From the Barbar Group

Stuwe H, Reardon PN, Yu Z, Shah S, Hughes K, Barbar EJ. 2024 May 7. Phosphorylation in the Ser/Arg-rich region of the nucleocapsid of SARS-CoV-2 regulates phase separation by inhibiting self-association of a distant helix. J Biol Chem.300(6):107354. doi: 10.1016/j.jbc.2024.107354. Online ahead of print. PMID: 38718862 PMCID: PMC11180338

From the Cooley Group

Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic encoding of phosphorylated amino acids into proteins. Chem Rev. 2024 May 22;124(10):6592-6642. doi: 10.1021/acs.chemrev.4c00110. Epub 2024 May 1. PMID: 38691379.

Eddins AJ, Pung AH, Cooley RB, Mehl RA. Tetrazine Amino Acid Encoding for Rapid and Complete Protein Bioconjugation. Bio Protoc. 2024 Aug 20;14(16):e5048. doi: 10.21769/ BioProtoc. 5048. PMID: 39210952; PMCID: PMC11349492.

Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. 2024 Jun 15. Phosphorylation code of human nucleophosmin includes four cryptic sites for hierarchical binding of 14-3-3 proteins. J Mol Biol 436(12):168592. doi: 10.1016/j.jmb.2024.168592. Epub 2024 May 1. PMID: 38702038 DOI: 10.1016/j.jmb.2024.168592

Chadda R, Kaushik V, Ahmad IM, Deveryshetty J, Holehouse AS, Sigurdsson ST, Biswas G, Levy Y, Bothner B, Cooley RB, Mehl RA, Dastvan R, Origanti S, Antony E. Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic Acids Res. 2024 Oct 28;52(19):11626-11640. doi: 10.1093/nar/gkae584. PMID: 38989614; PMCID: PMC11514480.

From the Cotten Group

A. Oludrian; A. Malik, A.C Zourou, Y. Wu, S.P. Gross, A. Siryapon, A. Poudel, K. Alleyne, S. Adams, Courson DS, Cotten ML , Purcell EB. Host-defense piscidin peptides as antibiotic adjuvants against Clostridioides difficile. PlosOne, 2024 22:e0295627.

Bepler T, Barrera MD, Rooney MT, Xiong Y, Kuang H, Goodell E, Goodwin MJ, Harbron E, Fu R, Mihailescu M, Narayanan A, and Cotten ML. Antiviral Activity of the Host Defense Peptide Piscidin 1: Investigating a Membrane-mediated Mode of Action. Front. Chem., 2024, 26:12:1379192. doi: 10.3389/fchem.2024.1379192.

Cotten ML, Starich MR, He Y, Yin J, Yuan Q, and Tjandra N. NMR chemical shift assignment of Drosophila odorant binding protein 44a in complex with 8(Z)-eicosenoic acid. Biomol. NMR Assign., 2024. doi: 10.1007/s12104-024-10178-2.

Miceli RT, Allen NG, Subramaniam B, Carmody L, Dordick JS, Corr DT, Cotten ML, Gross RA. Synergistic Treatment of Breast Cancer by Combining the Antimicrobial Peptide Piscidin with a Modified Glycolipid. ACS Omega, 2024, 9:33408-33424. doi: 10.1021/acsomega. 3c09902.

From the Franco Group

Nguyen KT, Sathler AR, Estevez AG, Logan IE, Franco MC. ProDiVis: a method to normalize fluorescence signal localization in 3D specimens. Front. Cell Dev. Biol. 22 September 2024. Sec. Cellular Biochemistry. Vol 12-2024. https://doi.org/10.3389/fcell.2024.1420161

Logan IE, Nguyen KT, Chatterjee T, Manivannan B, Paul NP, Kim SR, Sixta EM, Bastian LP, Marean-Reardon C, Karajannis MA, Fernández-Valle C, Estevez AG, Franco MC. Selective Nitration of Hsp90 Acts as a Metabolic Switch Promoting Tumor Cell Proliferation. 20240. Redox Biology, https://doi.org/10.1016/j.redox.2024.103249.

From the Freitag Group

Lax C, Mondo SJ, Osorio-Concepción M, Muszewska A, Corrochano-Luque M, Gutiérrez G, Riley R, Lipzen A, Guo J, Hundley H, Amirebrahimi M, Ng V, Lorenzo-Gutiérrez D, Binder U, Yang J, Song Y, Cánovas D, Navarro E, Freitag M, Gabaldón T, Grigoriev IV, Corrochano LM, Nicolás FE, Garre V. 2024 Symmetric and asymmetric DNA N6-adenine methylation regulates 4 different biological responses in Mucorales. Nat Commun. 15: 6066. doi: 10.1038/s41467-024- 50365-2. PMID: 39025853

From the Gombart Group

Nakamura Y, Kulkarni NN, Takahashi T, Alimohamadi H, Dokoshi T, Liu E, Shia M, Numata T, Luo EW, Gombart AF, Yang X, Secrest P, Gordts PL, Tsimikas S, Wong GC, Gallo RL. Increased LL37 in psoriasis and other inflammatory disorders promotes LDL uptake and atherosclerosis. J Clin Invest. 2024 Mar 1;134(5):e172578. doi: 10.1172/JCI172578. PMID: 38194294; PMCID: PMC10904043.

From the Reardon Group

Stuwe H, Reardon PN, Yu Z, Shah S, Hughes K, Barbar EJ. 2024 May 7. Phosphorylation in the Ser/Arg-rich region of the nucleocapsid of SARS-CoV-2 regulates phase separation by inhibiting self-association of a distant helix. J Biol Chem.300(6):107354. doi: 10.1016/j.jbc.2024.107354. Online ahead of print. PMID: 38718862 PMCID: PMC11180338

Eskew MW, Reardon PN, Benight AS. DNA-based assay for calorimetric determination of protein concentrations in pure or mixed solutions. PLoS One. 2024;19(3):e0298969. doi: 10.1371/journal.pone.0298969. eCollection 2024. PubMed PMID: 38427623; PubMed Central PMCID: PMC10906865.

From the Mehl Group

Mott TM, Wulffraat GC, Eddins AJ, Mehl RA, Senning EN. Fluorescence labeling strategies for cell surface expression of TRPV1. J Gen Physiol. 2024 Oct 7;156(10): e202313523. doi: 10.1085/jgp.202313523. Epub 2024 Aug 20. PMID: 39162763.

Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic encoding of phosphorylated amino acids into proteins. Chem Rev. 2024 May 22;124(10):6592-6642. doi: 10.1021/acs.chemrev.4c00110. Epub 2024 May 1. PMID: 38691379.

Eddins AJ, Pung AH, Cooley RB, Mehl RA. Tetrazine Amino Acid Encoding for Rapid and Complete Protein Bioconjugation. Bio Protoc. 2024 Aug 20;14(16):e5048. doi: 10.21769/ BioProtoc. 5048. PMID: 39210952; PMCID: PMC11349492.

Chadda R, Kaushik V, Ahmad IM, Deveryshetty J, Holehouse AS, Sigurdsson ST, Biswas G, Levy Y, Bothner B, Cooley RB, Mehl RA, Dastvan R, Origanti S, Antony E. Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic Acids Res. 2024 Oct 28;52(19):11626-11640. doi: 10.1093/nar/gkae584. PMID: 38989614; PMCID: PMC11514480.

From the Mortimer Group

Waring-Sparks AL, Waring-Sparks RA, Darner R, Mortimer NT. 2024. Advanced biology students’ individual conceptions of scientific researchers after participating in biomedically relevant CRE. J Microbiol Biol Educ.25:e00183-23.https://doi.org/10.1128/jmbe.00183-23

From the Vanegas Group

Poudel, B. & Vanegas, J. M. Structural Rearrangement of the AT1 Receptor Modulated by Membrane Thickness and Tension. J. Phys. Chem. B (2024) doi:10.1021/acs.jpcb.4c03325.

Leverant, C. J., Richards, D., Spoerke, E. D., Alcala, R., Jiang, Y-B., Percival, S., Vanegas, J. M., Rempe, S. B. Nanoconfinement of Carbon Dioxide within Interfacial Aqueous/Ionic Liquid Systems. Langmuir 40, 10615–10622 (2024).

Prignano, L. A., Stevens, M. J., Vanegas, J. M., Rempe, S. B. & Dempski, R. E. Metadynamics simulations reveal mechanisms of Na+ and Ca2+ transport in two open states of the channel rhodopsin chimera, C1C2. PLOS ONE 19, e0309553 (2024).

Harjoe CC, Wilson MN, Charbonneau N, Dalton LE, Van Zee K, Kiser S, Kayes L. Designing the biology classroom & lab to support blind & visually impaired learners. The American Biology Teacher 1 January 2023; 85 (1): 4–11. doi: https://doi.org/10.1525/abt.2023.85.1.4

From the Vrailas-Mortimer Group

Merkle, J.A., Devergne, O., Kelly, S. M., Croonquist, P.A., Evans, C.J., Hwalek, M.A, Straub, V.L., Hamill, D.R., Puthoff, D.P., Saville, K. J., Siders, J. L., Villanueva Gonzalez, Z. J., Wittke-Thompson, J.K., Bieser, K. L., Stamm, J., Vrailas-Mortimer, A. D., and Kagey, J. D. Fly-CURE, a multi-institutional CURE using drosophila, increases students' confidence, sense of Belonging, and persistence in research. 2023. Journal of Microbiology and Biology Education. Sept 21. doi.org/10.1128/jmbe.00245-22

Parkinsonism-Associated Metal Toxicity. 2022. Molecular Biology of the Cell. Oct 1;33(12):ar108. doi: 10.1091/mbc.E22-03-0096. Epub 2022 Aug 3.

Thompson, C.F., K.E. Hodges, N.T. Mortimer, A.D. Vrailas-Mortimer, S.K. Sakaluk, M.E. Hauber. 2022. Avian eggshell coloration predicts shell-matrix protoporphyrin content. Canadian Journal of Zoology, 100: 77-81. DOI: 10.1139/cjz-2021-0134.

Elizabeth Mast*, Kayla L Bieser*, Mary Abraham-Villa, Vanessa Adams, Akinwonuola J Akinlehin, Lynarose Z Aquino, Joseph L Austin, Abigail K Austin, Carissa N Beckham, Ethan J Bengson, Amanda Bieszk, Brianna Bogard, Rowan C Brennan, Rebecca M Brnot, Nicholas J Cirone, Mason R Clark, Brianna N Cooper, Dennys Cruz, Katlyn Daprizio, Jason DeBoe, Michaela M Dencker, Laura L Donnelly, Leanne Driscoll, Ryan J DuBeau, Sirada W Durso, Adam Ejub, Waad Elgosbi, Melanie Estrada, Kaeli Evins, Pearl D Fox, Jacob M France, Maira G Franco Hernandez, Lizbeth A Garcia, Olivia Garl, Myeerah R Gorsuch, Mikayla A Gorzeman-mohr, Madison E Grothouse, Megan E Gubbels, Romina Hakemiamjad, Chloé V Harvey, Madeline A Hoeppner, Jessica L Ivanov,Veronica M Johnson, Jessica L Johnson, Ashton Johnson, Kaleigh Johnston, Katie R Keller, Breanna T Kennedy, Levi R Killian, Marissa Klumb, Olivia L Koehn, Aaron S Koym, Kari J Kress, Regan E Landis, Kaitlyn N Lewis, Enosh Lim, Ilcen K Lopez, D’Artagnan Lowe, Paula Luengo Carretero, Grace Lunaburg, Samantha L Mallinder, Natalie A Marshall, Jessica Mathew, Jasmine Mathew, Hailee S Mcmanaway, Emily N Meegan, Jacob D Meyst, Meredith J Miller, Colin K Minogue, Alina A Mohr, Cristhian I Moran, Adrian Moran, Morgan D Morris, Michael D Morrison, Emmily A Moses, Cade J Mullins, Citlalli I Neri, Jess M Nichols, Breanna R Nickels, Akosua M Okai, Chiedu Okonmah, Makena Paramo, Meagan Paramo, Sydney L Parker, Neil K Parmar, Jacob Paschal, Prem Patel, Deep Patel, Erica B Perkins, Madelyn M Perry, Zachary Perry, Amanda A Pollock, Oxxyris Portalatin, Kamron S Proffitt, Jason T Queen, Alexis C Quemeneur, Amelia G Richardson, Kaylee Rosenberger, Allison M Rutherford, Itchel Santos-Perez, Christy Y Sarti, Lacey J Schouweiler, Lauren M Sessing, Sara O Setaro, Christopher F Silvestri, Olivia A Smith, Mackenzie J Smith, Jayson C Sumner, Rachel R Sutton, Lindsay Sweckard, Nicholas B Talbott, Peyton A Traxler, Jenna Truesdell, Aaron F Valenti, Leif Verace, Pragathi Vijayakumar, William L Wadley, Katherine E Walker, Ayanna R Williams, Trey J Wilson, Makayla A Witbeck, Trinity M Wobler, Lucas J Wright, Karolina A Zuczkowska, Olivier Devergne, Danielle R Hamill, Hemin P Shah, Jamie Siders, Elizabeth E Taylor, Alysia D Vrailas-Mortimer and Jacob D Kagey. Genetic mapping of Uba3O.2.2, a pupal lethal mutation in Drosophila melanogaster. 2022 microPublication Biology. 10.17912/micropub.biology.000542.

From the Barbar group

Rodriguez Galvan J, Donner B, Veseley CH, Reardon P, Forsythe HM, Howe J, Fujimura G, Barbar E. Human Parainfluenza Virus 3 Phosphoprotein Is a Tetramer and Shares Structural and Interaction Features with Ebola Phosphoprotein VP35. Biomolecules. 2021 Oct 29; 11(11):1603. https://doi.org/10.3390/biom11111603

Forsythe HM, Barbar E. The role of dancing duplexes in biology and disease. Prog Mol Biol Transl Sci. 2021;183:249-270. doi: 10.1016/bs.pmbts.2021.06.004. Epub 2021 Jun 30. PMID: 34656330.

Barbar E, Estelle A. A tail goes viral by forming an anchor and a tether. Structure. 2021 Aug 5;29(8):783-786. doi: 10.1016/j.str.2021.07.004. PMID: 34358464.

Morgan JL, Yeager A, Estelle AB, Gsponer J, Barbar E. Transient Tertiary Structures of Disordered Dynein Intermediate Chain Regulate its Interactions with Multiple Partners. J Mol Biol. 2021 Sep 3;433(18):167152. doi: 10.1016/j.jmb.2021.167152. Epub 2021 Jul 14. PMID: 34273400.

