocoll C, Cozzi F, Rasmussen S, Hamberger B, Hamberger B, Staerk D, Møller BL, Pateraki I. “Biosynthesis of bioactive diterpenoids in the medicinal plant Vitex agnus-castus.” Plant J. (2018) Mar;93(5):943-958. doi: 10.1111/tpj.13822

Xue S, Jones AD, Sousa L, Piotrowski J, Jin M, Sarks C, Dale BE, Balan V. “Water-soluble phenolic compounds produced from extractive ammonia pretreatment exerted binary inhibitory effects on yeast fermentation using synthetic hydrolysate.” PLoS One. (2018) Mar 15;13(3):e0194012. doi: 10.1371/journal.pone.0194012

Kaguni JM. “The Macromolecular Machines that Duplicate the Escherichia coli Chromosome as Targets for Drug Discovery.” Antibiotics (Basel). (2018) Mar 14;7:(1). doi: 10.3390/antibiotics7010023

Howe GA, Major IT, Koo AJ. “Modularity in Jasmonate Signaling for Multistress Resilience.” Annu Rev Plant Biol. (2018) Mar 14. doi: 10.1146/annurev-arplant-042817-040047

Poliner E, Takeuchi T, Du ZY, Benning C, Farré EM. “Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, Nannochloropsis oceanica CCMP1779.” ACS Synth Biol. (2018) Mar 14. doi: 10.1021/acssynbio.7b00362

Yang Y, Guo R, Gaffney K, Kim M, Muhammednazaar S, Tian W, Wang B, Liang J, Hong H. “Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-dependent Protease FtsH.” J Am Chem Soc. (2018) Mar 12. doi: 10.1021/jacs.8b00832

Scott KM, Williams J, Porter CMB, Russel S, Harmer TL, Paul JH, Antonen KM, Bridges MK, Camper GJ, Campla CK, Casella LG, Chase E, Conrad JW, Cruz MC, Dunlap DS, Duran L, Fahsbender EM, Goldsmith DB, Keeley RF, Kondoff MR, Kussy BI, Lane MK, Lawler S, Leigh BA, Lewis C, Lostal LM, Marking D, Mancera PA, McClenthan EC, McIntyre EA, Mine JA, Modi S, Moore BD, Morgan WA, Nelson KM, Nguyen KN, Ogburn N, Parrino DG, Pedapudi AD, Pelham RP, Preece AM, Rampersad EA, Richardson JC, Rodgers CM, Schaffer BL, Sheridan NE, Solone MR, Staley ZR, Tabuchi M, Waide RJ, Wanjugi PW, Young S, Clum A, Daum C, Huntemann M, Ivanova N, Kyrpides N, Mikhailova N, Palaniappan K, Pillay M, Reddy TBK, Shapiro N, Stamatis D, Varghese N, Woyke T, Boden R, Freyermuth SK, Kerfeld CA. “Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments.” Environ Microbiol. (2018) Mar 9. doi: 10.1111/1462-2920.14090

Poliner E, Farré EM, Benning C. “Advanced genetic tools enable synthetic biology in the oleaginous microalgae Nannochloropsis sp.” Plant Cell Rep. (2018) Mar 6. doi: 10.1007/s00299-018-2270-0

Kerfeld CA, Aussignargues C, Zarzycki J, Cai F, Sutter M. “Bacterial microcompartments.” Nat Rev Microbiol. (2018) Mar 5. doi: 10.1038/nrmicro.2018.10

Ligaba-Osena A, Jones J, Donkor E, Chandrayan S, Pole F, Wu CH, Vieille C, Adams MWW, Hankoua BB. “Novel Bioengineered Cassava Expressing an Archaeal Starch Degradation System and a Bacterial ADP-Glucose Pyrophosphorylase for Starch Self-Digestibility and Yield Increase.” Front Plant Sci. (2018) 9:192. doi: 10.3389/fpls.2018.00192

February 2018

Genoni A, Bucinsky L, Claiser N, Contreras-Garcia J, Dittrich B, Dominiak PM, Espinosa E, Gatti C, Giannozzi P, Gillet JM, Jayatilaka D, Macchi P, Madsen AØ, Massa LJ, Matta CF, Merz KM, Nakashima PNH, Ott H, Ryde U, Schwarz K, Sierka M, Grabowsky S. “Quantum Crystallography: Current Developments and Future Perspectives.” Chemistry. (2018) Feb 28. doi: 10.1002/chem.201705952

Rankin JA, Mauban RC, Fellner M, Desguin B, McCracken J, Hu J, Varganov SA, Hausinger RP. “The Lactate Racemase Nickel-Pincer Cofactor Operates by a Proton-Coupled Hydride Transfer Mechanism.” Biochemistry. (2018) Feb 28. doi: 10.1021/acs.biochem.8b00100

Yildirim A, Feig M. “High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization.” Nucleic Acids Res. (2018) Feb 26. doi: 10.1093/nar/gky141

Bohm K, Porwollik S, Chu W, Dover JA, Gilcrease EB, Casjens SR, McClelland M, Parent KN. “Genes affecting progression of bacteriophage P22 infection in Salmonella identified by transposon and single gene deletion screens.” Mol Microbiol. (2018) Feb 22. doi: 10.1111/mmi.13936

Jensen JK, Busse-Wicher M, Poulsen CP, Fangel JU, Smith PJ, Yang JY, Peña MJ, Dinesen MH, Martens HJ, Melkonian M, Wong GK, Moremen KW, Wilkerson CG, Scheller HV, Dupree P, Ulvskov P, Urbanowicz BR, Harholt J. “Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis.” New Phytol. (2018) Feb 20. doi: 10.1111/nph.15050

Dornbos P, LaPres JJ. “Incorporating population-level genetic variability within laboratory models in toxicology: From the individual to the population.” Toxicology. (2018) Feb 15;395:1-8. doi: 10.1016/j.tox.2017.12.007

Raschka S, Wolf AJ, Bemister-Buffington J, Kuhn LA. “Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes.” J Comput Aided Mol Des. (2018) Feb 12. doi: 10.1007/s10822-018-0105-2

Kim Y, Benning N, Pham K, Baghdadi A, Caruso G, Colligan M, Grayson A, Hurley A, Ignatoski N, Mcclure S, Mckaig K, Neag E, Showers C, Tangalos A, Vanells J, Padmanabhan K, Burton ZF. “Homology threading to generate RNA polymerase structures.” Protein Expr Purif. (2018) Feb 11. doi: 10.1016/j.pep.2018.02.002

Ciesielski GL, Nadalutti CA, Oliveira MT, Jacobs HT, Griffith JD, Kaguni LS. “Structural rearrangements in the mitochondrial genome of Drosophila melanogaster induced by elevated levels of the replicative DNA helicase.” Nucleic Acids Res. (2018) Feb 8. doi: 10.1093/nar/gky094

Bramer D, Wei GW. “Multiscale weighted colored graphs for protein flexibility and rigidity analysis.” J Chem Phys. (2018) Feb 7;148(5):054103. doi: 10.1063/1.5016562

Parent KN, Schrad JR, Cingolani G. “Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy.” Viruses. (2018) Feb 7;10:(2). doi: 10.3390/v10020067

Doore SM, Schrad JR, Dean WF, Dover JA, Parent KN. “Shigella phages isolated during a dysentery outbreak reveal uncommon structures and broad species diversity” J of Virology (2018) Feb 7. doi: 10.1128/JVI.02117-17

Du ZY, Lucker BF, Zienkiewicz K, Miller TE, Zienkiewicz A, Sears BB, Kramer DM, Benning C. “Galactoglycerolipid Lipase PGD1 Is Involved in Thylakoid Membrane Remodeling in Response to Adverse Environmental Conditions in Chlamydomonas.” Plant Cell. (2018) Feb 5. doi: 10.1105/tpc.17.00446

Fristedt R, Hu C, Wheatley N, Roy LM, Wachter RM, Savage L, Harbinson J, Kramer DM, Merchant SS, Yeates T, Croce R. “RAF2 is a Rubisco Assembly Factor in Arabidopsis thaliana.” Plant J. (2018) Feb 3;. doi: 10.1111/tpj.13849

Rohnke BA, Singh SP, Pattanaik B, Montgomery BL. “RcaE-Dependent Regulation of Carboxysome Structural Proteins Has a Central Role in Environmental Determination of Carboxysome Morphology and Abundance in Fremyella diplosiphon.” mSphere. (2018) Jan-Feb;3:(1). doi: 10.1128/mSphere.00617-17

January 2018

Wu K, Wei GW. “Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks.” J Chem Inf Model. (2018) Jan 31. doi: 10.1021/acs.jcim.7b00558

Raschka S, Scott AM, Liu N, Gunturu S, Huertas M, Li W, Kuhn LA. “Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control.” J Comput Aided Mol Des. (2018) Jan 30. doi: 10.1007/s10822-018-0100-7

Wei J, Zheng Y, Feng H, Qu H, Fan X, Yamaji N, Feng Ma J, Xu G, Takahashi H. “OsNRT2.4 encodes a dual-affinity nitrate transporter and functions in nitrate-regulated root growth and nitrate distribution in rice.” J Exp Bot. (2018) Jan 29. doi: 10.1093/jxb/erx486

Kim SJ, Zemelis-Durfee S, Jensen JK, Wilkerson CG, Keegstra K, Brandizzi F. “In the grass species Brachypodium distachyon, the production of mixed linkage (1,3;1,4)-Β-glucan (MLG) occurs in the Golgi apparatus.” Plant J. (2018) Jan 27. doi: 10.1111/tpj.13830

Pak D, Du N, Kim Y, Sun Y, Burton ZF. “Rooted tRNAomes and evolution of the genetic code.” Transcription. (2018) Jan 26;1-31. doi: 10.1080/21541264.2018.1429837

