Recent Publications

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

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

Hart R, Kuo MH. “Better Data Quality for Better Healthcare Research Results - A Case Study.” Stud Health Technol Inform. (2017) 234:161-166. doi: 10.3233/978-1-61499-742-9-161

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

April 2016

King BC, Vavitsas K, Ikram NK, Schrøder J, Scharff LB, Hamberger B, Jensen PE, Simonsen HT. “In vivo assembly of DNA-fragments in the moss, Physcomitrella patens.” Scientific Reports (2016) Apr 29;6:25030 doi: 10.1038/srep25030

Barbaglia AM, Tamot B, Greeve V, Hoffmann-Benning S. “Phloem proteomics reveals new lipid-binding proteins with a putative role in lipid-mediated signaling.” Frontiers in Plant Science/Plant Physiology; Research topic: How plants deal with stress: exploration through proteome investigation; Front. Plant Sci. (2016) Apr 28;7:563. doi: 10.3389/fpls.2016.00563

Schroeder F, McIntosh AL, Martin GG, Huang H, Landrock D, Chung S, Landrock KK, Dangott LJ, Li S, Kaczocha M, Murphy EJ, Atshaves BP, Kier AB. “Fatty Acid Binding Protein-1 (FABP1) and the Human FABP1 T94A Variant: Roles in the Endocannabinoid System and Dyslipidemias.” Lipids. (2016) Apr 27;. doi: 10.1007/s11745-016-4155-8

Aussignargues C, Pandelia ME, Sutter M, Plegaria JS, Zarzycki J, Turmo A, Huang J, Ducat DC, Hegg EL, Gibney BR, Kerfeld CA. “Structure and Function of a Bacterial Microcompartment Shell Protein Engineered to Bind a [4Fe-4S] Cluster.” J Am Chem Soc. (2016) Apr 27;138(16):5262-70. doi: 10.1021/jacs.5b11734


Feature Story
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) Apr 25;. doi: 10.1073/pnas.1600486113


Li P, Merz KM Jr. “MCPB.py: A Python Based Metal Center Parameter Builder.” J Chem Inf Model. (2016) Apr 25;56(4):599-604. doi: 10.1021/acs.jcim.5b00674

Montgomery BL, Lechno-Yossef S, Kerfeld CA. “Interrelated modules in cyanobacterial photosynthesis: the carbon-concentrating mechanism, photorespiration, and light perception.” J Exp Bot. (2016) Apr 25;. doi: 10.1093/jxb/erw162

Wubshet SG, Tahtah Y, Heskes AM, Kongstad KT, Pateraki I, Hamberger B, Møller BL, Staerk D. “Identification of PTP1B and α±-Glucosidase Inhibitory Serrulatanes from Eremophila spp. by Combined use of Dual High-Resolution PTP1B and α-Glucosidase Inhibition Profiling and HPLC-HRMS-SPE-NMR.” J Nat Prod. (2016) Apr 22;79(4):1063-72. doi: 10.1021/acs.jnatprod.5b01128

Haudek KC, Voss PG, Wang JL, Patterson RJ. “A 10S galectin-3-U1 snRNP complex assembles into active spliceosomes.” Nucleic Acids Res. (2016) Apr 21. pii: gkw303. doi: 10.1093/nar/gkw303

Hwang HJ, Dornbos P, Steidemann M, Dunivin TK, Rizzo M, LaPres JJ. “Mitochondrial-targeted aryl hydrocarbon receptor and the impact of 2,3,7,8-tetrachlorodibenzo-p-dioxin on cellular respiration and the mitochondrial proteome.” Toxicol Appl Pharmacol. (2016) Apr 20;. doi: 10.1016/j.taap.2016.04.005

Montgomery BL. “Spatiotemporal Phytochrome Signaling during Photomorphogenesis: From Physiology to Molecular Mechanisms and Back.” Front Plant Sci. (2016) Apr 11;7:480. doi: 10.3389/fpls.2016.00480

Kerfeld CA, Melnicki MR. “Assembly, function and evolution of cyanobacterial carboxysomes.” Curr Opin Plant Biol. (2016) Apr 6;31:66-75. doi: 10.1016/j.pbi.2016.03.009

Bohrer AS, Takahashi H. “Compartmentalization and Regulation of Sulfate Assimilation Pathways in Plants.” Int Rev Cell Mol Biol. (2016) Apr 20;326:1-31. doi: 10.1016/bs.ircmb.2016.03.001

Chodavarapu S, Kaguni JM. “Replication Initiation in Bacteria.” Enzymes. (2016) Apr 20;39:1-30. doi: 10.1016/bs.enz.2016.03.001

Jensen HM, TerAvest MA, Kokish MG, Ajo-Franklin CM. “CymA and Exogenous Flavins Improve Extracellular Electron Transfer and Couple It to Cell Growth in Mtr-Expressing Escherichia coli.” ACS Synth Biol. (2016) Apr 5;. doi: 10.1021/acssynbio.5b00279