White KA, McEntire KD, Buan NR, Robinson L, Barbar E. Charting a New Frontier Integrating Mathematical Modeling in Complex Biological Systems from Molecules to Ecosystems. Integr Comp Biol. 2021 Jul 20:icab165. doi: 10.1093/icb/icab165. Epub ahead of print. PMID: 34283225.

Loening NM, Barbar E. Structural characterization of the self-association domain of swallow. Protein Sci. 2021 May;30(5):1056-1063. doi: 10.1002/pro.4055. Epub 2021 Mar 9. PMID: 33641207; PMCID: PMC8040862.

Estelle AB, Reardon PN, Pinckney SH, Poole LB, Barbar E, Karplus PA. Native state fluctuations in a peroxiredoxin active site match motions needed for catalysis. Structure. 2021 Oct 21:S0969-2126(21)00369-5. doi: 10.1016/j.str.2021.10.001. Epub ahead of print. PMID: 34678159

Forsythe HM, Rodriguez Galvan J, Yu Z, Pinckney S, Reardon P, Cooley RB, Zhu P, Rolland AD, Prell JS, Barbar E. Multivalent binding of the partially disordered SARS-CoV-2 nucleocapsid phosphoprotein dimer to RNA. Biophys J. 2021 Jul 20;120(14):2890-2901. doi: 10.1016/j.bpj.2021.03.023. Epub 2021 Mar 29. PMID: 33794152; PMCID: PMC8007181.

Eastwood EL, Jara KA, Bornelöv S, Munafò M, Frantzis V, Kneuss E, Barbar EJ, Czech B, Hannon GJ. Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila. Elife. 2021 Feb 4;10:e65557. doi: 10.7554/eLife.65557. PMID: 33538693; PMCID: PMC7861614.

From the Cooley group

Sluchanko NN, Tugaeva KV, Gushchin I, Remeeva A, Kovalev K, Cooley RB. Crystal structure of human 14-3-3ζ complexed with the noncanonical phosphopeptide from proapoptotic BAD. Biochem Biophys Res Commun. 2021 Oct 26;583:100-105. doi: 10.1016/j.bbrc.2021.10.053. Epub ahead of print. PMID: 34735870.

Bednar RM, Jana S, Kuppa S, Franklin R, Beckman J, Antony E, Cooley RB, Mehl RA. Genetic Incorporation of Two Mutually Orthogonal Bioorthogonal Amino Acids That Enable Efficient Protein Dual-Labeling in Cells. ACS Chem Biol. 2021 Sep 30. doi: 10.1021/acschembio.1c00649. Epub ahead of print. PMID: 34590824.

Forsythe HM, Rodriguez Galvan J, Yu Z, Pinckney S, Reardon P, Cooley RB, Zhu P, Rolland AD, Prell JS, Barbar E. Multivalent binding of the partially disordered SARS-CoV-2 nucleocapsid phosphoprotein dimer to RNA. Biophys J. 2021 Jul 20;120(14):2890-2901. doi: 10.1016/j.bpj.2021.03.023. Epub 2021 Mar 29. PMID: 33794152; PMCID: PMC8007181.

From the Beckman group

Bednar RM, Jana S, Kuppa S, Franklin R, Beckman J, Antony E, Cooley RB, Mehl RA. Genetic Incorporation of Two Mutually Orthogonal Bioorthogonal Amino Acids That Enable Efficient Protein Dual-Labeling in Cells. ACS Chem Biol. 2021 Sep 30. doi: 10.1021/acschembio.1c00649. Epub ahead of print. PMID: 34590824.

Beckman JS, Voinov VG, Hare M, Sturgeon D, Vasil'ev Y, Oppenheimer D, Shaw JB, Wu S, Glaskin R, Klein C, Schwarzer C, Stafford G. Improved Protein and PTM Characterization with a Practical Electron-Based Fragmentation on Q-TOF Instruments. J Am Soc Mass Spectrom. 2021 Aug 4;32(8):2081-2091. doi: 10.1021/jasms.0c00482. Epub 2021 Apr 29. PMID: 33914527; PMCID: PMC8343505.

Shen X, Xu T, Hakkila B, Hare M, Wang Q, Wang Q, Beckman JS, Sun L. Capillary Zone Electrophoresis-Electron-Capture Collision-Induced Dissociation on a Quadrupole Time-of-Flight Mass Spectrometer for Top-Down Characterization of Intact Proteins. J Am Soc Mass Spectrom. 2021 Jun 2;32(6):1361-1369. doi: 10.1021/jasms.0c00484. Epub 2021 Mar 22. PMID:33749270; PMCID: PMC8576897.

From the Freitag group

Geiser DM, Al-Hatmi AMS, Aoki T, Arie T, Balmas V, Barnes I, Bergstrom GC, Bhattacharyya MK, Blomquist CL, Bowden RL, Brankovics B, Brown DW, Burgess LW, Bushley K, Busman M, Cano-Lira JF, Carrillo JD, Chang HX, Chen CY, Chen W, Freitag M, et al. Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex. Phytopathology. 2021 Jul;111(7):1064-1079. doi: 10.1094/PHYTO-08-20-0330-LE. Epub 2021 Sep 9. PMID: 33200960.

Alouane T, Rimbert H, Bormann J, González-Montiel GA, Loesgen S, Schäfer W, Freitag M, Langin T, Bonhomme L. Comparative Genomics of Eight Fusarium graminearum Strains with Contrasting Aggressiveness Reveals an Expanded Open Pangenome and Extended Effector Content Signatures. Int J Mol Sci. 2021 Jun 10;22(12):6257. doi: 10.3390/ijms22126257. PMID: 34200775; PMCID: PMC8230406.

Möller M, Habig M, Lorrain C, Feurtey A, Haueisen J, Fagundes WC, Alizadeh A, Freitag M, Stukenbrock EH. Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen. PLoS Genet. 2021 Mar 22;17(3):e1009448. doi: 10.1371/journal.pgen.1009448. PMID: 33750960; PMCID: PMC8016269.

From the Gombart group

Logan IE, Shulzhenko N, Sharpton TJ, Bobe G, Liu K, Nuss S, Jones ML, Miranda CL, Vasquez-Perez S, Pennington JM, Leonard SW, Choi J, Wu W, Gurung M, Kim JP, Lowry MB, Morgun A, Maier CS, Stevens JF, Gombart AF. Xanthohumol Requires the Intestinal Microbiota to Improve Glucose Metabolism in Diet-Induced Obese Mice. Mol Nutr Food Res. 2021 Nov;65(21):e2100389. doi: 10.1002/mnfr.202100389. Epub 2021 Oct 12. PMID: 34496124; PMCID: PMC8571065.

Zhang Y, Bobe G, Miranda CL, Lowry MB, Hsu VL, Lohr CV, Wong CP, Jump DB, Robinson MM, Sharpton TJ, Maier CS, Stevens JF, Gombart AF. Tetrahydroxanthohumol, a xanthohumol derivative, attenuates high-fat diet-induced hepatic steatosis by antagonizing PPARγ. Elife. 2021 Jun 15;10:e66398. doi: 10.7554/eLife.66398. PMID: 34128467; PMCID: PMC8205491.

From the Hagen group

Visioli F, Ingram A, Beckman JS, Magnusson KR, Hagen TM. Strategies to protect against age-related mitochondrial decay: Do natural products and their derivatives help? Free Radic Biol Med. 2022 Jan;178:330-346. doi: 10.1016/j.freeradbiomed.2021.12.008. Epub 2021 Dec 8.PMID: 34890770

Rodríguez E, Radke A, Hagen TM, Blier PU. Supercomplex organization of the electron transfer system in marine bivalves, a model of extreme longevity. J Gerontol A Biol Sci Med Sci. 2021 Dec 6:glab363. doi: 10.1093/gerona/glab363. Epub ahead of print. PMID: 34871395.

Rodríguez E, Hakkou M, Hagen TM, Lemieux H, Blier PU.J Gerontol A. Divergences in the Control of Mitochondrial Respiration Are Associated With Life-Span Variation in Marine Bivalves. Biol Sci Med Sci. 2021 Apr 30;76(5):796-804. doi: 10.1093/gerona/glaa301.PMID: 33257932

From the Hendrix group

Eriksen RL, Padgitt-Cobb LK, Randazzo AM, Hendrix DA, Henning JA. Gene Expression of Agronomically Important Secondary Metabolites in cv. ‘USDA Cascade’ Hop (Humulus lupulus L.) Cones during Critical Developmental Stages. Journal of the American Society of Brewing Chemists. 2021:1-14. doi: 10.1080/03610470.2021.1973328.

Padgitt-Cobb LK, Kothen-Hill S, Henning J, Hendrix DA, editors. The long-read genome assembly of hop (Humulus lupulus) uncovers the pseudoautosomal region and other genomic features. 2021: International Society for Horticultural Science (ISHS), Leuven, Belgium.

Padgitt-Cobb LK, Kingan SB, Wells J, Elser J, Kronmiller B, Moore D, Concepcion G, Peluso P, Rank D, Jaiswal P, Henning J, Hendrix DA. A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome. Plant Genome. 2021 Mar;14(1):e20072. doi: 10.1002/tpg2.20072. Epub 2021 Feb 18. PMID: 33605092.

From the Johnson group

Yan Q, Liu M, Kidarsa T, Johnson CP, Loper JE. Two Pathway-Specific Transcriptional Regulators, PltR and PltZ, Coordinate Autoinduction of Pyoluteorin in Pseudomonas protegens Pf-5. Microorganisms. 2021 Jul 13;9(7):1489. doi: 10.3390/microorganisms9071489. PMID: 34361923; PMCID: PMC8305169.

Manchanda A, Bonventre JA, Bugel SM, Chatterjee P, Tanguay R, Johnson CP. Truncation of the otoferlin transmembrane domain alters the development of hair cells and reduces membrane docking. Mol Biol Cell. 2021 Jul 1;32(14):1293-1305. doi: 10.1091/mbc.E20-10-0657. Epub 2021 May 12. PMID: 33979209; PMCID: PMC8351550.

Golbek TW, Otto SC, Roeters SJ, Weidner T, Johnson CP, Baio JE. Direct Evidence That Mutations within Dysferlin's C2A Domain Inhibit Lipid Clustering. J Phys Chem B. 2021 Jan 14;125(1):148-157. doi: 10.1021/acs.jpcb.0c07143. Epub 2020 Dec 23. PMID: 33355462.

From the Karplus group

Estelle AB, Reardon PN, Pinckney SH, Poole LB, Barbar E, Karplus PA. Native state fluctuations in a peroxiredoxin active site match motions needed for catalysis. Structure. 2021 Oct 21:S0969-2126(21)00369-5. doi: 10.1016/j.str.2021.10.001. Epub ahead of print. PMID: 34678159

Tronrud DE, Karplus PA. A complete Fourier-synthesis-based backbone-conformation-dependent library for proteins. Acta Crystallogr D Struct Biol. 2021 Feb 1;77(Pt 2):249-266. doi: 10.1107/S2059798320016344. Epub 2021 Feb 2. PMID: 33559613; PMCID: PMC7869903.

Peskin AV, Meotti FC, Kean KM, Göbl C, Peixoto AS, Pace PE, Horne CR, Heath SG, Crowther JM, Dobson RCJ, Karplus PA, Winterbourn CC. Modifying the resolving cysteine affects the structure and hydrogen peroxide reactivity of peroxiredoxin 2. J Biol Chem. 2021 Jan-Jun;296:100494. doi: 10.1016/j.jbc.2021.100494. Epub 2021 Mar 2. PMID: 33667550; PMCID: PMC8049995.

From the Mehl group

Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. Elife. 2021 Oct 8;10:e70236. doi: 10.7554/eLife.70236. PMID: 34623258; PMCID: PMC8500717.

Jones CM, Robkis DM, Blizzard RJ, Munari M, Venkatesh Y, Mihaila TS, Eddins AJ, Mehl RA, Zagotta WN, Gordon SE, Petersson EJ. Genetic encoding of a highly photostable, long lifetime fluorescent amino acid for imaging in mammalian cells. Chem Sci. 2021 Aug 3;12(36):11955-11964. doi: 10.1039/d1sc01914g. PMID: 34976337; PMCID: PMC8634729.

Chaparro Sosa AF, Bednar RM, Mehl RA, Schwartz DK, Kaar JL. Faster Surface Ligation Reactions Improve Immobilized Enzyme Structure and Activity. J Am Chem Soc. 2021 May 12;143(18):7154-7163. doi: 10.1021/jacs.1c02375. Epub 2021 Apr 29. PMID: 33914511; PMCID: PMC8574164.

Galles GD, Infield DT, Mehl RA, Ahern CA. Selection and validation of orthogonal tRNA/synthetase pairs for the encoding of unnatural amino acids across kingdoms. Methods Enzymol. 2021;654:3-18. doi: 10.1016/bs.mie.2021.03.009. Epub 2021 Apr 9. PMID: 34120719

Bednar RM, Jana S, Kuppa S, Franklin R, Beckman J, Antony E, Cooley RB, Mehl RA. Genetic Incorporation of Two Mutually Orthogonal Bioorthogonal Amino Acids That Enable Efficient Protein Dual-Labeling in Cells. ACS Chem Biol. 2021 Sep 30. doi: 10.1021/acschembio.1c00649. Epub ahead of print. PMID: 34590824.

From the Hsu group

Zhang Y, Bobe G, Miranda CL, Lowry MB, Hsu VL, Lohr CV, Wong CP, Jump DB, Robinson MM, Sharpton TJ, Maier CS, Stevens JF, Gombart AF. Tetrahydroxanthohumol, a xanthohumol derivative, attenuates high-fat diet-induced hepatic steatosis by antagonizing PPARγ. Elife. 2021 Jun 15;10:e66398. doi: 10.7554/eLife.66398. PMID: 34128467; PMCID: PMC8205491.

From the Nyarko group

Baker K, Kwok E, Reardon P, Rodriguez DJ, Rolland AD, Wilson JW, Prell JS, Nyarko A. Yorkie-Warts Complexes are an Ensemble of Interconverting Conformers Formed by Multivalent Interactions. J Mol Biol. 2021 Feb 19;433(4):166776. doi: 10.1016/j.jmb.2020.166776. Epub 2020 Dec 28. PMID: 33383033.

From the Perez group

Martin SA, Riordan RT, Wang R, Yu Z, Aguirre-Burk AM, Wong CP, Olson DA, Branscum AJ, Turner RT, Iwaniec UT, Perez VI. Rapamycin impairs bone accrual in young adult mice independent of Nrf2. Exp Gerontol. 2021 Oct 15;154:111516. doi: 10.1016/j.exger.2021.111516. Epub 2021 Aug 10. PMID: 34389472.