Liu D, Wang Q, Traverse CJ, Yang C, Young M, Kuttipillai PS, Lunt SY, Hamann TW, Lunt RR. “Impact of Ultrathin C60 on Perovskite Photovoltaic Devices.” ACS Nano. (2018) Jan 23;12(1):876-883. doi: 10.1021/acsnano.7b08561

Bhalla A, Bansal N, Pattathil S, Li M, Shen W, Particka CA, Karlen SD, Phongpreecha T, Semaan RR, Gonzales-Vigil E, Ralph J, Mansfield SD, Ding SY, Hodge DB, Hegg EL. ”Engineered Lignin in Poplar Biomass Facilitates Cu-Catalyzed Alkaline-Oxidative Pretreatment&lduo; ACS Sustainable Chemistry & Engineering (2018) Jan 22;6(3):2932-2941 doi: 10.1021/acssuschemeng.7b02067

Das A, Rahimi A, Ulbrich A, Alherech M, Motagamwala AH, Bhalla A, da Costa Sousa L, Balan V, Dumesic JA, Hegg EL, Dale BE, Ralph J, Coon JJ, Stahl SS. ”Lignin Conversion to Low-Molecular-Weight Aromatics via an Aerobic Oxidation-Hydrolysis Sequence: Comparison of Different Lignin Sources&dlquo; ACS Sustainable Chemistry & Engineering (2018) Jan 19;6(3):3367-3374 doi: 10.1021/acssuschemeng.7b03541

Wood RJ, Ormsby AR, Radwan M, Cox D, Sharma A, Vöpel T, Ebbinghaus S, Oliveberg M, Reid GE, Dickson A, Hatters DM. “A biosensor-based framework to measure latent proteostasis capacity.” Nat Commun. (2018) Jan 18;9(1):287. doi: 10.1038/s41467-017-02562-5

Gurchiek JK, Bao H, Domínguez-Martín MA, McGovern SE, Marquardt CE, Roscioli JD, Ghosh S, Kerfeld CA, Beck WF. “Fluorescence and Excited State Conformational Dynamics of the Orange Carotenoid Protein.” J Phys Chem B. (2018) Jan 18;. doi: 10.1021/acs.jpcb.7b09435

Howe GA. “Plant hormones: Metabolic end run to jasmonate.” Nat Chem Biol. (2018) Jan 16;14(2):109-110. doi: 10.1038/nchembio.2553

Watts J, Lokken A, Moauro A, Ralston A. “Capturing and Interconverting Embryonic Cell Fates in a Dish.” Curr Top Dev Biol. (2018) Jan 12. 128:181-202. doi: 10.1016/bs.ctdb.2017.11.008

Hodeib M, Ogrodzinski MP, Vergnes L, Reue K, Karlan BY, Lunt SY, Aspuria PP. “Metformin induces distinct bioenergetic and metabolic profiles in sensitive versus resistant high grade serous ovarian cancer and normal fallopian tube secretory epithelial cells.” Oncotarget. (2018) Jan 9;9(3):4044-4060. doi: 10.18632/oncotarget.23661

Hunter CT, Saunders JW, Magallanes-Lundback M, Christensen SA, Willett D, Stinard PS, Li QB, Lee K, DellaPenna D, Koch KE. “Maize w3 disrupts homogentisate solanesyl transferase (ZmHst) and reveals a plastoquinone-9 independent path for phytoene desaturation and tocopherol accumulation in kernels.” Plant J. (2018) Jan 8. doi: 10.1111/tpj.13821

Heskes AM, Sundram TCM, Boughton BA, Bjerg Jensen N, Hansen NL, Crocoll C, Cozzi F, Rasmussen S, Hamberger B, Hamberger B, Staerk D, Møller BL, Pateraki I. “Biosynthesis of bioactive diterpenoids in the medicinal plant Vitex agnus-castus.” Plant J. (2018) Jan 8. doi: 10.1111/tpj.13822

Cang Z, Mu L, Wei GW. “Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening.” PLoS Comput Biol. (2018) Jan 8;14(1):e1005929. doi: 10.1371/journal.pcbi.1005929

Lotz SD, Dickson A. “Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions.” J Am Chem Soc. (2018) Jan 5;. doi: 10.1021/jacs.7b08572

December 2017

Hu, J., Wille, H., and Schmitt-Ulms, G. “The Evolutionary unZIPping of a Dimerization Motif-A Comparison of ZIP and PrP Architectures.” Pathogens. (2017) Dec 29;7(1):4. doi: 10.3390/pathogens7010004

Tsai CH, Uygun S, Roston R, Shiu SH, Benning C. “Recovery from N Deprivation Is a Transcriptionally and Functionally Distinct State in Chlamydomonas.” Plant Physiol. (2017) Dec 29;. doi: 10.1104/pp.17.01546

Oakley CG, Savage L, Lotz S, Rudd Larson G, Thomashow MF, Kramer DM, Schemske DW. “Genetic basis of photosynthetic responses to cold in two locally adapted populations of Arabidopsis thaliana.” J Exp Bot. (2017) Dec 28;. doi: 10.1093/jxb/erx437

Zhang Q, Wijk RV, Shahbaz M, Roels W, Schooten BV, Vermeer JEM, Zarza X, Guardia A, Scuffi D, García-Mata C, Laha D, Williams P, Willems LAJ, Ligterink W, Hoffmann-Benning S, Gillaspy G, Schaaf G, Haring MA, Laxalt AM, Munnik T. “Arabidopsis Phospholipase C3 is Involved in Lateral Root Initiation and ABA Responses in Seed Germination and Stomatal Closure.” Plant Cell Physiol. (2017) Dec 22. doi: 10.1093/pcp/pcx194

Buehl CJ, Deng X, Luo J, Buranasudja V, Hazbun T, Kuo MH. “A Failsafe for Sensing Chromatid Tension in Mitosis with the Histone H3 Tail in Saccharomyces cerevisiae.” Genetics. (2017) Dec 14;. doi: 10.1534/genetics.117.300606

Fan P, Miller AM, Liu X, Jones AD, Last RL. “Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity.” Nat Commun. (2017) Dec 12;8(1):2080. doi: 10.1038/s41467-017-02045-7

Uyar A, Karamyan VT, Dickson A. “Long-Range Changes in Neurolysin Dynamics Upon Inhibitor Binding.” J Chem Theory Comput. (2017) Dec 8;. doi: 10.1021/acs.jctc.7b00944

Huang D, Guo G, Yuan P, Ralston A, Sun L, Huss M, Mistri T, Pinello L, Ng HH, Yuan G, Ji J, Rossant J, Robson P, Han X. “The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation.” Sci Rep. (2017) Dec 7;7(1):17156. doi: 10.1038/s41598-017-16009-w

Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM. “The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.” Plant Physiol. (2017) Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490

November 2017

Oh S, Montgomery BL. “Phytochromes: Where to Start?” Cell. (2017) Nov 30;171(6):1254-1256. doi: 10.1016/j.cell.2017.11.020

Nawrocki G, Wang PH, Yu I, Sugita Y, Feig M. “Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.” J Phys Chem B. (2017) Nov 30. doi: 10.1021/acs.jpcb.7b08785

Huot B, Castroverde CDM, Velásquez AC, Hubbard E, Pulman JA, Yao J, Childs KL, Tsuda K, Montgomery BL, He SY. “Dual impact of elevated temperature on plant defence and bacterial virulence in Arabidopsis.” Nat Commun. (2017) Nov 27;8(1):1808. doi: 10.1038/s41467-017-01674-2

Halder S, Parrell D, Whitten D, Feig M, Kroos L. “Interaction of intramembrane metalloprotease SpoIVFB with substrate Pro-σK.” Proc Natl Acad Sci U S A. (2017) Nov 27. doi: 10.1073/pnas.1711467114

Ralston A. “XEN and the Art of Stem Cell Maintenance: Molecular Mechanisms Maintaining Cell Fate and Self-Renewal in Extraembryonic Endoderm Stem (XEN) Cell Lines.” Adv Anat Embryol Cell Biol. (2017) Nov 25. 229:69-78. doi: 10.1007/978-3-319-63187-5_6

Dutagaci B, Feig M. “Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.” J Chem Inf Model. (2017) Nov 20. doi: 10.1021/acs.jcim.7b00510

Zeng B, Devadoss D, Wang S, Vomhof-DeKrey EE, Kuhn LA, Basson MD. “Inhibition of pressure-activated cancer cell adhesion by FAK-derived peptides.” Oncotarget. (2017) Nov 17;8(58):98051-98067. doi: 10.18632/oncotarget.20556

Yu Z, Li P, Merz KM. “The Extended Zinc AMBER Force Field (EZAFF).” J Chem Theory Comput. (2017) Nov 17. doi: 10.1021/acs.jctc.7b00773

Nagarajan S, Lapidus LJ. “Fluorescent Probe DCVJ Shows High Sensitivity for Characterization of Amyloid Β-Peptide Early in the Lag Phase.” Chembiochem. (2017) Nov 16;18(22):2205-2211. doi: 10.1002/cbic.201700387

Cang Z, Wei GW. “Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology.” Bioinformatics. (2017) Nov 15;33(22):3549-3557. doi: 10.1093/bioinformatics/btx460

Wang B, Wang C, Wu K, Wei GW. “Breaking the polar-nonpolar division in solvation free energy prediction.” J Comput Chem. (2017) Nov 11. doi: 10.1002/jcc.25107

Xu H, Moghe GD, Wiegert-Rininger K, Schilmiller AL, Barry CS, Last RL, Pichersky E. “Identification of dehydrogenases involved in the biosynthesis of the monoterpene moiety of pyrethrin.” Plant Physiol. (2017) Nov 9;. doi: 10.1104/pp.17.01330

