Recent Publications

November 2017

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

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

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

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

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

Hsieh CH, Chou YT, Kuo MH, Tsai HP, Chang JL, Wu CW. “A targetable HB-EGF-CITED4 axis controls oncogenesis in lung cancer.” Oncogene. (2017) Jan 16. doi: 10.1038/onc.2016.465

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