From the Qiu group

Xian Y, Xie Y, Silva SM, Karki CB, Qiu W, Li L. StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions. Front Mol Biosci. 2021 Jan 11;7:627087. doi: 10.3389/fmolb.2020.627087. PMID: 33505991; PMCID: PMC7831659.

From the Perez group

Sunchu B, Riordan RT, Yu Z, Almog I, Dimas-Munoz J, Drake AC, Perez VI. Aggresome-Like Formation Promotes Resistance to Proteotoxicity in Cells from Long-Lived Species. J Gerontol A Biol Sci Med Sci. 2020 Jul 13;75(8):1439-1447. doi: 10.1093/gerona/glaa069. PMID: 32515471; PMCID: PMC7357592.

Díaz-Valdivia NI, Díaz J, Contreras P, Campos A, Rojas-Celis V, Burgos-Ravanal RA, Lobos-González L, Torres VA, Perez VI, Frei B, Leyton L, Quest AFG. The non-receptor tyrosine phosphatase type 14 blocks caveolin-1-enhanced cancer cell metastasis. Oncogene. 2020 Apr;39(18):3693-3709. doi: 10.1038/s41388-020-1242-3. Epub 2020 Mar 9. PMID: 32152405; PMCID: PMC7190567.

From the Qiu group

Xian Y, Xie Y, Silva SM, Karki CB, Qiu W, Li L. StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions. Front Mol Biosci. 2021 Jan 11;7:627087. doi: 10.3389/fmolb.2020.627087. PMID: 33505991; PMCID: PMC7831659.

Swentowsky KW, Gent JI, Lowry EG, Schubert V, Ran X, Tseng KF, Harkess AE, Qiu W, Dawe RK. Distinct kinesin motors drive two types of maize neocentromeres. Genes Dev. 2020 Sep 1;34(17-18):1239-1251. doi: 10.1101/gad.340679.120. Epub 2020 Aug 20. PMID: 32820038; PMCID: PMC7462060.

2019 Biochemistry and Biophysics publications

From the Barbar group

Forsythe HM, Vetter CJ, Jara KA, Reardon PN, David LL, Barbar EJ, Lampi KJ. Altered Protein Dynamics and Increased Aggregation of Human γS-Crystallin Due to Cataract-Associated Deamidations. Biochemistry. 2019 Oct 8;58(40):4112-4124. doi: 10.1021/acs.biochem.9b00593. Epub 2019 Sep 26. PMID: 31490062.

Jespersen NE, Leyrat C, Gérard FC, Bourhis JM, Blondel D, Jamin M, Barbar E.The LC8-RavP ensemble Structure Evinces A Role for LC8 in Regulating Lyssavirus PolymeraseFunctionality. J Mol Biol. 2019 Dec 6;431(24):4959-4977. doi: 10.1016/j.jmb.2019.10.011. Epub 2019 Oct 18. PMID: 31634467; PMCID: PMC7060403.

From the Barbar and Hendrix group

Jespersen N, Estelle A, Waugh N, Davey NE, Blikstad C, Ammon YC, Akhmanova A, Ivarsson Y, Hendrix DA, Barbar E. Systematic identification of recognition motifs for the hub proteinLC8. Life Sci Alliance. 2019 Jul 2;2(4):e201900366. doi: 10.26508/lsa.201900366. PMID: 31266884; PMCID: PMC6607443.

From the Beckman group

Trias E, Kovacs M, King PH, Si Y, Kwon Y, Varela V, Ibarburu S, Moura IC, Hermine O, Beckman JS, Barbeito L. Schwann cells orchestrate peripheral nerve inflammation through theexpression of CSF1, IL-34, and SCF in amyotrophic lateral sclerosis. Glia. 2020 Jun;68(6):1165-1181. doi: 10.1002/glia.23768. Epub 2019 Dec 20. PMID: 31859421; PMCID: PMC7269115.

Shaw JB, Liu W, Vasil Ev YV, Bracken CC, Malhan N, Guthals A, Beckman JS, Voinov VG. Direct Determination of Antibody Chain Pairing by Top-down and Middle-down MassSpectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation. Anal Chem. 2020 Jan 7;92(1):766-773. doi: 10.1021/acs.analchem.9b03129. Epub 2019 Dec 12. PMID: 31769659; PMCID: PMC7819135.

Kovacs M, Trias E, Varela V, Ibarburu S, Beckman JS, Moura IC, Hermine O, King PH, Si Y, Kwon Y, Barbeito L. CD34Identifies a Subset of Proliferating Microglial Cells Associated withDegenerating Motor Neurons in ALS. Int J Mol Sci. 2019 Aug 9;20(16):3880. doi: 10.3390/ijms20163880. PMID: 31395804; PMCID: PMC6720880.

From the Estevez, Franco, and Beckman group

Strayer AL, Dennys-Rivers CN, Ricart KC, Bae N, Beckman JS, Franco MC, Estevez AG. Ligand-independent activation of the P2X7 receptor by Hsp90 inhibition stimulates motorneuron apoptosis. Exp Biol Med (Maywood). 2019 Aug;244(11):901-914. doi: 10.1177/1535370219853798. Epub 2019 May 29. PMID: 31142143; PMCID: PMC6690143.

From the Cooley group

Tugaeva KV, Kalacheva DI, Cooley RB, Strelkov SV, Sluchanko NN. Concatenation of 14-3-3 with partner phosphoproteins as a tool to study their interaction. Sci Rep. 2019 Oct 18;9(1):15007. doi: 10.1038/s41598-019-50941-3. PMID: 31628352; PMCID: PMC6802120.

Kitts G, Giglio KM, Zamorano-Sánchez D, Park JH, Townsley L, Cooley RB, Wucher BR, Klose KE, Nadell CD, Yildiz FH, Sondermann H. A Conserved Regulatory Circuit Controls Large Adhesins in Vibrio cholerae. mBio. 2019 Dec 3;10(6):e02822-19. doi: 10.1128/mBio.02822-19. PMID: 31796544

From the Franco group

Robinson MM, Sather BK, Burney ER, Ehrlicher SE, Stierwalt HD, Franco MC, Newsom SA. Robust intrinsic differences in mitochondrial respiration and H2O2 emission between L6 and C2C12 cells. Am J Physiol Cell Physiol. 2019 Aug 1;317(2):C339-C347. doi: 10.1152/ajpcell.00343.2018. Epub 2019 May 15. PMID: 31091142; PMCID: PMC6732423.

Pestoni JC, Klingeman Plati S, Valdivia Camacho OD, Fuse MA, Onatunde M, Sparrow NA, Karajannis MA, Fernández-Valle C, Franco MC. Peroxynitrite supports a metabolicreprogramming in merlin-deficient Schwann cells and promotes cell survival. J Biol Chem. 2019 Jul 26;294(30):11354-11368. doi: 10.1074/jbc.RA118.007152. Epub 2019 Jun 6. PMID: 31171721; PMCID: PMC6663865.

Tsakadze N, Catania J, Hoffmann M, Benes-Lima L, Estevez AG, Franco MC, Rossi F. “Case Report: Length-dependent Small Fiber Polyneuropathy Caused by Coxsackie and Influenza Virus Co-Infection”. 2019. J Neurol Exp Neurosci5(2): 103-105.

Fuse MA, Dinh CT, Vitte J, Kirkpatrick J, Mindos T, Klingeman Plati S, Young JI, Huang J, Carlstedt A, Franco MC, Brnjos K, Nagamoto J, Petrilli A, Copik AJ, Soulakova JN, Bracho O, Yan D, Mittal R, Shen R, Telischi FF, Morrison H, Giovannini M, Liu XZ, Chang LS, Fernandez-Valle C. “Preclinical Assessment of MEK1/2 Inhibitors for Neurofibromatosis Type 2-Associated Schwannomas Reveal Differences in Efficacy and Drug Resistance Development.” Neuro-Oncology. 2019. 18;21(4):486-497.

From the Freitag group

Adpressa DA, Connolly LR, Konkel ZM, Neuhaus GF, Chang XL, Pierce BR, Smith KM, Freitag M, Loesgen S. A metabolomics-guided approach to discover Fusarium graminearum metabolites after removal of a repressive histone modification. Fungal Genet Biol. 2019 Nov;132:103256. doi: 10.1016/j.fgb.2019.103256. Epub 2019 Jul 22. PMID: 31344458.

Bosnjak N, Smith KM, Asaria I, Lahola-Chomiak A, Kishore N, Todd AT, Freitag M, Nargang FE (2019) Involvement ofa GProtein Regulatory Circuit inAlternative Oxidase Production in Neurospora crassa. G3 (Bethesda) 9: 3453-3465. pii: g3.400522.2019. doi: 10.1534/g3.119.400522. PMID: 31444295

Adpressa DA , Connolly LR, Konkel ZM, Chang XL, Pierce BR, Smith KM, Freitag M, Loesgen S. (2019) Overexpression and discovery of new secondary metabolites Fusarium graminearum strains lacking the histone H3 lysine27 methyltransferase, KMT6. Fungal Genetics and Biology 132:103256. doi: 10.1016/j.fgb.2019.103256. PMID: 31344458

Möller M, Schotanus K, Soyer JL, Haueisen J, Happ K, Stralucke M, Happel P, Smith KM, Connolly LR, Freitag M, Stukenbrock EH (2019) Destabilization ofchromosome structure byhistone H3 lysine 27 methylation. PLoS Genet.15(4):e1008093. doi: 10.1371/journal.pgen.1008093. eCollection 2019 Apr. PMC6510446

From the Gombart group

Chen S, Ge L, Wang H, Cheng Y, Gorantla S, Poluektova LY, Gombart AF, Xie J. Eluted 25-hydroxyvitamin D3 from radially aligned nanofiber scaffolds enhances cathelicidin production while reducing inflammatory response in human immune system-engrafted mice. Acta Biomater. 2019 Oct 1;97:187-199. doi: 10.1016/j.actbio.2019.08.005. Epub 2019 Aug 3. PMID: 31386930; PMCID: PMC6801031.

Logan IE, Miranda CL, Lowry MB, Maier CS, Stevens JF, Gombart AF.Antiproliferative and Cytotoxic Activity of Xanthohumol and Its Non-Estrogenic Derivatives in Colon and Hepatocellular Carcinoma Cell Lines. Int J Mol Sci. 2019 Mar 9;20(5):1203. doi: 10.3390/ijms20051203. PMID: 30857300; PMCID: PMC6429097.

Paraiso IL, Plagmann LS, Yang L, Zielke R, Gombart AF, Maier CS, Sikora AE, Blakemore PR, Stevens JF. Reductive Metabolism of Xanthohumol and 8-Prenylnaringenin by the IntestinalBacterium Eubacterium ramulus. Mol Nutr Food Res. 2019 Jan;63(2):e1800923. doi: 10.1002/mnfr.201800923. Epub 2018 Dec 3. PMID: 30471194; PMCID: PMC6561348.

From the Hendrix group

Zhang Z, Garzotto M, Davis EW 2nd, Mori M, Stoller WA, Farris PE, Wong CP, Beaver LM, Thomas GV, Williams DE, Dashwood RH, Hendrix DA, Ho E, Shannon J. SulforaphaneBioavailability and Chemopreventive Activity in Men Presenting for Biopsy of the ProstateGland: A Randomized Controlled Trial. Nutr Cancer. 2020;72(1):74-87. doi: 10.1080/01635581.2019.1619783. Epub 2019 Jun 1. PMID: 31155953; PMCID: PMC8244813.

Bell J, Larson M, Kutzler M, Bionaz M, Löhr CV, Hendrix D. miRWoods: Enhanced precursordetection and stacked random forests for the sensitive detection of microRNAs. PLoS Comput Biol. 2019 Oct 9;15(10):e1007309. doi: 10.1371/journal.pcbi.1007309. PMID: 31596843; PMCID: PMC6785219.

Huang L, Zhang H, Deng D, Zhao K, Liu K, Hendrix DA, Mathews DH. LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search. Bioinformatics. 2019 Jul 15;35(14):i295-i304. doi: 10.1093/bioinformatics/btz375. PMID: 31510672; PMCID: PMC6681470.

Ritter N, Ali T, Kopitchinski N, Schuster P, Beisaw A, Hendrix DA, Schulz MH, Müller-McNicoll M, Dimmeler S, Grote P. ThelncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development. Dev Cell. 2019 Sep 9;50(5):644-657.e8. doi: 10.1016/j.devcel.2019.07.013. Epub 2019 Aug 15. PMID: 31422919.

Sall K, Dekkers BJW, Nonogaki M, Katsuragawa Y, Koyari R, Hendrix D, Willems LAJ, Bentsink L, Nonogaki H. DELAY OF GERMINATION 1-LIKE 4 acts as an inducer of seedreserve accumulation. Plant J. 2019 Oct;100(1):7-19. doi: 10.1111/tpj.14485. Epub 2019 Sep 9. PMID: 31359518.

From the Johnson group

Golbek TW, Padmanarayana M, Roeters SJ, Weidner T, Johnson CP, Baio JE. Otoferlin C2FDomain-Induced Changes in Membrane Structure Observed by Sum Frequency Generation. Biophys J. 2019 Nov 19;117(10):1820-1830. doi: 10.1016/j.bpj.2019.09.010. Epub 2019 Sep 17. PMID: 31587832; PMCID: PMC7019022.

Manchanda A, Chatterjee P, Bonventre JA, Haggard DE, Kindt KS, Tanguay RL, Johnson CP. Otoferlin Depletion Results in Abnormal Synaptic Ribbons and Altered Intracellular Calcium Levels in Zebrafish. Sci Rep. 2019 Oct 3;9(1):14273. doi: 10.1038/s41598-019-50710-2. PMID: 31582816; PMCID: PMC6776657.

Bonventre JA, Holman C, Manchanda A, Codding SJ, Chau T, Huegel J, Barton C, Tanguay R, Johnson CP. Fer1l6 is essential for the development of vertebrate muscle tissue in zebrafish. Mol Biol Cell. 2019 Feb 1;30(3):293-301. doi: 10.1091/mbc.E18-06-0401. Epub 2018 Dec 5. PMID: 30516436; PMCID: PMC6589578.

From the Mathews group

Mathews CK. Deoxyribonucleotide salvage falls short in wholeanimals. J Biol Chem. 2019 Nov 1;294(44):15898-15899. doi: 10.1074/jbc.H119.011335. PMID: 31676554; PMCID: PMC6827281.