Heo L, Feig M. “PREFMD: a web server for protein structure refinement via molecular dynamics simulations.” Bioinformatics. (2017) Nov 8;. doi: 10.1093/bioinformatics/btx726

October 2017

Müller TA, Struble SL, Meek K, Hausinger RP. “Characterization of human AlkB homolog 1 produced in mammalian cells and demonstration of mitochondrial dysfunction in ALKBH1-deficient cells.” Biochem Biophys Res Commun. (2017) Oct 30. doi: 10.1016/j.bbrc.2017.10.158

Diepenbrock CH, Kandianis CB, Lipka AE, Magallanes-Lundback M, Vaillancourt B, Góngora-Castillo E, Wallace JG, Cepela J, Mesberg A, Bradbury PJ, Ilut DC, Mateos-Hernandez M, Hamilton J, Owens BF, Tiede T, Buckler ES, Rocheford T, Buell CR, Gore MA, DellaPenna D. “Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain.” Plant Cell. (2017) Oct;29(10):2374-2392. doi: 10.1105/tpc.17.00475

Burns LA, Faver JC, Zheng Z, Marshall MS, Smith DGA, Vanommeslaeghe K, MacKerell AD Jr, Merz KM Jr, Sherrill CD. “The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions.” J Chem Phys. (2017) Oct 28;147(16):161727. doi: 10.1063/1.5001028

Chen C, MacCready JS, Ducat DC, Osteryoung KW. “The Molecular Machinery of Chloroplast Division.” Plant Physiol. (2017) Oct 27. doi: 10.1104/pp.17.01272

Felczak MM, Chodavarapu S, Kaguni JM. “DnaC, the indispensable companion of DnaB helicase, controls the accessibility of DnaB helicase by primase.” J Biol Chem. (2017) Oct 25. doi: 10.1074/jbc.M117.807644

Thornburg CK, Walter T, Walker KD. “Biocatalysis of a Paclitaxel Analogue: Conversion of Baccatin III to N-Debenzoyl-N-(2-furoyl)paclitaxel and Characterization of an Amino Phenylpropanoyl CoA Transferase” Biochemistry (2017) Oct 25. doi: 10.1021/acs.biochem.7b00912

Weiss TL, Young EJ, Ducat DC. “A synthetic, light-driven consortium of cyanobacteria and heterotrophic bacteria enables stable polyhydroxybutyrate production.” Metab Eng. (2017) Oct 20. doi: 10.1016/j.ymben.2017.10.009

Lindsey BE 3rd, Rivero L, Calhoun CS, Grotewold E, Brkljacic J. “Standardized Method for High-throughput Sterilization of Arabidopsis Seeds.” J Vis Exp. (2017) Oct 17. doi: 10.3791/56587

Plegaria JS, Kerfeld CA. “Engineering nanoreactors using bacterial microcompartment architectures.” Curr Opin Biotechnol. (2017) Oct 13;51:1-7. doi: 10.1016/j.copbio.2017.09.005

Teoh ST, Lunt SY. “Metabolism in cancer metastasis: bioenergetics, biosynthesis, and beyond.” Wiley Interdiscip Rev Syst Biol Med. (2017) Oct 9. doi: 10.1002/wsbm.1406

Kar P, Feig M. “Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.” J Chem Theory Comput. (2017) Oct 9. doi: 10.1021/acs.jctc.7b00840

Heo L, Feig M. “What makes it difficult to refine protein models further via molecular dynamics simulations?” Proteins. (2017) Oct 4;. doi: 10.1002/prot.25393

Turmo A, Gonzalez-Esquer CR, Kerfeld CA. “Carboxysomes: metabolic modules for CO2 fixation.” FEMS Microbiol Lett. (2017) Oct 2;364:(18). doi: 10.1093/femsle/fnx176

September 2017

Plegaria JS, Sutter M, Ferlez B, Aussignargues C, Niklas J, Poluektov OG, Fromwiller C, TerAvest M, Utschig LM, Tiede DM, Kerfeld CA. “Structural and Functional Characterization of a Short-Chain Flavodoxin Associated with a Non-Canonical PDU Bacterial Microcompartment.” Biochemistry. (2017) Sep 28. doi: 10.1021/acs.biochem.7b00682

Kerfeld CA. “A bioarchitectonic approach to the modular engineering of metabolism.” Philos Trans R Soc Lond B Biol Sci. (2017) Sep 26;372:(1730). doi:10.1098/rstb.2016.0387

Davis GA, Rutherford AW, Kramer DM. “Hacking the thylakoid proton motive force for improved photosynthesis: modulating ion flux rates that control proton motive force partitioning into Δφ and ΔpH.” Philos Trans R Soc Lond B Biol Sci. (2017) Sep 26;372:(1730). doi:10.1098/rstb.2016.0381

Lapidus LJ. “Protein unfolding mechanisms and their effects on folding experiments.” F1000Res. (2017) Sep 22;6:1723. doi: 10.12688/f1000research.12070.1

Morales A, Yin X, Harbinson J, Driever SM, Molenaar J, Kramer DM, Struik P. “In silico analysis of the regulation of the photosynthetic electron transport chain in C3 plants.” Plant Physiol. (2017) Sep 18. doi: 10.1104/pp.17.00779

Nagarajan S, Lapidus LJ. “Fluorescent probe DCVJ shows high sensitivity for characterization of amyloid beta peptide early in the lag phase.” Chembiochem. (2017) Sep 11. doi: 10.1002/cbic.201700387

Liu J, Last RL. “A chloroplast thylakoid lumen protein is required for proper photosynthetic acclimation of plants under fluctuating light environments.” Proc Natl Acad Sci U S A. (2017) Sep 5. doi: 10.1073/pnas.1712206114

Lucker B, Schwartz E, Kuhlgert S, Ostendorf E, Kramer DM. “Spectroanalysis in Native Gels (SING): Rapid Spectral Analysis of Pigmented Thylakoid Membrane Complexes Separated By Clear Native PAGE.” Plant J. (2017) Sep 2. doi: 10.1111/tpj.13703

Zhao D, Hamilton JP, Pham GM, Crisovan E, Wiegert-Rininger K, Vaillancourt B, DellaPenna D, Buell CR. “De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin.” Gigascience. (2017) Sep 1;6(9):1-7. doi: 10.1093/gigascience/gix065

August 2017

Nedialkov YA, Opron K, Caudill HL, Assaf F, Anderson AJ, Cukier RI, Wei G, Burton ZF. “Hinge action versus grip in translocation by RNA polymerase.” Transcription. (2017) Aug 30;e1330179. doi: 10.1080/21541264.2017.1330179

Moghe GD, Leong BJ, Hurney S, Jones AD, Last RL. “Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway.” Elife. (2017) Aug 30. doi: 10.7554/eLife.28468

Sharkey TD. “A dichotomy resolved: plant growth can control the rate of starch accumulation.” Plant Cell Environ. (2017) Aug 30. doi: 10.1111/pce.13059

Liu J, Hiser C, Ferguson-Miller S. “Role of conformational change and K-path ligands in controlling cytochrome c oxidase activity.” Biochem Soc Trans. (2017) Aug 24. doi: 10.1042/BST20160138

Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. “Improvements to the APBS biomolecular solvation software suite.” Protein Sci. (2017) Aug 24. doi: 10.1002/pro.3280

Leong BJ, Last RL. “Promiscuity, impersonation and accommodation: evolution of plant specialized metabolism.” Curr Opin Struct Biol. (2017) Aug 16;47:105-112. doi: 10.1016/j.sbi.2017.07.005

Terbush AD, MacCready JS, Chen C, Ducat DC, Osteryoung KW. “Conserved Dynamics of Chloroplast Cytoskeletal FtsZ Proteins Across Photosynthetic Lineages.” Plant Physiol. (2017) Aug 16. doi:10.1104/pp.17.00558

Matsushima Y, Hirofuji Y, Aihara M, Yue S, Uchiumi T, Kaguni LS, Kang D. “Drosophila protease ClpXP specifically degrades DmLRPPRC1 controlling mitochondrial mRNA and translation.” Sci Rep. (2017) Aug 16;7(1):8315. doi:10.1038/s41598-017-08088-6

Kieffer-Kwon K, McAndrew M, Floer M, et al. “Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation” Molecular Cell. (2017) Aug 11;67:1-13. doi: 10.1016/j.molcel.2017.07.013

Pak D, Root-Bernstein R, Burton ZF. “tRNA structure and evolution and standardization to the three nucleotide genetic code.” Transcription. (2017) Aug 8;8(4):205-219. doi: 10.1080/21541264.2017.1318811

Chakraborty D, Benham V, Bullard B, Kearney T, Hsia HC, Gibbon D, Demireva EY, Lunt SY, Bernard JJ. “Fibroblast growth factor receptor is a mechanistic link between visceral adiposity and cancer.” Oncogene. (2017) Aug 7. doi: 10.1038/onc.2017.278

Fellner M, Desguin B, Hausinger RP, Hu J. “Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.” Proc Natl Acad Sci U S A. (2017) Aug 7. pii: 201704967. doi: 10.1073/pnas.1704967114

Martinez S, Fellner M, Herr CQ, Ritchie A, Hu J, Hausinger RP. “Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist.” J Am Chem Soc. (2017) Aug 5. doi: 10.1021/jacs.7b06186

Zhang T, Liu J, Fellner M, Zhang C, Sui D, Hu J. “Crystal structures of a ZIP zinc transporter reveal a binuclear metal center in the transport pathway.” Sci Adv. (2017) Aug;3(8):e1700344. doi: 10.1126/sciadv.1700344