From the Mehl group

Porter JJ, Jang HS, Haque MM, Stuehr DJ, Mehl RA.Tyrosine nitration on calmodulin enhancescalcium-dependent association and activation of nitric-oxide synthase. J Biol Chem. 2020 Feb 21;295(8):2203-2211. doi: 10.1074/jbc.RA119.010999. Epub 2019 Dec 30. PMID: 31914408; PMCID: PMC7039552.

Tugaeva KV, Kalacheva DI, Cooley RB, Strelkov SV, Sluchanko NN. Concatenation of 14-3-3with partner phosphoproteins as a tool to study their interaction. Sci Rep. 2019 Oct 18;9(1):15007. doi: 10.1038/s41598-019-50941-3. PMID: 31628352; PMCID: PMC6802120.

Bednar RM, Golbek TW, Kean KM, Brown WJ, Jana S, Baio JE, Karplus PA, Mehl RA. Immobilization of Proteins with Controlled Load and Orientation. ACS Appl Mater Interfaces. 2019 Oct 9;11(40):36391-36398. doi: 10.1021/acsami.9b12746. Epub 2019 Sep 26. PMID: 31525993.

Van Fossen EM, Bednar RM, Mehl RA. Engineering Spatial Orthogonality into Protein Translation. Biochemistry. 2019 Aug 6;58(31):3325-3327. doi: 10.1021/acs.biochem.9b00569. Epub 2019 Jul 25. PMID: 31343161.

Randall LM, Dalla Rizza J, Parsonage D, Santos J, Mehl RA, Lowther WT, Poole LB, Denicola A. Unraveling the effects of peroxiredoxin 2 nitration; role of C-terminal tyrosine 193. Free Radic Biol Med. 2019 Sep;141:492-501. doi: 10.1016/j.freeradbiomed.2019.07.016. Epub 2019 Jul 16. PMID: 31323313; PMCID: PMC6749834.

From the Mehl and Cooley

Zhu P, Gafken PR, Mehl RA, Cooley RB. A Highly Versatile Expression System for the Production of Multiply Phosphorylated Proteins. ACS Chem Biol. 2019 Jul 19;14(7):1564-1572. doi: 10.1021/acschembio.9b00307. Epub 2019 Jun 17. PMID: 31243963; PMCID: PMC7737670.

Porter JJ, Jang HS, Van Fossen EM, Nguyen DP, Willi TS, Cooley RB, Mehl RA.Genetically Encoded Protein Tyrosine Nitration in Mammalian Cells. ACS Chem Biol. 2019 Jun 21;14(6):1328-1336. doi: 10.1021/acschembio.9b00371. Epub 2019 Jun 4.PMID: 31117397 \

From the Merrill group

Shearn CT, Fennimore B, Orlicky DJ, Gao YR, Saba LM, Battista KD, Aivazidis S, Assiri M, Harris PS, Michel C, Merrill GF, Schmidt EE, Colgan SP, Petersen DR. Cholestatic liver disease results increased production of reactive aldehydes and an atypical periportal hepatic antioxidant response. Free Radic Biol Med. 2019 Nov 1;143:101-114. doi: 10.1016/j.freeradbiomed.2019.07.036. Epub 2019 Aug 1. PMID: 31377417; PMCID: PMC6848778.

From the Nyarko group

Kwok E, Rodriguez DJ, Kremerskothen J, Nyarko A. Intrinsic disorder and amino acidspecificity modulate binding of the WW2 domain in kidney and brain protein (KIBRA) to synaptopodin. J Biol Chem. 2019 Nov 15;294(46):17383-17394. doi: 10.1074/jbc.RA119.009589. Epub 2019 Oct 9. PMID: 31597702; PMCID: PMC6873182.

From the Reardon group

Keller RMoon, Beaver LM, Reardon PN, Prater MC, Truong L, Robinson MM, Tanguay RL, Stevens JFred, Hord NG. 2021. Nitrate-induced improvements in exercise performance are coincident with exuberant changes in metabolic genes and the metabolome in zebrafish skeletal muscle.. J Appl Physiol (1985).

Long DM, Frame AK, Reardon PN, Cumming RC, Hendrix DA, Kretzschmar D, Giebultowicz JM. 2020. Lactate dehydrogenase expression modulates longevity and neurodegeneration in .. Aging (Albany NY). 12

Schwichtenberg T, Bogdan D, Carignan CC, Reardon P, Rewerts J, Wanzek T, Field JA. 2020. PFAS and Dissolved Organic Carbon Enrichment in Surface Water Foams on a Northern U.S. Freshwater Lake.. Environ Sci Technol. 54(22):14455-14464.

Brinson RG, Marino JP, Delaglio F, Arbogast LW, Evans RM, Kearsley A, Gingras G, Ghasriani H, Aubin Y, Pierens GK et al.. 2019. Enabling adoption of 2D-NMR for the higher order structure assessment of monoclonal antibody therapeutics.. MAbs. 11(1):94-105.

Ceja-Navarro JA, Karaoz U, Bill M, Hao Z, White RA, Arellano A, Ramanculova L, Filley TR, Berry TD, Conrad ME et al.. 2019. Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle.. Nat Microbiol. 4(5):864-875.

Lande C, Rao S, Morré JT, Galindo G, Kirby J, Reardon PN, Bobe G, Stevens JFrederik. 2019. Linden (Tilia cordata) associated bumble bee mortality: Metabolomic analysis of nectar and bee muscle.. PLoS One. 14(7):e0218406.

Chacon SS, Reardon PN, Burgess CJ, Purvine S, Chu RK, Clauss TR, Walter E, Myrold DD, Washton N, Kleber M. 2019. Mineral Surfaces as Agents of Environmental Proteolysis: Mechanisms and Controls.. Environ Sci Technol. 53(6):3018-3026.

Viviana Pérez

Maciel-Barón LÁ, Morales-Rosales SL, Silva-Palacios A, Rodríguez-Barrera RH, García-Álvarez JA, Luna-López A, Pérez VI, Torres C, Königsberg M. (2018) The secretory phenotype of senescent astrocytes isolated from Wistar newborn rats changes with anti-inflammatory drugs, but does not have a short-term effect on neuronal mitochondrial potential. Biogerontology. Oct;19(5):415-433. doi: 10.1007/s10522-018-9767-3. Epub 2018 Aug 10.

Alghamdi M, Zhang J, Oswalt A, Porter JJ, Mehl RA, Kong W. (2017) Doping of Green Fluorescent Protein into Superfluid Helium Droplets: Size and Velocity of Doped Droplets. J Phys Chem A. Sep 14;121(36):6671-6678. doi: 10.1021/acs.jpca.7b05718. Epub 2017 Aug 31.

Lambert WD, Scinto SL, Dmitrenko O, Boyd SJ, Magboo R, Mehl RA, Chin JW, Fox JM, Wallace S. (2017) Computationally guided discovery of a reactive, hydrophilic trans-5-oxocene dienophile for bioorthogonal labeling. Org Biomol Chem. Aug 9;15(31):6640-6644. doi: 10.1039/c7ob01707c. Correction in Org Biomol Chem. 15(35):7476.

Row RD, Shih HW, Alexander AT, Mehl RA, Prescher JA. (2017) Cyclopropenones for Metabolic Targeting and Sequential Bioorthogonal Labeling. J Am Chem Soc. May 31;139(21):7370-7375. doi: 10.1021/jacs.7b03010. Epub 2017 May 17.

Sungwienwong I, Hostetler ZM, Blizzard RJ, Porter JJ, Driggers CM, Mbengi LZ, Villegas JA, Speight LC, Saven JG, Perona JJ, Kohli RM, Mehl RA, Petersson EJ. (2017) Improving target amino acid selectivity in a permissive aminoacyl tRNA synthetase through counter-selection. Org Biomol Chem. May 3;15(17):3603-3610. doi: 10.1039/c7ob00582b.

Scholfield MR, Ford MC, Carlsson AC, Butta H, Mehl RA, Ho PS. (2017) Structure-Energy Relationships of Halogen Bonds in Proteins. Biochemistry. Jun 6;56(22):2794-2802. doi: 10.1021/acs.biochem.7b00022. Epub 2017 Apr 22.

Viviana Perez

Maciel-Barón LÁ, Pérez VI, Torres C, González-Puertos VY, Konigsberg M, López-Diazguerrero NE. (2017) [Cellular senescence as a common denominator in age-related diseases]. Rev Med Inst Mex Seguro Soc. Jul-Aug;55(4):490-497. Spanish.

Wang R, Yu Z, Sunchu B, Shoaf J, Dang I, Zhao S, Caples K, Bradley L, Beaver LM, Ho E, Löhr CV, Perez VI. (2017) Rapamycin inhibits the secretory phenotype of senescent cells by a Nrf2-independent mechanism. Aging Cell. Jun;16(3):564-574. doi: 10.1111/acel.12587. Epub 2017 Mar 31.

Wang R, Sunchu B, Perez VI. (2017) Rapamycin and the inhibition of the secretory phenotype. Exp Gerontol. Aug;94:89-92. doi: 10.1016/j.exger.2017.01.026. Epub 2017 Feb 4.

Indira Rajagopal

Ahern K, Rajagopal I, Tan T (2016) Biochemistry Free For All

Weijian Zhang

Li C, Zhang WJ, Choi J, Frei B. (2016) Quercetin affects glutathione levels and redox ratio in human aortic endothelial cells not through oxidation but formation and cellular export of quercetin-glutathione conjugates and upregulation of glutamate-cysteine ligase. Redox Biol. Oct;9:220-228. doi: 10.1016/j.redox.2016.08.012.

Li C, Zhang WJ, Frei B. (2016) Quercetin inhibits LPS-induced adhesion molecule expression and oxidant production in human aortic endothelial cells by p38-mediated Nrf2 activation and antioxidant enzyme induction. Redox Biol. Oct;9:104-113. doi: 10.1016/j.redox.2016.06.006.

Afua Nyarko

Baßler J, Paternoga H, Holdermann I, Thoms M, Granneman S, Barrio-Garcia C, Nyarko A, Lee W, Stier G, Clark SA, Schraivogel D, Kallas M, Beckmann R, Tollervey D, Barbar E, Sinning I, Hurt E. (2015) A network of assembly factors is involved in remodeling rRNA elements during preribosome maturation. J Cell Biol. Jul 6;210(1):169-70. doi: 10.1083/jcb.20140811106112015c. No abstract

Barbar E, Nyarko A. (2015) Polybivalency and disordered proteins in ordering macromolecular assemblies. Semin Cell Dev Biol. Jan;37:20-5. doi: 10.1016/j.semcdb.2014.09.016. Epub 2014 Sep 27. Review.

Viviana Perez

Watson GW, Wickramasekara S, Fang Y, Maier CS, Williams DE, Dashwood RH, Perez VI, Ho E. (2015) HDAC6 activity is not required for basal autophagic flux in metastatic prostate cancer cells. Exp Biol Med (Maywood). Dec 6. pii: 1535370215618518. [Epub ahead of print]

Watson GW, Wickramasekara S, Fang Y, Palomera-Sanchez Z, Maier CS, Williams DE, Dashwood RH, Perez VI, Ho E. (2015) Analysis of autophagic flux in response to sulforaphane in metastatic prostate cancer cells. Mol Nutr Food Res. Oct;59(10):1954-61. doi: 10.1002/mnfr.201500283. Epub 2015 Aug 13.

Yu Z, Sunchu B, Fok WC, Alshaikh N, Pérez VI. (2015) Gene expression in the liver of female,but not male mice treated with rapamycin resembles changes observed under dietary restriction. Springerplus. Apr 11;4:174. doi: 10.1186/s40064-015-0909-7. eCollection 2015.

Pride H, Yu Z, Sunchu B, Mochnick J, Coles A, Zhang Y, Buffenstein R, Hornsby PJ, Austad SN, Pérez VI. (2015) Long-lived species have improved proteostasis compared to phylogenetically-related shorter-lived species. Biochem Biophys Res Commun. Feb 20;457(4):669-75. doi: 10.1016/j.bbrc.2015.01.046. Epub 2015 Jan 21.

Yu Z, Wang R, Fok WC, Coles A, Salmon AB, Pérez VI. (2015) Rapamycin and dietary restriction induce metabolically distinctive changes in mouse liver. J Gerontol A Biol Sci Med Sci. Apr;70(4):410-20. doi: 10.1093/gerona/glu053. Epub 2014 Apr 22.

Weijian Zhang

Zhang WJ, Frei B. (2015) Astragaloside IV inhibits NF- κ B activation and inflammatory gene expression in LPS-treated mice. Mediators Inflamm. 2015:274314. doi: 10.1155/2015/274314. Epub 2015 Apr 16.

Nyarko, Afua

Nyarko, A., Singarapu, K, Figueroa, M., Manning, V.A. Pandelova, I., Wolpert, T.J., Ciufetti, L*. & Barbar, E* (2014) Solution Structures of Ptr ToxB and its Inactive Homolog Highlight Protein Dynamics as a Modulator of Toxin Activity. J. Biol. Chem. 289:25946-56.

Barbar, E* & Nyarko, A. (2014) NMR Characterization of Self-Association Domains Promoted by Interactions with LC8 Hub Protein. Computational and Structural Biotechnology Journal. 9, e201402003.

Barbar, E.* & Nyarko, A. (2014) Polybivalency in Allosteric Regulation of Large Molecular Machines. Seminars in Cell & Developmental Biology 14, 00271-7.

Baßler J, Paternoga H, Holdermann I, Thoms M, Granneman S, Barrio-Garcia C, Nyarko A, Stier G, Clark SA, Schraivogel D, Kallas M, Beckmann R, Tollervey D, Barbar E*, Sinning I* & Hurt E*. (2014) A Network of Assembly Factors Is Involved in Remodeling rRNA Elements during Preribosome Maturation. J Cell Biol. 207, 481-98. Featured in ’News in Focus’ in the same issue

Perez, Viviana

Fok WC, Livi C, Bokov A, Yu Z, Chen Y, Richardson A, Pérez VI (2014) Short-term rapamycin treatment in mice has few effects on the transcriptome of white adipose tissue compared to dietary restriction. Mech Ageing Dev. 140, 23-9. doi:10.1016/j.mad.2014.07.004.

Yu Z, Wang R, Fok WC, Coles A, Salmon AB, Pérez VI (2014) Rapamycin and Dietary Restriction Induce Metabolically Distinctive Changes in Mouse Liver. J Gerontol A Biol Sci Med Sci. Apr 22. [Epub ahead of print]

Fok WC, Chen Y, Bokov A, Zhang Y, Salmon AB, Diaz V, Javors M, Wood WH 3rd, Zhang Y, Becker KG, Pérez VI, Richardson A. (2014) Mice fed rapamycin have an increase in lifespan associated with major changes in the liver transcriptome. PLoS One 9, e83988. doi: 10.1371/journal.pone.0083988. eCollection 2014. Erratum in: PLoS One. 2014;9(4):e92346.