Desguin B, Soumillion P, Hausinger RP, Hols P. “Unexpected complexity in the lactate racemization system of lactic acid bacteria.” FEMS Microbiol Rev. (2017) Aug 1;41(Supp_1):S71-S83. doi: 10.1093/femsre/fux021

Tietz S, Hall CC, Cruz JA, Kramer DM. “NPQ((T)) : a chlorophyll fluorescence parameter for rapid estimation and imaging of non-photochemical quenching of excitons in photosystem-II-associated antenna complexes.” Plant Cell Environ. (2017) Aug;40(8):1243-1255. doi: 10.1111/pce.12924

Feller A, Yuan L, Grotewold E. “The BIF Domain in Plant bHLH Proteins Is an ACT-Like Domain.” Plant Cell. (2017) Aug;29(8):1800-1802. doi: 10.1105/tpc.17.00356

July 2017

Young EJ, Burton R, Mahalik JP, Sumpter BG, Fuentes-Cabrera M, Kerfeld CA, Ducat DC. “Engineering the Bacterial Microcompartment Domain for Molecular Scaffolding Applications.” Front Microbiol. (2017) Jul 31;8:1441. doi: 10.3389/fmicb.2017.01441

Cang Z, Wei GW. “TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions.” PLoS Comput Biol. (2017) Jul 27;13(7):e1005690. doi: 10.1371/journal.pcbi.1005690

Nguyen DD, Xiao T, Wang M, Wei GW. “Rigidity Strengthening: A Mechanism for Protein-Ligand Binding.” J Chem Inf Model. (2017) Jul 24;57(7):1715-1721. doi: 10.1021/acs.jcim.7b00226

Kohzuma K, Froehlich JE, Davis GA, Temple JA, Minhas D, Dhingra A, Cruz JA, Kramer DM. “The Role of Light-Dark Regulation of the Chloroplast ATP Synthase.” Front Plant Sci. (2017) Jul 24;8:1248. doi: 10.3389/fpls.2017.01248

Pickens CA, Vazquez AI, Jones AD, Fenton JI. “Obesity, adipokines, and C-peptide are associated with distinct plasma phospholipid profiles in adult males, an untargeted lipidomic approach.” Sci Rep. (2017) Jul 24;7(1):6335. doi: 10.1038/s41598-017-05785-0

Fader KA, Nault R, Zhang C, Kumagai K, Harkema JR, Zacharewski TR. “2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-elicited effects on bile acid homeostasis: Alterations in biosynthesis, enterohepatic circulation, and microbial metabolism.” Sci Rep. (2017) Jul 19;7(1):5921. doi: 10.1038/s41598-017-05656-8

Ogrodzinski MP, Bernard JJ, Lunt SY. “Deciphering metabolic rewiring in breast cancer subtypes.” Transl Res. (2017) Jul 15. pii: S1931-5244(17)30234-7. doi: 10.1016/j.trsl.2017.07.004

Cang Z, Wei GW. “Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology.” Bioinformatics. (2017) Jul 14. doi: 10.1093/bioinformatics/btx460

White NA, Hoogstraten CG. “Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.” Biophys Chem. (2017) Jul 8;228:62-68. doi: 10.1016/j.bpc.2017.07.001

Nadakuduti SS, Uebler JB, Liu X, Jones AD, Barry CS. “Characterization of trichome-expressed BAHDs in Petunia reveals distinct acylsugar assembly mechanisms.” Plant Physiol. (2017) Jul 12. pii: pp.00538.2017. doi: 10.1104/pp.17.00538

Bao H, Melnicki MR, Pawlowski EG, Sutter M, Agostoni M, Lechno-Yossef S, Cai F, Montgomery BL, Kerfeld CA. “Additional families of orange carotenoid proteins in the photoprotective system of cyanobacteria.” Nat Plants. (2017) Jul 10;3:17089. doi: 10.1038/nplants.2017.89

Wang K, Froehlich JE, Zienkiewicz A, Hersh HL, Benning C. “A Plastid Phosphatidylglycerol Lipase Contributes to the Export of Acyl Groups from Plastids for Seed Oil Biosynthesis.” Plant Cell. (2017) Jul 6. pii: tpc.00397.2017. doi: 10.1105/tpc.17.00397

Cang Z, Wei GW. “Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction.” Int J Numer Method Biomed Eng. (2017) Jul 5. doi: 10.1002/cnm.2914

Parrell D, Zhang Y, Olenic S, Kroos L. “Bacillus subtilis Intramembrane Protease RasP Activity in Escherichia coli and in Vitro.” J Bacteriol. (2017) Jul 3. pii: JB.00381-17. doi: 10.1128/JB.00381-17

June 2017

Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. “Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.” J Phys Chem B. (2017) Jun 30. doi: 10.1021/acs.jpcb.7b03570

Major IT, Yoshida Y, Campos ML, Kapali G, Xin XF, Sugimoto K, de Oliveira Ferreira D, He SY, Howe GA. “Regulation of growth-defense balance by the JASMONATE ZIM-DOMAIN (JAZ)-MYC transcriptional module.” New Phytol. (2017) Jun 26. doi: 10.1111/nph.14638

Dutta S, Cruz JA, Imran SM, Chen J, Kramer DM, Osteryoung KW. “Variations in chloroplast movement and chlorophyll fluorescence among chloroplast division mutants under light stress.” J Exp Bot. (2017) Jun 22. doi: 10.1093/jxb/erx203

Kuhn MJ, Mavangira V, Gandy JC, Zhang C, Jones AD, Sordillo LM. “Differences in the Oxylipid Profiles of Bovine Milk and Plasma at Different Stages of Lactation.” J Agric Food Chem. (2017) Jun 21;65(24):4980-4988. doi: 10.1021/acs.jafc.7b01602

Martinez S, Hausinger RP. “Correction to Biochemical and Spectroscopic Characterization of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme from Pseudomonas syringae pv. phaseolicola PK2.” Biochemistry. (2017) Jun 20;56(24):3158. doi: 10.1021/acs.biochem.7b00502

Mukundi E, Gomez-Cano F, Ouma WZ, Grotewold E. “Design of Knowledge Bases for Plant Gene Regulatory Networks.” Methods Mol Biol. (2017) Jun 17;1629:207-223. doi: 10.1007/978-1-4939-7125-1_14

Forman V, Callari R, Folly C, Heider H, Hamberger B. “Production of Putative Diterpene Carboxylic Acid Intermediates of Triptolide in Yeast.” Molecules. (2017) Jun 13;22(6). pii: E981. doi: 10.3390/molecules22060981

Poliner E, Pulman JA, Zienkiewicz K, Childs K, Benning C, Farré EM. “A toolkit for Nannochloropsis oceanica CCMP1779 enables gene stacking and genetic engineering of the eicosapentaenoic acid pathway for enhanced long-chain polyunsaturated fatty acid production.” Plant Biotechnol J. (2017) Jun 12. doi: 10.1111/pbi.12772

de Bang TC, Lay KS, Scheible WR, Takahashi H. “Small peptide signaling pathways modulating macronutrient utilization in plants.” Curr Opin Plant Biol. (2017) Jun 2;39:31-39. doi: 10.1016/j.pbi.2017.05.005

May 2017

Strand DD, Fisher N, Kramer DM. “The higher plant plastid NAD(P)H dehydrogenase-like complex (NDH) is a high efficiency proton pump that increases ATP production by cyclic electron flow.” J Biol Chem. (2017) May 30. pii: jbc.M116.770792. doi: 10.1074/jbc.M116.770792

Mansfeld BN, Colle M, Kang Y, Jones AD, Grumet R. “Transcriptomic and metabolomic analyses of cucumber fruit peels reveal a developmental increase in terpenoid glycosides associated with age-related resistance to Phytophthora capsici.” Hortic Res. (2017) May 24;4:17022. doi: 10.1038/hortres.2017.22

Yang Y, Zienkiewicz A, Lavell A, Benning C. “Co-evolution of Domain Interactions in the Chloroplast TGD1, 2, 3 Lipid Transfer Complex Specific to Brassicaceae and Poaceae Plants.” Plant Cell. (2017) May 19. pii: tpc.00182.2017. doi: 10.1105/tpc.17.00182

Xing A, Last RL. “A Regulatory Hierarchy of the Arabidopsis Branched-chain Amino Acid Metabolic Network.” Plant Cell. (2017) May 18. pii: tpc.00186.2017. doi: 10.1105/tpc.17.00186

Lechno-Yossef S, Melnicki MR, Bao H, Montgomery BL, Kerfeld CA. “Synthetic OCP Heterodimers are Photoactive and Recapitulate the Fusion of Two Primitive Carotenoproteins in the Evolution of Cyanobacterial Photoprotection.” Plant J. (2017) May 15. doi: 10.1111/tpj.13593

Kanazawa A, Ostendorf E, Kohzuma K, Hoh D, Strand DD, Sato-Cruz M, Savage L, Cruz JA, Fisher N, Froehlich JE, Kramer DM. “Chloroplast ATP Synthase Modulation of the Thylakoid Proton Motive Force: Implications for Photosystem I and Photosystem II Photoprotection.” Front Plant Sci. (2017) May 3;8:719. doi: 10.3389/fpls.2017.00719

Dutagaci B, Wittayanarakul K, Mori T, Feig M. “Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.” J Chem Theory Comput. (2017) May 11. doi: 10.1021/acs.jctc.7b00254

Morin JA, Cerrón F, Jarillo J, Beltran-Heredia E, Ciesielski GL, Arias-Gonzalez JR, Kaguni LS, Cao FJ, Ibarra B. “DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein.” Nucleic Acids Res. (2017) May 9. doi: 10.1093/nar/gkx395