Triana-Martínez F, López-Diazguerrero NE, Maciel-Barón LA, Morales-Rosales SL, Galván-Arzate S, Fernandez-Perrino FJ, Zentella A, Pérez VI, Gomez-Quiroz LE, Königsberg M (2014) Cell proliferation arrest and redox state status as part of different stages during senescence establishment in mouse fibroblasts. Biogerontology 15, 165-76. doi: 10.1007/s10522-013-9488-6. Epub 2013 Dec 18.

Fok WC, Bokov A, Gelfond J, Yu Z, Zhang Y, Doderer M, Chen Y, Javors M, Wood WH 3rd, Zhang Y, Becker KG, Richardson A, Pérez VI (2014) Combined treatment of rapamycin and dietary restriction has a larger effect on the transcriptome and metabolome of liver. Aging Cell. 13, 311-9. doi: 10.1111/acel.12175. Epub 2013 Dec 5.

Zhang, Weijian

Wei, H., Zhang, W.J., LeBoeuf, R.C., Frei, B. (2014) Copper Induces - and Copper Chelation by Tetrathiomolybdate Inhibits -Endothelial Activation in Vitro. Redox Report 19, 40-48

Wu IL, Patterson MA, Carpenter Desai HE, Mehl RA, Giorgi G, Conticello VP. (2013) Multiple site-selective insertions of noncanonical amino acids into sequence-repetitive polypeptides. Chembiochem. 2013 May 27;14(8):968-78.

Franco MC, Ye Y, Refakis CA*, Feldman JL*, Stokes AL*, Basso M, Melero RM, de Mera F, Sparrow NA, Calingasan NY, Kiaei M, Rhoads TW, Ma T, Grumet M, Barnes S, Beal MF, Beckman JS, Mehl R, Estévez AG. (2013) Nitration of Hsp90 induces cell death. PNAS, 110(12) E1102-E1111.

Merrill, Gary

Hyter S, Coleman DJ, Ganguli-Indra, Merrill GF, Ma S, Yanagisawa M, Indra AK. (2013) Endothelin-1 is a transcriptional target of p53 in epidermal keratinocytes and regulates UV induced melanocyte homeostasis. Pigment Cell Melanoma Res. 26:247-258. doi: 10.1111/pcmr.12063. Epub 2013 Jan 24.

Van Zee, Kari

Ding J, Bierma J, Smith MR, Poliner E, Wolfe C, Hadduck AN, Zara S, Jirikovic M, van Zee K, Penner MH, Patton-Vogt J, Bakalinsky AT. (2013). Acetic acid inhibits nutrient uptake in Saccharomyces cerevisiae: auxotrophy confounds use of yeast deletion libraries for strain improvement. Appl Microbiol Biotechnol 97:7405?7416.

Zhang, Weijian

Wei H, Zhang WJ, McMillen TS, Leboeuf RC, Frei B. (2012) Copper chelation by tetrathiomolybdate inhibits vascular inflammation and atherosclerotic lesion development in apolipoprotein E-deficient mice. Atherosclerosis. 223(2):306-13.

Ahern, Kevin

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 51, #5, p. 297

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 51, #4, p. 227

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 51, #3, p. 155

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 51, #2, p. 83

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 51, #1, p. 19

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 50, #6, p. 355

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 50, #5, p. 283

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 50, #4, p. 211

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 50, #3, p. 147

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 50, #2, p. 85

Ahern, K. “WebWatch,” BioTechniques (2011), Vol. 50, #1, p. 17

Ahern, Kevin (2011) The Latest, Greatest Wildly Popular Metabolic Melodies Songbook. Lulu publishers. ISBN: 978-1-257-79645-8

Ahern, Kevin . “Good Protein Synthesis” Biochemistry and Molecular Biology Education (2011), 39, 468.

Ahern, Kevin. “The Three R’s of DNA,” Biochemistry and Molecular Biology Education (2011), 39, 401.

Ahern, Kevin. “The Way They Work,” Biochemistry and Molecular Biology Education (2011), 39, 331. Ahern, Kevin. “They Call the Stuff Urea,” Biochemistry and Molecular Biology Education (2011), 39, p. 247.

Ahern, Kevin. “To Make a Cholesterol,” Biochemistry and Molecular Biology Education (2011), 39, p. 80.

Baird, William

Andrysík Z, Vondráček J, Marvanová S, Ciganek M, Neča J, Pěnčíková K, Mahadevan B, Topinka J, Baird WM, Kozubík A, Machala M. (2011)Activation of the aryl hydrocarbon receptor is the major toxic mode of action of an organic extract of a reference urban dust particulate matter mixture: the role of polycyclic aromatic hydrocarbons. Mutat Res. 2011 Sep 1;714(1-2):53-62. Epub 2011 Jul 5.

Barbar, Elisar

Barbar, E. & Nyarko A. (2011) Assembly and Regulation of Dynein Light Chains. Handbook of Dynein, CRC Press.

Nyarko, A. & Barbar, E.* (2011) Light chain dependent self-association of dynein intermediate chain. J. Biol. Chem. 286,1556-66

Nyarko, A., Hall, J., Hall, A., Hare, M., Kremerskothen, J., & Barbar, E.* (2011) Conformational dynamics promote binding diversity of dynein light chain LC8. Biophysical Chemistry. 159, 41-7. Available online 6 May 2011.

Morgan, J.L., Song, Y., & Barbar, E.* (2011) Structural dynamics and multi-region interactions in dynein- dynactin recognition. J. Biol. Chem. 286, 39349-59

Powell JD, Barbar E, Dreher TW*. (2011) Turnip yellow mosaic virus forms infectious particles without the native beta annulus structure and flexible coat protein N-terminus. Virology. Epub ahead of print.

Frei, Balz

Bowman, G.L., Shannon, J., Ho, E., Traber, M.G., Frei, B., Oken, B.S., Kaye, J.A., and Quinn, J.F. (2011) Reliability and validity of plasma nutrients and food frequency questionnaire estimates in elders with and without mild cognitive impairment. Alzheimer. Dis. Assoc. Disord., 25, 49-57.

Zhu, B.Z., Mao, L., Fan, R.M., Zhu, J.G., Zhang, Y.N., Wang, J., Kalyanaraman, B., Frei B. (2011) Ergothioneine prevents copper-induced oxidative damage to DNA and protein by formation of a redox-inactive ergothioneine-copper complex. Chem. Res. Toxicol. 24, 30-34.

Zhang, W.J., Wei, H., Tien, Y.T., and Frei, B. (2011) Genetic ablation of phagocytic NADPH oxidase in mice limits TNFα-induced inflammation in the lungs but not other tissues. Free Radic. Biol. Med. 50, 1517-1525.

Lotito, S.B., Zhang, W.J., Yang, C.S., Crozier, A., and Frei, B. (2011) Metabolic conversion of dietary flavonoids alters their anti-inflammatory and antioxidant properties. Free Radic. Biol. Med. 51, 454-463.

Wei, H., Frei, B., Beckman, J.S., and Zhang, W.J. (2011) Copper chelation by tetrathiomolybdate inhibits lipopolysaccharide-induced inflammatory responses in vivo. Am J Physiol Heart Circ Physiol. 301:H712-20.

Finlay, L.A., Michels, A.J., Butler, J.A., Smith, E.J., Monette, J.S., Moreau, R.F., Petersen Shay, K., Frei, B., and Hagen. T.M. (2011) R-α-lipoic acid does not reverse hepatic inflammation of aging, but lowers lipid anabolism while accentuating circadian rhythm transcript profiles. Am. J. Physiol. Regul. Integr. Comp. Physiol. 2011 Nov 2. [Epub ahead of print]

Drake, V.J., and Frei, B. (2011) Vitamin C in human disease prevention. In: Vitamins in the Prevention of Human Diseases (Herrmann, W. and Obeid, R., eds), pp. 347-362, Walter de Gruyter, Berlin, Germany.

Beckman, Joseph

Drechsel DA, Estévez AG, Barbeito L, Beckman JS. Nitric Oxide-Mediated Oxidative Damage and the Progressive Demise of Motor Neurons in ALS. Neurotox Res. 2012 Apr 10. [Epub ahead of print]

Trumbull KA, McAllister D, Gandelman MM, Fung WY, Lew T, Brennan L, Lopez N, Morré J, Kalyanaraman B, Beckman JS. Diapocynin and apocynin administration fails to significantly extend survival in G93A SOD1 ALS mice. Neurobiol Dis. 2012 Jan;45(1):137-44. Epub 2011 Jul 28. PubMed

Díaz-Amarilla P, Olivera-Bravo S, Trias E, Cragnolini A, Martínez-Palma L, Cassina P, Beckman J, Barbeito L. Phenotypically aberrant astrocytes that promote motoneuron damage in a model of inherited amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A. 2011 Nov 1;108(44):18126-31. Epub 2011 Oct 18.

Wei H, Frei B, Beckman JS, Zhang WJ. Copper chelation by tetrathiomolybdate inhibits lipopolysaccharide-induced inflammatory responses in vivo. Am J Physiol Heart Circ Physiol. 2011 Sep;301(3):H712-20. Epub 2011 Jul 1.

Voinov VG, Deinzer ML, Beckman JS, Barofsky DF. Electron capture, collision-induced, and electron capture-collision induced dissociation in Q-TOF. J Am Soc Mass Spectrom. 2011 Apr;22(4):607-11. Epub 2011 Feb 12.

Rhoads TW, Lopez NI, Zollinger DR, Morré JT, Arbogast BL, Maier CS, DeNoyer L, Beckman JS. Measuring copper and zinc superoxide dismutase from spinal cord tissue using electrospray mass spectrometry. Anal Biochem. 2011 Aug 1;415(1):52-8. Epub 2011 Mar 29.

Freitag, Michael

K. K. Adhvaryu, E. Berge, H. Tamaru, M. Freitag4 and E. U. Selker (2011) Substitutions in the amino-terminal tail of histone H3 have varied effects of DNA methylation. PLoS Genetics 7: e1002423 (doi:10.1371/journal.pgen.1002423) PMID: 22242002.

K. M. Smith*, P. A. Phatale**, C. M. Sullivan, K. R. Pomraning** and M. Freitag1 (2011) Heterochromatin is required for normal distribution of Neurospora CenH3. Molecular and Cellular Biology 31: 2528-2542 (doi:10.1128/MCB.01285-10) PMID: 21505064.

K. R. Pomraning**, K. M. Smith* and M. Freitag1 (2011) Bulk segregant analysis followed by high-throughput sequencing reveals the Neurospora cell cycle gene, ndc-1, to be allelic with the gene for ornithine decarboxylase, spe-1. Eukaryotic Cell 10: 724-733 (doi:10.1128/EC.00016-11) PMID: 21515825.

M. Riquelme, O. Yarden, S. Bartnicki-Garcia, B. Bowman, E. Castro-Longoria, S. Free, A. Fleißner, M. Freitag4, R.R. Lew, R. Mouriño-Pérez, M. Plamann, C. Rasmussen, C. Richthammer, R. W. Roberson, E. Sanchez-Leon, S. Seiler, and M. K. Watters. 2011. Architecture and development of the Neurospora crassa hypha – a model cell for polarized growth. Fungal Biology, 115: 446-474. (doi:10.1016/j.funbio.2011.02.008) PMID: 21640311.

E. Sánchez-León, J. Verdín, M. Freitag4, R. W. Roberson, S. Bartnicki-Garcia and M. Riquelme. 2011. Traffic of chitin synthase 1 (CHS-1) to the Spitzenkörper and developing septa in hyphae of Neurospora crassa: actin dependence and evidence of distinct microvesicle populations. Eukaryotic Cell 10: 683-695 (published ahead of print on 4 February 2011, doi:10.1128/EC.00280-10) PMID: 21296914. Cover image.

Greenwood, J.

Ma, L., Greenwood, J.A., and Schachner, M. (2011) CRP1, a protein localized in filopodia of growth cones, is involved in dendritic growth. J. Neurosci. 31, 16781-91.

Hagen, Tory

Gomez, LA, Heath, SH, and Hagen TM. (2012) Acetyl-l-carnitine supplementation reverses the age-related decline in carnitine palmitoyltransferase I (CPT 1) activity in interfibrillar mitochondria without changing the L-carnitine content in the rat heart. Mech. Ageing Dev. Feb. 1 (Epub ahead of print)

Albright, RK, Goska, BJ, Hagen TM, Chi MI, Cauwenberghs G., Chiang PY. (2011) OLAM: a wearable, non-contact sensor forcontinuous heart-rate and activity monitoring. Conf Proc IEEE Eng. Med BiolSoc. 2011: 5625-5628.

Shenvi, SV, Smith E, Hagen TM. (2011) Identification of age-specific Nrf2 binding to a novel antioxidant responseelement locus in the Gclc promoter: a compensatory means for the loss of glutathione synthetic capacity in the aging rat liver? Aging Cell. Doi: 10.1111/j. 1474-9726.2011.00788 (Epub ahead of print). NIHMSID:NIMH346900

Finlay LA, Michels, AJ, Butler JA, Smith EJ, Monette JS, Moreau, RF, Shay KP, Frei B, and Hagen TM. (2011) R-a-lipoic acid does not reverse hepatic inflammation of aging, but lowers lipid anabolism while accentuating circadian rhythm transcript profiles. Am J Physiol, Regul. Integr. Comp Physiol. (Epub ahead of print). PMCID:PMC Journal—In Process

Visioli FV, and Hagen TM (2011) Antioxidant to enhance fertility: role of eNOS and potential benefits. Pharmacol. Res. 64: 431-437.

Monette JS, Gómez LA, Moreau RF, Dunn KC, Butler JA, Finlay LA, Michels AJ, Shay KP, Smith EJ, Hagen TM. (2011) (R)-alpha-Lipoic acid treatment restores ceramide balance in aging rat cardiac mitochondria. Pharmacol Res. 63:23-29. Epub 2010 Oct 8.PMID 20934512

Hsu, Victor

Hsu, Victor. Fleishman, S.J. et al. (2011) "Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology" J. Mol Biol., 414 (2):289-302.

Johnson, Colin

Johnson, Colin. Mechanism and function of synaptotagmin-mediated membrane apposition. Hui E, Gaffaney JD, Wang Z, Johnson CP, Evans CS, Chapman ER. Nat Struct Mol Biol. 2011 Jun 5;18(7):813-21. doi: 10.1038/nsmb.2075. PMID: 21642967 [PubMed - indexed for MEDLINE]

Karplus, P. Andrew

Nirudodhi, S., Parsonage, D., Karplus, P.A., Poole, L.B. & Maier, C.S. (2011) “Conformational studies of the robust 2-Cys peroxiredoxin Salmonella typhimurium AhpC by solution phase hydrogen/deuterium (H/D) exchange monitored by electrospray ionization mass spectrometry ” Int. J. Mass Spec. 302, 93-100.

Cooley, RB, Rhoads, T.W., Arp, D.J. & Karplus, P.A. (2011) “A diiron protein auto-generates a valine-phenylalanine crosslink” Science 332, 929.

Tronrud, D.E. & Karplus, P.A. (2011) A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution. Acta Cryst D67, 699-706.

Carter, E.L., Tronrud, D.E., Taber, S.R., Karplus, P.A. & Hausinger, R.P. (2011) “Iron-Containing Urease in a Pathogenic Bacterium” Proc. Nat. Acad. Sci. 108, 13095-13099.

Cooley, R.B., Arp, D.J. & Karplus, P.A. (2011) “Symerythrin structures at atomic resolution and the origins of rubrerythrins and the ferritin-like superfamily” J. Mol. Biol. 413, 177-194.

Stipanuk, M.H., Dominy, J.E. Jr., Simmons, C.R. & Karplus , P.A. (2011) “Thiol Dioxygenases: Unique Families of Cupin Proteins” Amino Acids 41, 91-102.

Klomsiri, C., Karplus, P.A. & Poole, L.B. (2011) “Cysteine-based redox switches in enzymes” Antioxidants & Redox Signaling, 14, 1065-71.

Hall, A.R., Nelson, K.J., Poole, L.B. & Karplus, P.A. (2011) “Structure-based insights into the catalytic power and conformational dexterity of peroxiredoxins.” Antioxidants & Redox Signaling,15, 795-815.

Mathews, Chris

Wheeler, L. J., and C. K. Mathews (2011) Nucleoside triphosphate pool asymmetry in mammalian mitochondria. J. Biol. Chem. 286, 16992-16996.

Mehl, Ryan

Jason L. Seitchik*, Jennifer C. Peeler*, Michael T. Taylor, Melissa L. Blackman, Timothy W. Rhoads, Richard B. Cooley, Christian Refakis*, Joseph M. Fox, and Ryan A. Mehl. Genetically Encoded Tetrazine Amino Acid Directs Rapid Site-Specific in Vivo Bioorthogonal Ligation with trans-Cyclooctenes. J. Am. Chem. Soc. 2012, 134(6), 2898-901.

Ryan A. Mehl. Engineered Unnatural Animals: Tools for Multicellular Biochemistry. ChemBioChem. 2012 13(2), 186-8.

Saadyah Averick, Antonina Simakova, Sangwoo Park, Dominik Konkolewicz, Andrew J. D. Magenau, Ryan A. Mehl, and Krzysztof Matyjaszewski. ATRP under Biologically Relevant Conditions: Grafting from a Protein. ACS Macro Letters, 2012, 1, 6-10.

Saadyah Averick, Eduardo Paredes, Debasish Grahacharya, Bradley F. Woodman*, Shigeki J. Miyake-Stoner*, Ryan A. Mehl, Krzysztof Matyjaszewski, Subha R. Das. A Protein-Polymer Hybrid Mediated By DNA. Langmuir 2012, 28(4), 1954-8.

R. Daniel Libby, Ryan A. Mehl. Characterization of covalent Ene adduct intermediates in ‘‘hydride equivalent’’ transfers in a dihydropyridine model for NADH reduction reactions. Bioorganic Chemistry. 2012, 40(1), 57-66.

Saadyah Averick, Antonina Simakova, Andrew Magenau, Andrew Seong, Bradley F. Woodman*, Ryan A. Mehl, Krzysztof Matyjaszewski. Covalently Incorporated Protein-Nanogels using AGET ATRP in Inverse Miniemulsion. Polymer Chem. Comm. 2011, 2 (7), 1476-1478.

Jennifer C. Peeler*, Ryan A. Mehl. Methods in Molecular Biology series, “Unnatural amino acids”. Site-Specific incorporation of unnatural amino acids as probes for protein conformational changes Springer Science, Methods in Molecular Biology 2012. 794, 125-134.

Zhang, Weijian

Zhang WJ*, Wei H, Tien YT, Frei B*. (2011) Genetic ablation of phagocytic NADPH oxidase in mice limits TNFα-induced inflammation in the lungs but not other tissues. Free Radic. Biol. Med. 50:1517-1525.

Lotito SB, Zhang WJ, Yang CS, Crozier A, and Frei B. (2011) Metabolic conversion of dietary flavonoids alters their anti-inflammatory and antioxidant properties. Free Radic. Biol. Med. 51:454-463

Wei H, Frei B, Beckman JS, Zhang WJ. (2011) Copper chelation by tetrathiomolybdate inhibits lipopolysaccharide-induced inflammatory responses in vivo. Am J Physiol Heart Circ Physiol. 301:H712-720.

Program Postdocs and Courtesy Faculty

Cooley, Richard

Cooley, RB, Arp DJ and Karplus, PA. (2011) “Symerythrin structures at atomic resolution and the origins of rubrerythrins and the ferritin-like superfamily." J. Mol. Biol. 413, 177-194.

Cooley, RB, Rhoads, T., Arp DJ and Karplus, PA. (2011) "A diiron protein autogenerates a valine-phenylalanine cross-link." Science, 332 (6032), 929.

Research Associates

Smith, Kristina

K.M. Smith, P.A. Phatale, C.M. Sullivan, K.R. Pomraning, and M. Freitag. Heterochromatin is required for normal distribution Neurospora crassa CenH3. Mol Cell Biol. 31: 2528-42, 2011.

K.R. Pomraning, K.M. Smith, and M. Freitag. Bulk segregant analysis followed by high-throughput sequencing reveals the Neurospora cell cycle gene, ndc-1, to be allelic with the gene for ornithine decarboxylase, spe-1. Eukaryotic Cell 10: 724-33, 2011.

Ahern, Kevin

Educational Songs

Ahern, K. (2010) "Catalyze" Biochem. Mol. Biol. Educ. 38, 335.

Ahern, K. (2010) "Photosynthesis is Divine" Biochem. Mol. Biol. Educ., 38, 58.

Ahern, K. (2010) "Web Watch", Biotechniques 48, #5, in press. Ahern, K. (2010) "Web Watch", Biotechniques 48, #4, 265.

Ahern, K. (2010) "Web Watch", Biotechniques 48, #3, 183.

Ahern, K. (2010) "Web Watch", Biotechniques 48, #2, 93.

Ahern, K. (2010) "Web Watch", Biotechniques 48, #1, 23.

Ahern, K. (2010) "Web Watch", Biotechniques 47, #6, 1003.

Ahern, K. (2010) "Web Watch", Biotechniques 47, #5, 909.

Ahern, K. (2010) "Web Watch", Biotechniques 47, #4, 815.

Ahern, K. (2010) "Web Watch", Biotechniques 47, #3, 725.

Ahern, K. (2010) "Web Watch", Biotechniques 47, #2, 657.

Ahern, K. (2010) "Web Watch", Biotechniques 47, #1, 577.

Baird, William

Luch, A. and Baird, W.M. (2010) Carcinogenic Polycyclic Aromatic Hydrocarbons. In: Charlene A. McQueen, Comprehensive Toxicology Vol14 pp85-123 Oxford: Academic Press.

Barbar, Elisar

Hall, J., Song, Y., Karplus, P.A. and Barbar, E. (2010) The crystal structure of dynein intermediate chain-light chain roadblock complex gives new insights into dynein assembly. J. Biol. Chem. 285, 22566-22575.

Nyarko, A. and Barbar, E. (2010) Light chain dependent self-association of dynein intermediate chain. J. Biol. Chem. Oct 25. [Epub ahead of print]

Frei, Balz

Bowman, G.L., Shannon, J., Frei, B., Kaye, J.A. and Quinn, J.F. (2010) Uric acid as a central nervous system antioxidant. J. Alzheimers Dis. 19, 1331-1336.

Zhang, W.J., Wei, H. and Frei, B. (2010) The iron chelator, desferrioxamine, reduces inflammation and atherosclerotic lesion development in experimental mice. Exp. Biol. Med. 235, 633-641.

Li, L., Smith, A., Hagen, T.M. and Frei, B. (2010) Vascular oxidative stress and inflammation increase with age: Ameliorating effects of α-lipoic acid supplementation. Ann. N.Y. Acad. Sci. 1203, 151-159.

Traber, M.G. and Frei, B. (2010) Micronutrient concentrations and subclinical atherosclerosis in adults with HIV. Am. J. Clin. Nutr. 92, 266-267. PubMed PMID: 20463044.

Wu, R., Frei, B., Kennedy, J.A. and Zhao, Y. (2010) Effects of refrigerated storage and processing technologies on the bioactive compounds and antioxidant capacities of 'Marion' and 'Evergreen' blackberries. Food Science and Technology 43, 1253-1264.

Michels, A.J., Hagen, T.M. and Frei, B. (2010) A new twist on an old vitamin: human polymorphisms in the gene encoding the sodium-dependent vitamin C transporter 1. Am. J. Clin. Nutr. 92, 271-272.

Drake, V.J. and Frei, B. (2010) Vitamin C in human disease prevention. In: Vitamins and Vitamin-Like Nutrients for Prevention of Human Diseases (Obeid, R. and Herrmann, W., eds), Walter de Gruyter, Berlin, Germany, in press.

Bowman, G.L., Shannon, J., Ho, E., Traber, M.G., Frei, B., Oken, B.S., Kaye, J.A. and Quinn, J.F. (2010) Reliability and validity of plasma nutrients and food frequency questionnaire estimates in elders with and without mild cognitive impairment. Alzheimer. Dis. Assoc. Disord. Nov 3. [Epub ahead of print]

Zhu, B.Z., Zhang, Y.N., Wang, J. and Frei, B. (2010) Ergothioneine prevents copper-induced oxidative damage to DNA and protein by formation of a redox-inactive ergothioneine-copper complex. Chem. Res. Toxicol. Nov 3. [Epub ahead of print]

Freitag, Michael

Smith, K.M., Sancar, G., Dekhang, R., Sullivan, C.M., Li, S., Tag, A.G., Sancar, C., Bredeweg, E.L., Priest, H.D., McCormick, R.F., Thomas, T.L., Carrington, J.C., Stajich, J.E., Bell-Pedersen, D., Brunner, M. and Freitag, M. (2010) Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for Neurospora white collar complex. Eukaryotic Cell 9, 1549-1556.

Lee, H-C., Li, L., Gu, W., Xue, Z., Crosthwaite, S.K., Lewis, Z.A., Freitag, M., Selker, E.U., Mello, C. and Liu, Y. (2010). Origin and biogenesis of microRNAs and dicer-independent small interfering RNAs: Multiple mechanisms for small RNA production in fungi. Molecular Cell 38, 1-12, (doi:10.1016/j.molcel.2010.04.005).

Ma, L.-J., van der Does, H.C., Borkovich, K.A., Coleman, J.J., Daboussi, M.-J., Di Pietro, A., Dufresne, M., Freitag, M., Grabherr, M., Henrissat, B., Houterman, P.M., Shim, W.-B., Woloshuk, C., Xie, X., Xu, J.-R., Antoniw, J., Baker, S.E., Bluhm, B.H., Breakspear, A., Brown, D.W., Butchko, R.A.E., Chapman, S., Coulson, R., Coutinho, P.M., Danchin, E.G.J., Diener, A., Gale, L.R., Gardiner, D.M., Goff, S., Hammond-Kosack, K.E., Hilburn,

K., Hua-Van, A., Jonkers, W., Kazan, K., Kodira, C.D., Koehrsen, M., Kumar, L., Lee, Y.-H., Li, L., Manners, J.M., Miranda-Saavedra, D., Mukherjee, M., Park, G., Park, J., Park, S.-Y., Proctor, R., Regev, A., Ruiz-Roldan, M.C., Sain, D., Sakthikumar, S., Sykes, S., Schwartz, D.C., Turgeon, G., Wapinski, I., Yoder, O., Young, S., Zeng, Q., Zhou, S., Galagan, J., Cuomo, C.A., Kistler, H.C. and Rep, M. (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium oxysporum. Nature 464, 367-373.

Nowrousian, M., Stajich, J., Engh, I., Espagne, E., Kamerewerd, J., Kempken, F., Kuo, H.-C., Osiewacz, H.D., Pöggeler, S., Read, N., Seiler, S., Smith, K.M., Zickler, D., Kück, U. and Freitag, M. (2010) Next-generation sequencing of the 40 Mb genome of the filamentous fungus Sordaria macrospora. PLoS Genetics 6, e1000891.

Roca, M.G., Kuo, H.-C., Lichius, A., Freitag, M. and Read, N.D. (2010) Nuclear dynamics and mitosis during the early stages of colony establishment in Neurospora crassa. Eukaryotic Cell 9, 1171-1183 (online 12 March 2010, doi:10.1128/EC.00329-09). Cover image (August 2010).

Delgado-Alvarez, D.L., Smith, L.G., Callejas-Negrete, O.A., Freitag, M., Roberson, R.W., Gómez, N. and Mouriño-Pérez, R.R. (2010) F-actin localization and dynamics determined by live cell imaging in Neurospora crassa. Fungal Genetics and Biology 47, 573-586. (doi:10.1016/j.fgb.2010.03.004).

Rowe, J., Harbertson, J., Osborne, J., Freitag, M., Lim, J. and Bakalinsky, A. (2010) Mannoproteins are enriched in model wine aged 9 months on the yeast lees. Journal of Agricultural and Food Chemistry 58, 2337-2346.

Gombart, Fritz

Akagi, T., Thoennissen, N.H., George, A., Crooks, G., Song, J.H., Okamoto, R., Nowak, D., Gombart, A.F. and Koeffler, H.P. (2010) In vivo deficiency of both C/EBPβ and C/EBPε results in highly defective myeloid differentiation and lack of cytokine response. PLoS One Nov 3;5(11):e15419.

Greenwood, J.

Jang, H.S., Lal, S. and Greenwood, J.A. (2010) Calpain 2 is required for glioblastoma cell invasion: regulation of matrix metalloproteinase 2. Neurochem. Res. 35, 1796-1804.

Hagen, Tory

Monette, J.S., Gómez, L.A., Moreau, R.F., Dunn, K.C., Butler, J.A., Finlay, L.A., Michels, A.J., Shay, K.P., Smith, E.J. and Hagen, T.M. (2010) (R)-α -Lipoic acid treatment restores ceramide balance in aging rat cardiac mitochondria. Pharmacol. Res., in press.