Stedtfeld RD, Stedtfeld TM, Fader KA, Williams MR, Bhaduri P, Quensen J, Zacharewski TR, Tiedje JM, Hashsham SA. “TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome.” FEMS Microbiol Ecol. (2017) May 4. doi: 10.1093/femsec/fix058

Yang Y, Xu L, Feng Z, Cruz JA, Savage LJ, Kramer DM, Chen J. “PhenoCurve: capturing dynamic phenotype-environment relationships using phenomics data.” Bioinformatics. (2017) May 1;33(9):1370-1378. doi: 10.1093/bioinformatics/btw673

Benning C. “Plant science from The Plant Journal Editors' perspective.” Plant J. (2017) May;90(4):625-627. doi: 10.1111/tpj.13565

April 2017

Liban TJ, Medina EM, Tripathi S, Sengupta S, Henry RW, Buchler NE, Rubin SM. “Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family.” Proc Natl Acad Sci U S A. (2017) Apr 24. pii: 201619170. doi: 10.1073/pnas.1619170114

Nurminen A, Farnum GA, Kaguni LS. “Pathogenicity in POLG syndromes: DNA polymerase gamma pathogenicity prediction server and database.” BBA Clin. (2017) Apr 18;7:147-156. doi: 10.1016/j.bbacli.2017.04.001

Dickson A, Tiwary P, Vashisth H. “Kinetics of Ligand Binding Through Advanced Computational Approaches: A Review.” Curr Top Med Chem. (2017) Apr 14. doi: 10.2174/1568026617666170414142908

Montgomery BL. “Seeing new light: recent insights into the occurrence and regulation of chromatic acclimation in cyanobacteria.” Curr Opin Plant Biol. (2017) Apr 6;37:18-23. doi: 10.1016/j.pbi.2017.03.009

Bao H, Melnicki MR, Kerfeld CA. “Structure and functions of Orange Carotenoid Protein homologs in cyanobacteria.” Curr Opin Plant Biol. (2017) Apr 5;37:1-9. doi: 10.1016/j.pbi.2017.03.010

March 2017

Srivastava KR, Lapidus LJ. “Prion protein dynamics before aggregation.” Proc Natl Acad Sci U S A. (2017) Mar 20. pii: 201620400. doi: 10.1073/pnas.1620400114

Roushangar R, Mias GI. “MathIOmica-MSViewer: A Dynamic Viewer for Mass Spectrometry Files for Mathematica.” J Mass Spectrom. (2017) Mar 15. doi: 10.1002/jms.3928

Müller TA, Tobar MA, Perian MN, Hausinger RP. “Biochemical characterization of AP lyase and m(6)A demethylase activities of human AlkB homolog 1 (ALKBH1).” Biochemistry. (2017) Mar 14. doi: 10.1021/acs.biochem.7b00060

Pateraki I, Andersen-Ranberg J, Jensen NB, Wubshet SG, Heskes AM, Forman V, Hallström B, Hamberger B, Motawia MS, Olsen CE, Staerk D, Hansen J, Møller BL, Hamberger B. “Total biosynthesis of the cyclic AMP booster forskolin from Coleus forskohlii.” Elife. (2017) Mar 14;6. pii: e23001. doi: 10.7554/eLife.23001

González-Reymúndez A, de Los Campos G, Gutiérrez L, Lunt SY, Vazquez AI. “Prediction of years of life after diagnosis of breast cancer using omics and omic-by-treatment interactions.” Eur J Hum Genet. (2017) Mar 8. doi: 10.1038/ejhg.2017.12

Rajagopalan R, Kroos L. “The dev Operon Regulates the Timing of Sporulation during Myxococcus xanthus Development.” J Bacteriol. (2017) Mar 6. pii: JB.00788-16. doi: 10.1128/JB.00788-16

Hansen NL, Nissen JN, Hamberger B. “Two residues determine the product profile of the class II diterpene synthases TPS14 and TPS21 of Tripterygium wilfordii.” Phytochemistry. (2017) Mar 6. pii: S0031-9422(17)30093-6. doi: j.phytochem.2017.02.022

Walker RG, Czepnik M, Goebel EJ, McCoy JC, Vujic A, Cho M, Oh J, Aykul S, Walton KL, Schang G, Bernard DJ, Hinck AP, Harrison CA, Martinez-Hackert E, Wagers AJ, Lee RT, Thompson TB. “Structural basis for potency differences between GDF8 and GDF11.” BMC Biol. (2017) Mar 3;15(1):19. doi: 10.1186/s12915-017-0350-1

Jensen JK, Wilkerson CG. “Brachypodium as an experimental system for the study of stem parenchyma biology in grasses.” PLoS One. (2017) Mar 1;12(3):e0173095. doi: 10.1371/journal.pone.0173095

February 2017

Dickson A, Lotz SD. “Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore.” Biophys J. (2017) Feb 28;112(4):620-629. doi: 10.1016/j.bpj.2017.01.006

Nault R, Fader KA, Lydic TA, Zacharewski TR. “Lipidomic evaluation of aryl hydrocarbon receptor-mediated hepatic steatosis in male and female mice by 2,3,7,8-tetrachlorodibenzo-p-dioxin.” Chem Res Toxicol. (2017) Feb 27. doi: 10.1021/acs.chemrestox.6b00430

Jordan A, Chandler J, MacCready JS, Huang J, Osteryoung KW, Ducat DC. “Engineering Cyanobacterial Cell Morphology for Enhanced Recovery and Processing of Biomass.” Appl Environ Microbiol. (2017) Feb 24. pii: AEM.00053-17. doi: 10.1128/AEM.00053-17

Wang B, Sexton RE, Feig M. “Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.” Biochim Biophys Acta. (2017) Feb 24. pii: S1874-9399(16)30280-2. doi: 10.1016/j.bbagrm.2017.02.008

Walker AR, Silvestrov P, Müller TA, Podolsky RH, Dyson G, Hausinger RP, Cisneros GA. “ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding.” PLoS Comput Biol. (2017) Feb 23;13(2):e1005345. doi: 10.1371/journal.pcbi.1005345

Busch AW, Montgomery BL. “Distinct light-, stress-, and nutrient-dependent regulation of three tryptophan-rich sensory protein (TSPO) genes in the cyanobacterium Fremyella diplosiphon.” Plant Signal Behav. (2017) Feb 21:0. doi: 10.1080/15592324.2017.1293221

Nguyen DD, Wang B, Wei GW. “Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies.” J Comput Chem. (2017) Feb 16. doi: 10.1002/jcc.24757

Salminen TS, Oliveira MT, Cannino G, Lillsunde P, Jacobs HT, Kaguni LS. “Mitochondrial genotype modulates mtDNA copy number and organismal phenotype in Drosophila. Mitochondrion.” (2017) Feb 15. pii: S1567-7249(16)30075-7. doi: 10.1016/j.mito.2017.02.001

Henderson KL, Li M, Martinez S, Lewis EA, Hausinger RP, Emerson JP. “Global stability of an α-ketoglutarate-dependent dioxygenase (TauD) and its related complexes.” Biochim Biophys Acta. (2017) Feb 15. pii: S0304-4165(17)30066-1. doi: 10.1016/j.bbagen.2017.02.018

Ghosh B, Jones AD. “Profiling, characterization, and analysis of natural and synthetic acylsugars (sugar esters)” Analytical Methods. (2017) Feb 14; 9(6):892-905. doi: 10.1039/C6AY02944B

Schrad JR, Young EJ, Abrahão JS, Cortines JR, Parent KN. “Microscopic Characterization of the Brazilian Giant Samba Virus.” Viruses. (2017) Feb 14;9(2). pii: E30. doi: 10.3390/v9020030

Fader KA, Nault R, Kirby MP, Markous G, Matthews J, Zacharewski TR. “Convergence of hepcidin deficiency, systemic iron overloading, heme accumulation, and REV-ERBα/β activation in aryl hydrocarbon receptor-elicited hepatotoxicity.” Toxicol Appl Pharmacol. (2017) Feb 14. pii: S0041-008X(17)30064-9. doi: 10.1016/j.taap.2017.02.006

Kim JS, Nanfara MT, Chodavarapu S, Jin KS, Babu VM, Ghazy MA, Chung S, Kaguni JM, Sutton MD, Cho Y. “Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing.&rdqup; Nucleic Acids Res. (2017) Feb 7. doi: 10.1093/nar/gkx081

Dutagaci B, Sayadi M, Feig M. “Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices.” J Comput Chem. (2017) Feb 4. doi: 10.1002/jcc.24691

Sharkey TD, Monson RK. “Isoprene research - 60 years later, the biology is still enigmatic.” Plant Cell Environ. (2017) Feb 4. doi: 10.1111/pce.12930

Fader KA, Zacharewski TR. “Beyond the Aryl Hydrocarbon Receptor: Pathway Interactions in the Hepatotoxicity of 2,3,7,8-Tetrachlorodibenzo-<i>p</i>-dioxin and Related Compounds.” Curr Opin Toxicol. (2017) Feb;2:36-41. doi: 10.1016/j.cotox.2017.01.010

Hansen NL, Heskes AM, Hamberger B, Olsen CE, Hallström BM, Andersen-Ranberg J, Hamberger B. “The terpene synthase gene family in Tripterygium wilfordii harbors a labdane-type diterpene synthase among the monoterpene synthase TPS-b subfamily.” Plant J. (2017) Feb;89(3):429-441. doi: 10.1111/tpj.13410

January 2017

Lokareddy RK, Sankhala RS, Roy A, Afonine PV, Motwani T, Teschke CM, Parent KN, Cingolani G. “Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation.” Nat Commun. (2017) Jan 30;8:14310. doi: 10.1038/ncomms14310