Li, L., Smith, A., Hagen, T.M. and Frei, B. (2010) Vascular oxidative stress and inflammation increase with age: ameliorating effects of alpha-lipoic acid supplementation. Ann. N.Y. Acad. Sci. 1203,151-159.

Widlansky, M.E., Wang, J., Shenouda, S.M., Hagen, T.M., Smith, A.R., Kizhakekuttu, T.J., Kluge, M.A., Weihrauch, D., Gutterman, D.D. and Vita, J.A. (2010) Altered mitochondrial membrane potential, mass, and morphology in the mononuclear cells of humans with type 2 diabetes. Transl. Res. 156, 15-25.

Monette, J.S., Gómez, L.A., Moreau, R.F., Bemer, B.A., Taylor, A.W. and Hagen, T.M.. (2010) Characteristics of the rat cardiac sphingolipid pool in two mitochondrial subpopulations. Biochem. Biophys. Res. Commun. 398, 272-277.

Michels AJ, Hagen, TM, and Frei B. (2010) A new twist on an old vitamin: human polymorphisms in the gene encoding the sodium-dependent vitamin C transporter 1. Am J Clin Nutr 92, 271-272.

Monette, J.S., Gomez, L.A., Moreau, R., Bemer, B.A., Taylor, A.W. and Hagen, T.M. (2010) Characteristics of the rat cardiac spingolipid pool in two mitochondrial subpopulations. Biochemical and Biophysical Research Communications 398, 272-277.

Karplus, P. Andrew

Berkholz, D.S., Krenesky, P.b., Davidson, J.R. and Karplus, P.A. (2010) Protein geometry database: A flexible engine to explore backbone conformations and their relationships with covalent geometry. Nucleic Acids Res. 38, D320-325.

Hall, J., Karplus, P.A. and Barbar, E. (2010) The crystal structure of dynein intermediate chain-light chain roadblock complex gives new insights into dynein assembly. J. Biol. Chem. 285, 22566-22575.

Tronrud, D.E., Berkholz, D.S. and Karplus, P.A. (2010) Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins. Acta Cryst. D66, 834-842.

Hall, A., Parsonage, D., Poole, L.B. and Karplus, P.A. (2010) Structural evidence that peroxiredoxin catalytic power in based on transition state stabilization. J. Mol. Biol. 402, 194-209.

Cooley, R.B., Arp, D.J. and Karplus, P.A. (2010) Evolutionary origin of a secondary structure: pi-helices as cryptic but widespread insertional variations of alpha-helices that enhance protein functionality. J. Mol. Biol. 404, 232-246.

Parsonage, D., Reeves, S.A., Karplus, P.A. and Poole, L.B. (2010) Engineering of fluorescent reporters into redox domains to monitor electron transfers. Meth. Enzymol. 474, 1-21.

Hollingsworth, S.A. and Karplus, P.A. (2010) A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. Biomolecular Concepts 1, 271-283.

Mathews, Chris

Mathews, C.K. (2010) Bacteriophage T4. In: Encyclopedia of Life Sciences 2010, John Wiley & Sons, Ltd: Chichester [DOI: 10.1002/9780470015902.a0000784.pub3]

Mathews, C.K. (2010) The Tao of Chemistry and Life, A Scientific Journey (book review), Biochem. Mol. Biol. Educ. 38, 130.

Hogan, C., Aligianni, S., Durand-Dubief, M., Persson, J., Will, W., Wheeler, J., Mathews, C.K. and Varga-Weisz, P. (2010) Fission yeast Iec1-Ino80-mediated nucleosome eviction regulates nucleotide and phosphate metabolism. Mol. Cell Biol. 30, 657-674.

Merrill, Gary

Rollins, M.F., van der Heide, D.M., Weisend, C.M., Kundert, J.A., Comstock. K.M., Suvorova, E.S., Capecchi, M.R., Merrill, G.F. and Schmidt, E.E. (2010) Hepatocytes lacking thioredoxin reductase 1 have normal replicative potential during development and regeneration. J. Cell Sci. 5(123), 2402-2412. PMID: 20571049.

Moreau, Regis

Monette, J.S., Gomez, L.A., Moreau, R., Dunn, K.C., Butler, J.A., Finlay, L.A., Michels, A.J., Petersen Shay, K., Smith, E.J. and Hagen, T.M. (2010) (R)-a-Lipoic acid treatment restores ceramide balance in aging rat cardiac mitochondria. Pharmacological Research, in press.

Monette, J.S., Gomez, L.A., Moreau, R., Bemer, B.A., Taylor, A.W. and Hagen, T.M. (2010) Characteristics of the rat cardiac spingolipid pool in two mitochondrial subpopulations. Biochemical and Biophysical Research Communications 398, 272-277.

Zhang, Weijian

Zhang, W.J., Wei, H. and Frei, B. (2010) The iron chelator, desferrioxamine, reduces inflammation and atherosclerotic lesion development in experimental mice. Exp. Biol. Med. 235, 633-641.

Program Graduate and Undergraduate Students with Affiliate Faculty

Hadduck, A.N., Hindagolla, V., Contreras, A., Li, Q., Bakalinsky, A.T. (2010) Does aqueous fullerene inhibit growth of yeast or E. coli? Appl. Env. Micro. 76, 8239-8242.

Bollmann, S. R., Tominey, C.M., Hoffman, P.D., Hoffman, T.M.C. and Hays, J.B. (2011) Reversion-reporter transgenes to analyze all six base-substitution pathways in arabidopsis. Plant Physiology 155.

Furukawa, T., Curtis, M.J., Tominey, C.M., Duong, Y.H., Wilcox, B.W.L., Aggoune, D., Hays, J.B. and Britt, A.B. (2010) A shared DNA-damage-response pathway for induction of stem-cell death by UVB and by gamma irradiation. DNA Repair 9, 940-948.

Curtin, M.J., Belcram, K., Bollmann, S.R., Tominey, C.M., Hoffman, P.D., Mercier, R. and Hays, J.B. (2009) Reciprocal chromosome translocation associated with TDNA-insertion mutation in Arabidopsis: genetic and cytological analyses of consequences for gametophyte development and for construction of doubly mutant lines. Planta 229, 731-745.

Program Postdocs and Courtesy Faculty

Baase, W.A., Liu, L., Tronrud, D.E., Matthews, B.W. (2010) Lessons from the lysozyme of phage T4. Protein Sci. 19, 631-641.

Carpenter, R.A., Zhan, X., Ellis, H.R. (2010) Catalytic role of a conserved cysteine residue in the desulfonation reaction by the alkanesulfonate monooxygenase enzyme. Biochim. Biophys. Acta 1804, 97-105.

Ahern, Kevin

Educational Songs

Ahern, K. "Catalyze" Biochem. Mol. Biol. Educ., submitted.

Ahern, K. and Rajagopal, I. "Photosynthesis is Divine" Biochem. Mol. Biol. Educ., in press. Ahern, K. (2009) "Enzymes" Biochem. Mol. Biol. Educ. 37, 260.

Rajagopal, I. and Ahern, K. (2009) "Central Dogma Zen" Biochem. Mol. Biol. Educ. 37, p. 68.

Baird, William

Bailey, G.S., Reddy, A.P., Pereira, C.B., Harttig, U., Baird, W., Spitsbergen, J.M., Hendricks, J.D., Orner, G.A., Williams, D.E. and Swenberg, J.A. (2009) Nonlinear cancer response at ultralow dose: A 40800-animal ED₀₀₁ tumor and biomarker. Chem. Res. Toxicol. 22, 1264-1276.

Barbar, Elisar

Benison, G., Chiodo, M.P., Karplus, P.A. and Barbar, E. (2009) Structural, thermodynamic, and kinetic effects of a phosphomimetic mutation in dynein light chain LC8. Biochemistry 48, 11381-11389.

Hall, J., Karplus, P.A. and Barbar, E. (2009) Multivalency in the assembly of intrinsically disordered dynein intermediate chain. J. Biol. Chem. 284, 33115-33121.

Hall, A., Parsonage, D., Horita, D., Karplus, P.A., Poole, L.B. and Barbar, E. (2009) Redox-dependent dynamics of a dual thioredoxin fold protein: evolution of specialized folds. Biochemistry 48, 5984-5993.

Benison, G. and Barbar, E. (2009) NMR analysis of dynein light chain dimerization and interactions with diverse ligands. Methods Enzymol. 455, 237-258.

Beckman, Joe

Voinov, V.G., Beckman, J.S., Deinzer, M.L. and Barofsky, D.F. (2009) Electron-capture dissociation (ECD), collision-induced dissociation (CID) and ECD/CID in a linear radio-frequency-free magnetic cell. Rapid Commun. Mass Spectrom. 23, 3028-3030.

Beckman, J.S. (2009) Understanding peroxynitrite biochemistry and its potential for treating human diseases. Arch. Biochem. Biophys. 484, 114-116.

Sotelo-Silveira, J.R., Lepanto, P., Elizondo, V., Horjales, S., Palacios, F., Martinez-Palma, L., Marin, M., Beckman, J.S. and Barbeito, L. (2009) Axonal mitochondrial clusters containing mutant SOD1 in transgenic models of ALS. Antioxid. Redox Signal. 11, 1535-1545.

Trumbull, K.A. and Beckman, J.S. (2009) A role for copper in the toxicity of zinc-deficient superoxide dismutase to motor neurons in amyotrophic lateral sclerosis. Antioxid. Redox Signal. 11, 1627-1639.

Frei, Balz

Zhang, W.J., Wei, H. and Frei, B. (2009) Genetic deficiency of NADPH oxidase does not diminish but rather enhances LPS-induced acute inflammatory responses in vivo. Free Radic. Biol. Med. 46, 791-798. PMCID: 2659145.

Bowman, G.L., Dodge, H., Frei, B., Calabrese, C., Oken, B.S., Kaye, J.A. and Quinn, J.F. (2009) Ascorbic acid and rates of cognitive decline in Alzheimer’s disease. J. Alzheimers Dis. 16, 93-98. PMCID: 2674290.

Popkin, B.M., Bray, G.M., Caballero, B., Frei, B. and Willett, W.C. (2009) The role of beverages in a healthy diet: key issues and guidelines. In: Functional and Speciality Beverage Technology (Paquin, P., ed.), pp. 451-483, Woodhead Publishing, Cambridge, England.

Li, L. and Frei, B. (2009) Prolonged exposure to LPS increases iron, heme, and p22^phox levels and NADPH oxidase activity in human aortic endothelial cells. Inhibition by Desferrioxamine. Arterioscler. Thromb. Vasc. Biol. 29, 732-738. PMCID: 2724965.

Roberts, L.J., Traber, M.G. and Frei, B. (2009) Vitamins E and C in the prevention of cardiovascular disease and cancer in men. Free Radic. Biol. Med. 46, 1558.

Freitag, Michael

Bowman, B.J., Draskovic, M., Freitag, M. and Bowman, E.J. (2009) Structure and distribution of organelles and the cellular location of calcium transporters in Neurospora crassa. Eukaryotic Cell 8, 1845-1855 (online 2 October 2009, EC.00174-09v1).

Coleman, J.J., Rounsley, S.D., Rodriguez-Carres, M., Kuo, A., Wasmann, C.C., Grimwood, J., Schmutz, J., Taga, M., White, G.J., Zhou, S., Schwartz, D.C., Freitag, M., Ma, L.-J., Danchin, E.G.J., Henrissat, B., Coutinho, P.M., Nelson, D.R., Straney, D., Napoli, C.A., Gribskov, M., Rep, M., Kroken, S., Molnár, I., Rensing, C., Kennell, J.C., Zamora, J., Farman, M.L., Selker, E.U., Salamov, A., Shapiro, H., Pangilinan, J., Lindquist, E., Lamers, C., Grigoriev, I., Geiser, D.M., Covert, S.F., Temporini, E. and Van Etten, H.D. (2009) The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion. PLoS Genetics 5, e1000618. doi:10.1371/journal.pgen.1000618.

Ramos-Garcia, S.L., Roberson, R.W., Freitag, M., Bartnicki-García, S. and Mouriño-Pérez, R.R. (2009) Cytoplasmic bulk flow propels nuclei in mature hyphae of Neurospora crassa. Eukaryotic Cell 8, 1880-1890 (online 14 August 2009, EC.00062-09v1).

Cosseau, C., Azzi, A., Smith, K.M., Freitag, M., Mitta, G. and Grunau, C. (2009) Native chromatin immunoprecipitation (N-ChIP) and ChIP-Seq of Schistosoma masoni: critical experimental parameters. Mol. Biochem. Parasitology 166, 70-76 (online 9 March 2009, doi:10.1016/j.molbiopara.2009.02015).

Lewis, Z.A., Honda, S., Khlafallah, T.K., Jeffress, J.K., Freitag, M., Mohn, F., Schübeler, D. and Selker, E.U. (2009) Relics of repeat-induced point mutation direct heterochromatin organization in Neurospora crassa. Genome Research 19, 427-437.

Pomraning, K.R., Smith, K.M. and Freitag, M. (2009) Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47, 142-150. (doi:10.1016/j.ymeth.2008.09.022).

Gombart, Fritz

Gombart, A.F. (2009) The vitamin D-antimicrobial peptide pathway and its role in protection against infection. Future Microbiol. 4, 1151-1165. PMID: 19895218

Uh, A., Simmons, C.F., Bresee, C., Khoury, N., Gombart, A.F., Nicholson, R.C., Kocak, H. and Equils, O. (2009) MyD88 and TRIF mediate the cyclic adenosine monophosphate (cAMP) induced corticotropin releasing hormone (CRH) expression in JEG3 choriocarcinoma cell line. Reprod. Biol. Endocrinol. 7, 74. PMID: 19615077

Gombart, A.F., Saito, T. and Koeffler, H.P. (2009) Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates. BMC Genomics. 10, 321. PMID: 19607716

Adams, J.S., Re,n S., Liu, P.T., Chun, R.F., Lagishetty, V., Gombart, A.F., Borregaard, N., Modlin, R.L. and Hewison, M. (2009) Vitamin d-directed rheostatic regulation of monocyte antibacterial responses. J. Immunol. 182, 4289-4295. PMID: 19299728

Gombart, A.F., Bhan, I., Borregaard, N., Tamez, H., Camargo, C.A. Jr., Koeffler, H.P. and Thadhani, R. (2009) Low plasma level of cathelicidin antimicrobial peptide (hCAP18) predicts increased infectious disease mortality in patients undergoing hemodialysis.. Clin. Infect. Dis. 48, 418-424. PMID: 19133797

Greenwood, J.