Zhang F, Ke J, Zhang L, Chen R, Sugimoto K, Howe GA, Xu HE, Zhou M, He SY, Melcher K. “Structural insights into alternative splicing-mediated desensitization of jasmonate signaling.” Proc Natl Acad Sci U S A. (2017) Jan 30. pii: 201616938. doi: 10.1073/pnas.1616938114

Aykul S, Parenti A, Chu KY, Reske J, Floer M, Ralston A, Martinez-Hackert E. “Biochemical and cellular analysis reveals ligand binding specificities, a molecular basis for ligand recognition, and membrane association dependent activities of Cripto-1 and Cryptic.” J Biol Chem. (2017) Jan 26. pii: jbc.M116.747501. doi: 10.1074/jbc.M116.747501

Hays SG, Yan LL, Silver PA, Ducat DC. “Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction.” J Biol Eng. (2017) Jan 23;11:4. doi: 10.1186/s13036-017-0048-5

Strand DD, Livingston AK, Satoh-Cruz M, Koepke T, Enlow HM, Fisher N, Froehlich JE, Cruz JA, Minhas D, Hixson KK, Kohzuma K, Lipton M, Dhingra A, Kramer DM. “Defects in the Expression of Chloroplast Proteins Leads to H(2)O(2) Accumulation and Activation of Cyclic Electron Flow around Photosystem I.” Front Plant Sci. (2017) Jan 13;7:2073. doi: 10.3389/fpls.2016.02073

Masukawa H, Sakurai H, Hausinger RP, Inoue K. “Increased heterocyst frequency by patN disruption in Anabaena leads to enhanced photobiological hydrogen production at high light intensity and high cell density.” Appl Microbiol Biotechnol. (2017) Jan 7. doi: 10.1007/s00253-016-8078-3

Liu B, Wang B, Zhao R, Tong Y, Wei GW. “ESES: Software for Eulerian solvent excluded surface.” J Comput Chem. (2017) Jan 4. doi: 10.1002/jcc.24682

Zienkiewicz K, Zienkiewicz A, Poliner E, Du ZY, Vollheyde K, Herrfurth C, Marmon S, Farré EM, Feussner I, Benning C. “ldqou;Nannochloropsis, a rich source of diacylglycerol acyltransferases for engineering of triacylglycerol content in different hosts.” Biotechnol Biofuels. (2017) Jan 3;10:8. doi: 10.1186/s13068-016-0686-8

December 2016

Reese KL, Jones AD, Smith RW. “Characterization of smokeless powders using multiplexed collision-induced dissociation mass spectrometry and chemometric procedures.” Forensic Sci Int. (2016) Dec 21;272:16-27. doi: 10.1016/j.forsciint.2016.12.021

Konishi N, Ishiyama K, Beier MP, Inoue E, Kanno K, Yamaya T, Takahashi H, Kojima S. “Contributions of two cytosolic glutamine synthetase isozymes to ammonium assimilation in Arabidopsis roots.” J Exp Bot. (2016) Dec 21. pii: erw454. doi: 10.1093/jxb/erw454

Martin-Diaconescu V, Joseph CA, Boer JL, Mulrooney SB, Hausinger RP, Maroney MJ. “Non-thiolate ligation of nickel by nucleotide-free UreG of Klebsiella aerogenes.” J Biol Inorg Chem. (2016) Dec 21. doi: 10.1007/s00775-016-1429-9

Busch AW, WareJoncas Z, Montgomery BL. “Tryptophan-Rich Sensory Protein/Translocator Protein (TSPO) from Cyanobacterium Fremyella diplosiphon Binds a Broad Range of Functionally Relevant Tetrapyrroles.” Biochemistry. (2016) Dec 19. doi: 10.1021/acs.biochem.6b01019

Kopec AK, Joshi N, Cline-Fedewa H, Wojcicki AV, Ray JL, Sullivan BP, Froehlich JE, Johnson BF, Flick MJ, Luyendyk JP. “Fibri(nogen) drives repair after acetaminophen-induced liver injury via leukocyte αMβ2 integrin-dependent upregulation of MMP12.” J Hepatol. (2016) Dec 10. pii: S0168-8278(16)30709-7. doi: 10.1016/j.jhep.2016.12.004

Uygun S, Peng C, Lehti-Shiu MD, Last RL, Shiu SH. “Utility and Limitations of Using Gene Expression Data to Identify Functional Associations.” PLoS Comput Biol. (2016) Dec 9;12(12):e1005244. doi: 10.1371/journal.pcbi.1005244

Kempf H, Olmer R, Haase A, Franke A, Bolesani E, Schwanke K, Robles-Diaz D, Coffee M, Göhring G, Dräger G, Pötz O, Joos T, Martinez-Hackert E, Haverich A, Buettner FF, Martin U, Zweigerdt R. &ldqup;Bulk cell density and Wnt/TGFbeta signalling regulate mesendodermal patterning of human pluripotent stem cells.” Nat Commun. (2016) Dec 9;7:13602. doi: 10.1038/ncomms13602

Kirilovsky D, Kerfeld CA. “Cyanobacterial photoprotection by the orange carotenoid protein.” Nat Plants. (2016) Dec 2;2(12):16180. doi: 10.1038/nplants.2016.180

Kroos L. “Highly Signal-Responsive Gene Regulatory Network Governing Myxococcus Development.” Trends Genet. (2016) Dec 1. pii: S0168-9525(16)30145-7. doi: 10.1016/j.tig.2016.10.006

November 2016

Kovalova N, Nault R, Crawford R, Zacharewski TR, Kaminski NE. “Comparative analysis of TCDD-induced AhR-mediated gene expression in human, mouse and rat primary B cells.” Toxicol Appl Pharmacol. (2016) Nov 29. pii: S0041-008X(16)30364-7. doi: 10.1016/j.taap.2016.11.009

Mias GI, Yusufaly T, Roushangar R, Brooks LR, Singh VV, Christou C. “MathIOmica: An Integrative Platform for Dynamic Omics.” Sci Rep. (2016) Nov 24;6:37237. doi: 10.1038/srep37237

Angelovici R, Batushansky A, Deason N, Gonzalez-Jorge S, Gore MA, Fait A, DellaPenna D. Network-guided GWAS improves identification of genes affecting free amino acids. Plant Physiol. 2016 Nov 21. pii: pp.01287.2016. doi: 10.1104/pp.16.01287

Laursen T, Borch J, Knudsen C, Bavishi K, Torta F, Martens HJ, Silvestro D, Hatzakis NS, Wenk MR, Dafforn TR, Olsen CE, Motawia MS, Hamberger B, Møller BL, Bassard JE. “Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum.” Science. (2016) Nov 18;354(6314):890-893. doi: 10.1126/science.aag2347

Liu A, Sui D, Wu D, Hu J. “The activation loop of PIP5K functions as a membrane sensor essential for lipid substrate processing.” Science Advances. (2016) Nov 18;2(11). doi: 10.1126/sciadv.1600925

Ong RG, Higbee A, Bottoms S, Dickinson Q, Xie D, Smith SA, Serate J, Pohlmann E, Jones AD, Coon JJ, Sato TK, Sanford GR, Eilert D, Oates LG, Piotrowski JS, Bates DM, Cavalier D, Zhang Y. “Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate. Biotechnol Biofuels.” (2016) Nov 8;9:237. doi: 10.1186/s13068-016-0657-0

Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, MacKerell AD Jr. “CHARMM36m: an improved force field for folded and intrinsically disordered proteins.” Nat Methods. (2016) Nov 7. doi: 10.1038/nmeth.4067

MacCready JS, Schossau J, Osteryoung KW, Ducat DC. “Robust Min-system oscillation in the presence of internal photosynthetic membranes in cyanobacteria.” Mol Microbiol. (2016) Nov 5. doi: 10.1111/mmi.13571

Dutta G, Nagarajan S, Lapidus LJ, Lillehoj PB. “Enzyme-free electrochemical immunosensor based on methylene blue and the electro-oxidation of hydrazine on Pt nanoparticles.” Biosens Bioelectron. (2016) Nov 3. pii: S0956-5663(16)31136-8. doi: 10.1016/j.bios.2016.10.094

Proshlyakov DA, McCracken J, Hausinger RP. “Spectroscopic analyses of 2-oxoglutarate-dependent oxygenases: TauD as a case study.” J Biol Inorg Chem. (2016) Nov 3;. doi: 10.1007/s00775-016-1406-3

Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M. “Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.” Elife. (2016) Nov 1;. doi: 10.7554/eLife.19274

Burton, ZF. “Herpes Simplex Virus Serotype 2 Oral Infection.” JSM Biochem Mol Biol (2016) 3(1):1015.

Krishnan A, Zhang R, Yao V, Theesfeld CL, Wong AK, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya OG. “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.” Nat Neurosci. (2016) Nov;19(11):1454-1462. doi: 10.1038/nn.4353

Jagalski V, Barker R, Topgaard D, Günther-Pomorski T, Hamberger B, Cárdenas M. “Biophysical study of resin acid effects on phospholipid membrane structure and properties.” Biochim Biophys Acta. (2016) Nov;1858(11):2827-2838. doi: 10.1016/j.bbamem.2016.08.008

October 2016

Stiban J, So M, Kaguni LS. “Iron-Sulfur Clusters in Mitochondrial Metabolism: Multifaceted Roles of a Simple Cofactor.” Biochemistry (Mosc). (2016) Oct;81(10):1066-1080. doi: 10.1134/S0006297916100059

Ando T, Yu I, Feig M, Sugita Y. “Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.” J Phys Chem B. (2016) Oct 31;. doi: 10.1021/acs.jpcb.6b06243

Fedeson DT, Ducat DC. “Cyanobacterial surface display system mediates engineered interspecies and abiotic binding.” ACS Synth Biol. (2016) Oct 30;. doi: 10.1021/acssynbio.6b00254

Kuhlgert S, Austic G, Zegarac R, Osei-Bonsu I, Hoh D, Chilvers MI, Roth MG, Bi K, TerAvest D, Weebadde P, Kramer DM. “MultispeQ Beta: a tool for large-scale plant phenotyping connected to the open PhotosynQ network.” R Soc Open Sci. (2016) Oct 26;3(10):160592 doi: 10.1098/rsos.160592

Yang Y, Xu L, Feng Z, Cruz JA, Savage LJ, Kramer DM, Chen J. “PhenoCurve: Capturing Dynamic Phenotype-Environment Relationships using Phenomics Data.” Bioinformatics. (2016) Oct 24;. doi: 10.1093/bioinformatics/btw673

Dickson A, Bailey CT, Karanicolas J. “Optimal allosteric stabilization sites using contact stabilization analysis.” J Comput Chem. (2016) Oct 24. doi: 10.1002/jcc.24517

Wang B, Francis J, Sharma M, Law SM, Predeus AV, Feig M. “Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways.” PLoS Comput Biol. (2016) Oct 21;12(10):e1005159. doi: 10.1371/journal.pcbi.1005159

Martinez S, Hausinger RP. “Biochemical and Spectroscopic Characterization of the Non-Heme Fe(II) and 2-Oxoglutarate Dependent Ethylene-Forming Enzyme from Pseudomonas syringae pv. phaseolicola PK2.” Biochemistry. (2016) Oct 17. doi: 10.1021/acs.biochem.6b00890

Abramson BW, Kachel B, Kramer DM, Ducat DC. “Increased Photochemical Efficiency in Cyanobacteria via an Engineered Sucrose Sink.” Plant Cell Physiol. (2016) Oct 13. pii: pcw169. doi: 10.1093/pcp/pcw169

Kerfeld CA. “Rewiring Escherichia coli for carbon-dioxide fixation.” Nat Biotechnol. (2016) Oct 11;34(10):1035-1036. doi: 10.1038/nbt.3693

Nguyen DD, Wei GW. “The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling.” J Comput Chem. (2016) Oct 8. doi: 10.1002/jcc.24512

Aarabi F, Kusajima M, Tohge T, Konishi T, Gigolashvili T, Takamune M, Sasazaki Y, Watanabe M, Nakashita H, Fernie AR, Saito K, Takahashi H, Hubberten HM, Hoefgen R, Maruyama-Nakashita A. Sulfur deficiency-induced repressor proteins optimize glucosinolate biosynthesis in plants. Sci Adv. 2016 Oct 7;2(10):e1601087. PubMed PMID: 27730214

Ochieng PO, White NA, Feig M, Hoogstraten CG. “Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation.” J Phys Chem B. (2016) Oct 5. doi: 10.1021/acs.jpcb.6b05606

Davis GA, Kanazawa A, Schöttler MA, Kohzuma K, Froehlich JE, Rutherford AW, Satoh-Cruz M, Minhas D, Tietz S, Dhingra A, Kramer DM. “Limitations to photosynthesis by proton motive force-induced photosystem II photodamage.” Elife. (2016) Oct 4;5. pii: e16921. doi: 10.7554/eLife.16921

Raschka S, Bemister-Buffington J, Kuhn LA. “Detecting the native ligand orientation by interfacial rigidity: SiteInterlock.” Proteins. (2016) Oct 3. doi: 10.1002/prot.25172

Wei Y, Gokhale RH, Sonnenschein A, Montgomery KM, Ingersoll A, Arnosti DN. “Complex cis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator.” Development (2016) Oct 1;143:3591-3603. doi: 10.1242/dev.138073

September 2016

Wang B, Zhao Z, Wei GW. “Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies.” J Chem Phys. (2016) Sep 28;145(12):124110. doi: 10.1063/1.4963193

Luo J, Deng X, Buehl C, Xu X, Kuo MH. “Identification of Tension Sensing Motif of Histone H3 in Saccharomyces cerevisiae and Its Regulation by Histone Modifying Enzymes.” Genetics. (2016) Sep 26;. doi: 10.1534/genetics.116.192443

Kim BJ, Chu I, Jusuf S, Kuo T, TerAvest MA, Angenent LT, Wu M. “Oxygen Tension and Riboflavin Gradients Cooperatively Regulate the Migration of Shewanella oneidensis MR-1 Revealed by a Hydrogel-Based Microfluidic Device.” Front Microbiol. (2016) Sep 20;7:1438. doi: 10.3389/fmicb.2016.01438

Goodman KM, Yamagata M, Jin X, Mannepalli S, Katsamba PS, Ahlsén G, Sergeeva AP, Honig B, Sanes JR, Shapiro L. “Molecular basis of sidekick-mediated cell-cell adhesion and specificity.” Elife. (2016) Sep 19;. doi: 10.7554/eLife.19058

Renda BA, Chan C, Parent KN, Barrick JE. “Emergence of a competence reducing filamentous phage from the genome of Acinetobacter baylyi ADP1.” J Bacteriol. (2016) Sep 19. pii: JB.00424-16. doi: 10.1128/JB.00424-16

Ye ZW, Lung SC, Hu TH, Chen QF, Suen YL, Wang M, Hoffmann-Benning S, Yeung E, Chye ML. Arabidopsis acyl-CoA-binding protein ACBP6 localizes in the phloem and affects jasmonate composition. Plant Mol Biol. 2016 Sep 19. doi: 10.1007/s11103-016-0541-0

Root-Bernstein R, Kim Y, Sanjay A, Burton ZF. “tRNA evolution from the proto-tRNA minihelix world.” Transcription. (2016) Sep 16;. doi: 10.1080/21541264.2016.1235527

Horn PJ, Benning C. “The plant lipidome in human and environmental health.” Science. (2016) Sep 16;353(6305):1228-32. doi: 10.1126/science.aaf6206

Nault R, Fader KA, Kopec AK, Harkema JR, Zacharewski TR, Luyendyk JP. “Coagulation-driven hepatic fibrosis requires protease activated receptor-1 (PAR-1) in a mouse model of TCDD-elicited steatohepatitis.” Toxicol Sci. (2016) Sep 9. pii: kfw175. doi: 10.1093/toxsci/kfw175

Kelly AA, Kalisch B, Hölzl G, Schulze S, Thiele J, Melzer M, Roston RL, Benning C, Dörmann P. “Synthesis and transfer of galactolipids in the chloroplast envelope membranes of Arabidopsis thaliana.” Proc Natl Acad Sci U S A. (2016) Sep 6. pii: 201609184. doi: 10.1073/pnas.1609184113

Wang K, Hersh HL, Benning C. “SENSITIVE TO FREEZING2 aides in resilience to salt and drought in freezing-sensitive tomato.” Plant Physiol. (2016) Sep 6. pii: pp.01183.2016. doi: 10.1104/pp.16.01183

August 2016

Araya T, von Wirén N, Takahashi H. “CLE peptide signaling and nitrogen interactions in plant root development.” Plant Mol Biol. (2016) Aug;91(6):607-15. doi: 10.1007/s11103-016-0472-9

Campos ML, Yoshida Y, Major IT, de Oliveira Ferreira D, Weraduwage SM, Froehlich JE, Johnson BF, Kramer DM, Jander G, Sharkey TD, Howe GA. “Rewiring of jasmonate and phytochrome B signalling uncouples plant growth-defense tradeoffs.” Nat Commun. (2016) Aug 30;7:12570. doi: 10.1038/ncomms12570

Nault R, Fader KA, Ammendolia DA, Dornbos P, Potter D, Sharratt B, Kumagai K, Harkema JR, Lunt SY, Matthews J, Zacharewski T. “Dose-dependent metabolic reprogramming and differential gene expression in TCDD-elicited hepatic fibrosis.” Toxicol Sci. (2016) Aug 25. pii: kfw163. doi: 10.1093/toxsci/kfw163

Liu C, Chan C. “An Approach to Enhance Alignment and Myelination of Dorsal Root Ganglion Neurons.” J Vis Exp. (2016) Aug 24;(114). doi: 10.3791/54085

Bilgin B, Nath A, Chan C, Walton SP. “Characterization of transcription factor response kinetics in parallel.” BMC Biotechnol. (2016) Aug 24;16(1):62. doi: 10.1186/s12896-016-0293-6

Bansal N, Zheng Z, Merz KM Jr. “Incorporation of side chain flexibility into protein binding pockets using MT<sub>flex</sub>.” Bioorg Med Chem. (2016) Aug 23;. doi: 10.1016/j.bmc.2016.08.030

Ralston A. “Investigations at the 'Four-Front' of Mammalian Development.” Trends Genet. (2016) Aug;32(8):457-8. doi: 10.1016/j.tig.2016.05.005

Banerjee A, Preiser AL, Sharkey TD. “Engineering of Recombinant Poplar Deoxy-D-Xylulose-5-Phosphate Synthase (PtDXS) by Site-Directed Mutagenesis Improves Its Activity.” PLoS One. 2016 Aug 22;11(8):e0161534. doi: 10.1371/journal.pone.0161534
Correction: doi: 10.1371/journal.pone.0165028

Dover JA, Burmeister AR, Molineux IJ, Parent KN. “Evolved populations of Shigella flexneri phage Sf6 acquire large deletions, altered genomic architecture, and faster life cycles.” Genome Biol Evol. (2016) Aug 6. pii: evw177. doi: 10.1093/gbe/evw177

July 2016

Benning C, Sweetlove L. “Synthetic biology for basic and applied plant research.” Plant J. (2016) Jul;87(1):3-4. doi: 10.1111/tpj.13245. doi: 10.1111/tpj.13245

Kang JH, Campos ML, Zemelis-Durfee S, Al-Haddad JM, Jones AD, Telewski FW, Brandizzi F, Howe GA. “Molecular cloning of the tomato Hairless gene implicates actin dynamics in trichome-mediated defense and mechanical properties of stem tissue.” J Exp Bot. (2016) Jul 31. pii: erw292. doi: 10.1093/jxb/erw292

Dornbos P, Crawford RB, Kaminski NE, Hession SL, LaPres JJ. “The Influence of Human Inter-individual Variability on the Low-dose Region of Dose-Response Curve Induced by 2,3,7,8-Tetrachlorodibenzo-p-dioxin in Primary B Cells.” Toxicol Sci. (2016) Jul 29. pii: kfw128. doi: 10.1093/toxsci/kfw128

Sadre R, Magallanes-Lundback M, Pradhan S, Salim V, Mesberg A, Jones AD, DellaPenna D. “Metabolite diversity in alkaloid biosynthesis: A multi-lane (diastereomer) highway for camptothecin synthesis in Camptotheca acuminata”. Plant Cell. 2016 Jul 18. pii: tpc.00193.2016. doi: 10.1105/tpc.16.00193

Luo D, Callari R, Hamberger B, Wubshet SG, Nielsen MT, Anderson-Randberg J, Hallstrom BM, Cozzi F, Heider H, Lindberg Moller B, Staerk D, Hamberger B. “Oxidation and cyclization of casbene in the biosynthesis of Euphorbia factors from mature seeds of Euphorbia lanthyris L.“ PNAS (2016) Jul 6. doi: 10.1073/pnas.1607504113

Feig M. “Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.” J Chem Inf Model. (2016) Jul 5. doi: 10.1021/acs.jcim.6b00222

McAndrew MJ, Gjidoda A, Tagore M, Miksanek T, Floer M. “Chromatin remodeler recruitment during macrophage differentiation facilitates transcription factor binding to enhancers in mature cells.” J Biol Chem. (2016) Jul 5. pii:jbc.M116.734186. doi: 10.1074/jbc.M116.734186

June 2016

Aykul S, Martinez-Hackert E. “Determination of half-maximal inhibitory concentration using biosensor-based protein interaction analysis.” Anal Biochem. (2016) Jun 27. pii: S0003-2697(16)30160-9. doi: 10.1016/j.ab.2016.06.025

Cruz JA, Savage LJ, Zegarac R, Hall CC, Satoh-Cruz M, Davis GA, Kovac WK, Chen J, Kramer DM. “Dynamic Environmental Photosynthetic Imaging Reveals Emergent Phenotypes.” Cell Syst. (2016) Jun 22;2(6):365-77. doi: 10.1016/j.cels.2016.06.001

Ma W, Kong Q, Mantyla JJ, Yang Y, Ohlrogge JB, Benning C. “14-3-3 protein mediates plant seed oil biosynthesis through interaction with AtWRI1.” Plant J. (2016) Jun 20. doi: 10.1111/tpj.13244

Shi H, Xagoraraki I, Parent KN, Bruening ML, Tarabara VV. “Elution is a critical step for human adenovirus 40 recovery from tap and surface water by crossflow ultrafiltration.” Appl Environ Microbiol. (2016) Jun 10. pii:AEM.00870-16. doi: 10.1128/AEM.00870-16

Dickson A, Lotz SD. “Ligand Release Pathways Obtained with WExplore: Residence Times and Mechanisms.” J Phys Chem B. (2016) Jun 8. doi: 10.1021/acs.jpcb.6b04012

May 2016

Opron K, Xia K, Burton Z, Wei GW. “Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.” J Comput Chem. (2016) May 30;37(14):1283-95. doi: 10.1002/jcc.24320

Carrillo LR, Froehlich JE, Cruz JA, Savage L, Kramer DM. “Multi-level regulation of the chloroplast ATP synthase: The chloroplast NADPH thioredoxin reductase C (NTRC) is required for redox modulation specifically under low irradiance.” Plant J. (2016) May 28. doi: 10.1111/tpj.13226

Feature Story
Zhang C, Zhang T, Zou J, Miller CL, Gorkhali R, Yang J, Schilmiller A, Wang S, Huang K, Brown EM, Moreman KW, Hu J, Yang JJ. “Structural basis for regulation of human calcium-sensing receptor by magnesium ions and an unexpected tryptophan derivative co-agonist.” ScienceAdvances. (2016) May 27. 2:e1600241. doi: 10.1126/sciadv.1600241

Barnes AC, Benning C, Roston R. “Chloroplast membrane remodeling during freezing stress is accompanied by cytoplasmic acidification activating SENSITIVE TO FREEZING 2.” Plant Physiol. (2016) May 27. pii:.00286.2016. doi: 10.1104/pp.16.00286

Li X, Handee W, Kuo MH. “The slim, the fat, and the obese: guess who lives the longest?” Curr Genet. (2016) May 26. doi: 10.1007/s00294-016-0617-z

Liu C, Kray J, Toomajian V, Chan C. “Schwann Cell Migration on Patterned PDMS Microgrooved Surface.” Tissue Eng Part C Methods. (2016) May 23. doi: 10.1089/ten.TEC.2015.0539

Montgomery BL. “Mechanisms and fitness implications of photomorphogenesis during chromatic acclimation in cyanobacteria.” J Exp Bot. (2016) May 23. pii:erw206. doi: 10.1093/jxb/erw206

Hwang HJ, Dornbos P, LaPres JJ. “Data on AHR-dependent changes in the mitochondrial proteome in response to 2,3,7,8-tetrachlorodibenzo-p-dioxin.” Data Brief. (2016) May 20;8:191-5. doi: 10.1016/j.dib.2016.05.023

Hwang HJ, Steidemann M, Dunivin TK, Rizzo M, LaPres JJ. “Data of enzymatic activities of the electron transport chain and ATP synthase complexes in mouse hepatoma cells following exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD).” Data Brief. (2016) May 20;8:93-7. doi: 10.1016/j.dib.2016.05.018

Desguin B, Soumillion P, Hols P, Hausinger RP. “Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium carboxylation and LarE-dependent sacrificial sulfur insertion.” Proc Natl Acad Sci U S A. (2016) May 17;113(20):5598-603. doi: 10.1073/pnas.1600486113

López-Igual R, Wilson A, Leverenz RL, Melnicki MR, Bourcier de Carbon C, Sutter M, Turmo A, Perreau F, Kerfeld CA, Kirilovsky D. “Different functions of the paralogs to the N-terminal domain of the Orange Carotenoid Protein in the cyanobacterium Anabaena sp. PCC 7120.” Plant Physiol. (2016) May 13. pii:pp.00502.2016. doi: 10.1104/pp.16.00502

Gonzalez-Jorge S, Mehrshahi P, Magallanes-Lundback M, Lipka AE, Angelovici R, Gore MA, DellaPenna D. “ZEAXANTHIN EPOXIDASE activity potentiates carotenoid degradation in maturing Arabidopsis seed.” Plant Physiol. (2016) May 6. pii:pp.00604.2016. doi: 10.1104/pp.16.00604

Cornish AJ, Ginovska B, Thelen A, Da Silva JC, Soares TA, Raugei S, Dupuis M, Shaw WJ, Hegg EL. “Single Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase.” Biochemistry.(2016) May 17. doi: 10.1021/acs.biochem.5b01044

Cho S, Dong S, Parent KN, Chen M. “Immune-tolerant elastin-like polypeptides (iTEPs) and their application as CTL vaccine carriers.” J Drug Target. (2016) May 15;24(4):328-39. doi: 10.3109/1061186X.2015.1077847

Zhang X, Zhao Y, Yan H, Cao Z, Mo Y. “Combined QM(DFT)/MM molecular dynamics simulations of the deamination of cytosine by yeast cytosine deaminase (yCD).” J Comput Chem. (2016) May 15;37(13):1163-74. doi: 10.1002/jcc.24306

Li F, Liu J, Liu N, Kuhn LA, Garavito RM, Ferguson-Miller S. “Translocator Protein 18 kDa (TSPO): An Old Protein with New Functions?” Biochemistry. (2016) May 9;. doi: 10.1021/acs.biochem.6b00142

Ciesielski GL, Oliveira MT, Kaguni LS. “Animal Mitochondrial DNA Replication.” Enzymes. (2016) May 9;39:255-92. doi: 10.1016/bs.enz.2016.03.006


Feature Story
Sayal R, Dresch JM, Pushel I, Taylor BR, Arnosti DN. “Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo.” Elife. (2016) May 6;. doi: 10.7554/eLife.08445


Najt CP, Senthivinayagam S, Aljazi MB, Fader KA, Olenic SD, Brock JR, Lydic TA, Jones AD, Atshaves BP. “Liver-specific loss of Perilipin 2 alleviates diet-induced hepatic steatosis, inflammation, and fibrosis.” Am J Physiol Gastrointest Liver Physiol. (2016) May 1;310(9):G726-38. doi: 10.1152/ajpgi.00436.2015

Guo R, Gaffney K, Yang Z, Kim M, Sungsuwan S, Huang X, Hubbell WL, Hong H. “Steric trapping reveals a cooperativity network in the intramembrane protease GlpG.” Nat Chem Biol. (2016) May;12(5):353-60. doi: 10.1038/nchembio.2048

Sharkey TD, Govindjee. “Hartmut Lichtenthaler: an authority on chloroplast structure and isoprenoid biochemistry.” Photosynth Res. (2016) May;128(2):117-23. doi: 10.1007/s11120-015-0211-0