Jang, H.S. and Greenwood, J.A. (2009) Gylcine-rich region regulates cysteine-rich protein 1 binding to actin cytoskeleton. Biochem. Biophys. Res. Commun. 380, 484-488.

Hagen, Tory

Michels, A.J. and Hagen, T.M. (2009) Hepatocyte nuclear factor 1 is essential for transcription of sodium-dependent vitamin C transporter protein 1. Am. J. Physiol. Cell Physiol. 297 C1220-1227. PMID: 19741195

Gómez, L.A., Monette, J.S., Chavez, J.D., Maier, C.S. and Hagen, T.M. (2009) Supercomplexes of the mitochondrial electron transport chain decline in the aging rat heart. Arch. Biochem. Biophys. 490, 30-35. PMID: 19679098

Shay, K.P., Moreau, R.F., Smith, E.J., Smith, A.R. and Hagen, T.M. (2009) Alpha-lipoic acid as a dietary supplement: molecular mechanisms and therapeutic potential. Biochim. Biophys. Acta 1790, 1149-1160. PMID: 19664690

Shenvi, S.V., Smith, E.J. and Hagen, T.M. (2009) Transcriptional regulation of rat gamma-glutamate cysteine ligase catalytic subunit gene is mediated through a distal antioxidant response element. Pharmacol. Res. 60, 229-236. PMID: 19540342

Butler, J.A., Hagen, T.M. and Moreau, R. (2009) Lipoic acid improves hypertriglyceridemia by stimulating triacylglycerol clearance and downregulating liver triacylglycerol secretion. Arch. Biochem. Biophys. 485, 63-71. PMID: 19232511

Hsu, Victor

Koerner, J.L., Hsu, V.L., Lee, J. and Kennedy, J.A. (2009) Determination of proanthocyanidin A2 content in phenolic polymer isolates by reversed-phase high-performance liquid chromatography. J. Chromatog. A 1216, 1403-1409.

Karplus, P. Andrew

Krueger, S.K., Henderson, M.C., Siddens, L.K., VanDyke, J.E., Benninghoff, A.D., Karplus, P.A., Furnes, B., Schlenk^, D. and Williams, D.E. (2009) Characterization of Sulfoxygenation and Structural Implications of Human Flavin-Containing Monooxygenase Isoform 2 (FMO2.1) Variants S195L and N413K. Drug Metab. And Disp. 37,1785-1791 (PMID: 19420133).

Hollingsworth, S, Berkholz, D.S. and Karplus, P.A. (2009) On the occurrence of linear groups in proteins. Protein Sci. 18, 1321-1325. (PMID: 19472372).

Hall, A., Parsonage, D., Horita, D., Karplus, P.A., Poole, L.B. and Barbar, E. (2009) Redox-dependent dynamics of a dual thioredoxin-fold protein: evolution of specialized folds. Biochemistry 48, 5984-5993. (PMID: 19459661).

Hall, A., Parsonage, D., Poole, L.B. and Karplus, P.A. (2009) Structural changes common to catalysis in the Tpx peroxiredoxin subfamily. J. Mol. Biol. 393, 867-881. (PMID: 19699750).

Khayrutdinov, B.I., Bae, W.J., Yun, Y.M., Lee, J.H., Tsuyama, T., Kim, J.J., Hwang, E., Ryu, K.S., Cheong, H.K., Cheong, C., Ko, J.S., Enomoto, T., Karplus, P.A., Güntert, P., Tada, S., Jeon, Y.H. and Cho, Y. (2009) Structure of the Cdt1 C-terminal domain: Conservation of the winged helix fold in replication licensing factors. Prot. Sci. 18, 2252-2264. (PMID: 19722278).

Wallen, J.R., Mallett, T.C., Boles, W., Parsonage, D., Furdui, C.M., Karplus, P.A. and Claiborne, A. (2009) Crystal structure and catalytic properties of Bacillus anthracis CoADR-RHD: Implications for flavin-linked sulfur trafficking. Biochemistry 48, 9650-9667 (PMID 19725515).

Berkholz, D.S., Shapavalov, M.D., Dunbrack, R.S. Jr. and Karplus, P.A. (2009) Conformation Dependence of Backbone Geometry in Proteins. Structure 17, 1316-1325.

Hall, J., Karplus, P.A. and Barbar, E. (2009) Multivalency in the assembly of intrinsically disordered dynein intermediate chain. J. Biol. Chem. 284, 33115-33121. (PMID: 19759397).

Benison, G., Chiodo, M., Karplus, P.A., and Barbar, E. (2009) Structural, Thermodynamic, and Kinetic Effects of a Phosphomimetic Mutation in Dynein Light Chain LC8. Biochemistry 48, 11381-11389. (PMID: 19863079).

Hall, A., Karplus, P.A., and Poole, L.B. (2009) Typical 2-Cys peroxiredoxins: Structures, mechanisms and functions. FEBS Journal 276, 2469-2477. (PMID: 19476488).

Mathews, Chris

Mathews, C.K. and Wheeler, L.J. (2009) Measuring DNA Precursor Pools in Mitochondria. In J.A. Stuart (ed.) Mitochondrial DNA: Methods and Protocols, Second Edition. Methods in Molecular Biology Series, Humana Press, Totowa, NJ, pp. 371-381.

Muniyappa, H., Song, S., Mathews, C.K. and Das, K.C. (2009) Reactive Oxygen Species-Independent Oxidation of Thioredoxin in Hypoxia: Inactivation of Ribonucleotide Reductase and Redox-Mediated Checkpoint Control. J. Biol. Chem. 284, 17069-17081.

Chimploy, K., Diaz, G.D., Li, Q., Carter, O., Dashwood, W-M., Mathews, C.K., Williams, D.E., Bailey, G.S. and Dashwood, R.H. (2009) E2F4 and ribonucleotide reductase mediate S-phase arrest in colon cancer sells treated with chlorophyllin. Int. J. Cancer, 125, 2086-2094.

Merrill, Gary

Stoner, C.S., Pearson, G.D., Koç, A., Merwin, J.R., Lopez, N.I. and G.F. Merrill, G.F. (2009) Effect of thioredoxin reductase deletion and p53 cysteine replacement on human p53 activity in wild-type and thioredoxin reductase null yeast. Biochemistry 48, 9156-9169.

Suvorora, E.S., Lucas, O., Eisand, C.M., Rollins, M.F., Merrill, G.F., Capecchi, M.R. and Schmidt, E.E. (2009) Cytoprotective Nrf2 pathway is induced in chronically Txnrd1-deficient hepatocytes. PLoS One 4(7):e6158.

Long, C.M., Rohrmann, G.F. and Merrill, G.F. (May 2009) The conserved baculovirus protein p33 (Ac92) is a flavin adenine dinucleotide-linked sulfydryl oxidase. Virology 388, 231-235.

Zhang, Weijian

Zhang, W.J., Wei, H. and Frei, B. (2009) Genetic deficiency of NADPH oxidase does not diminish, but rather enhances, LPS-induced acute inflammatory responses in vivo. Free Radical Biology & Medicine. 46, 791-798.

Program graduate students with affiliate faculty

Cooley, R.B., Bottomley, P.J. and Arp, D.J. (2009) Growth of a non-methanotroph on natural gas: ignoring the obvious to focus on the obscure. Environ. Microbiol. Rep. 1, 408-413.

Cooley, R.B., Dubbels, B.L., Sayavedra-Soto, L.A., Bottomley, P.J. and Arp, D.J. (2009) Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly 'Pseudomonas butanovora'. Microbiology 155, 2086-2096.

Nian, H., Bisson, W.H., Dashwood, W.M., Pinto, J.T., Dashwood, R.H. (2009) Alpha-keto acid metabolites of organoselenium compounds inhibit histone deacetylase activity in human colon cancer cells. Carcinogenesis Aug;30(8),1416-1423. Epub 2009 Jun 15.

Nian, H., Delage, B., Ho, E., Dashwood, R.H. (2009) Modulation of histone deacetylase activity by dietary isothiocyanates and allyl sulfides: studies with sulforaphane and garlic organosulfur compounds. Environ. Mol. Mutagen. Apr;50(3), 213-221. Review.

Ahern, Kevin

Educational Songs

Ahern, K. and Rajagopal, I. (2008) "Central Dogma Zen", Biochem. Mol. Biol. Educ.

Ahern, K. (2008) "Gluconeogenesis", Biochem. Mol. Biol. Educ.

Ahern, K. (2008) “Translation” Biochem. Mol. Biol. Educ. 36, p. 88.

Ahern, K. (2008) “When Acids Are Synthesized” Biochem. Mol. Biol. Educ. 36, p. 243 Ahern, K. (2008) “Biochemistry Pie” Biochem. Mol. Biol. Educ. 36, 380-381.

Ahern, K. (2008) “Gluconeogenesis” Biochem. Mol. Biol. Educ. 36, 443.

Columns

Ahern, K. (2008) “WebWatch,” BioTechniques, Vol. 44, 12 columns. Ahern, K. (2008) “Best of the Web,” Gen. Eng. News, Vol. 28, 22 columns.

Baird, William

Hooven, L. and Baird, W. (2008) Proteomic Analysis of MCF-7 Cells Treated with Benzo[a]pyrene, Dibenzo[a]pyrene, Coal Tar Extract, and Diesel Exhaust Extract. J. Toxicology.

Barbar, Elisar

Benison, G., Karplus, P.A. and Barbar, E. (2008) Interplay of Ligand Binding and Quaternary Structure in the Diverse Interactions of Dynein Light Chain LC8. J. Mol. Biol. 384, 954-966.

Hall, J., Hall, A., Pursifull, N. and Barbar, E. (2008) Differences in Dynamic Structure of LC8 Monomer, Dimer and Dimer-Peptide Complexes. Biochemistry 47, 11940-11952.

Barbar, E. (2008) Dynein Light Chain LC8 is a Dimerization Hub Essential in Diverse Protein Networks. Biochemistry 47, 503-508. (New Concepts in Biochemistry—chosen as a Hot Article).

Beckman, Joe

Vargas, M.R., Pehar, M., Díaz-Amarilla, P.J., Beckman, J.S., Barbeito, L. (2008) Transcriptional profile of primary astrocytes expressing ALS-linked mutant SOD1. J. Neurosci. Res. 86, 3515-1525.

Robinson, K.M., Janes, M.S., Beckman, J.S. (2008) The selective detection of mitochondrial superoxide by live cell imaging. Nat. Protoc. 3, 941-947.

Cassina, P., Cassina, A., Pehar, M., Castellanos, R., Gandelman, M., de León, A., Robinson, K.M., Mason, R.P., Beckman, J.S., Barbeito, L. and Radi, R. (2008) Mitochondrial dysfunction in SOD1G93A-bearing astrocytes promotes motor neuron degeneration: prevention by mitochondrial-targeted antioxidants. J. Neurosci. 28, 4115-4122.

Traber, M.G., Frei, B. and Beckman, J.S. (2008) Vitamin E revisited: do new data validate benefits for chronic disease prevention? Curr. Opin. Lipidol. 19, 30-38.

Frei, Balz

Drake, V.J., Frei, B. and Bouley, L.M. (2008) An error in the US Department of Agriculture nutrition database results in vitamin A values that are 6 times too high. Am. J. Clin. Nutr. 87, 1067-1068.

Frei, B. and Lawson, S. (2008) Vitamin C and cancer revisited. Proc. Natl. Acad. Sci. USA 105, 11037-11038.

Visioli, F., Smith, A., Frei, B. and Hagen, T. (2008) Lipoic acid significantly restores, in rats, the age-related decline in vasomotion. Br. J. Pharmacol. 153, 1615-1622.

Zhang, W., Bird, K.E., McMillen, T.S., LeBoeuf, R.C., Hagen, T.M. and Frei, B. (2008) Dietary α-lipoic acid supplementation inhibits atherosclerotic lesion development in apoE-/- and apoE/LDL receptor-/- mice. Circulation 117, 421-428.

Traber, M.G., Frei, B. and Beckman, J.S. (2008) Vitamin E revisited: do new data validate benefits for chronic disease prevention? Current Opinion in Lipidology 19, 30-38.

Frei, B., Lawson, S., Levine, M., Chen, Q. and Espey, M.G. (2008) Reply to Borst: Randomized clinical trials of high-dose intravenous vitamin C in cancer patients are warranted. Proc. Natl. Acad. Sci. USA 105, E96. www.pnas.org/cgi/doi/10.1073/pnas.0810008105.

Freitag, Michael

Lewis, Z.A., Honda, S., Khlafallah, T.K., Jeffress, J.K., Freitag, M., Mohn, F., Schübeler, D. and Selker, E.U. (2008) Relics of repeat-induced point mutation direct heterochromatin organization in Neurospora crassa. Genome Research (in press).

Pomraning, K.R., Smith, K.M. and Freitag, M. (2008) Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods (doi:10.1016/j.ymeth.2008.09.022) [Published online Oct. 21, 2008].

Smith, K.M., Kothe, G.O., Matsen, C.B., Khlafallah, T.K., Adhvaryu, K.K., Hemphill, M., Freitag, M., Motamedi, M.R. and Selker, E.U. (2008) The fungus Neurospora crassa displays telomeric silencing mediated by multiple sirtuins and by methylation of histone H3 lysine 9. Epigenetics & Chromatin 1:5 (doi:10.1186/1756-8935-1-5).

Lee, D.W., Freitag, M., Selker, E.U. and Aramayo, R. (2008) A cytosine methyltransferase homologue is essential for sexual development in Aspergillus nidulans. PLoS ONE 3:e2531.doi:10.1371/journal.pone.0002531.

Freitag, C.M., Cabrera, Y., Williams, M., Freitag, M. and Morrell, J.J. (2008) Fungi colonizing exposed durable wood in Hilo, HI. Inoculum 59, 29.

Uchida, M., Mouriño-Pérez, R.R., Freitag, M., Bartnicki-García, S. and Roberson, R.W. (2008) Microtubule Dynamics and the Role of Molecular Motors in Neurospora crassa. Fungal Genetics and Biology 45, 683-692.

Jacobson, D.J., Raju, N.B. and Freitag, M. (2008) Evidence for the absence of meiotic silencing by unpairied DNA in Neurospora tetrasperma. Fungal Genetics and Biology 45, 351-362. This work was also featured on the journal cover.

Gombart, Fritz

Gombart, A.F., Bhan, I., Borregaard, N., Tamez, H., Camargo, C. Jr., Koeffler, H.P. and Thadhani, R. Low plasma cathelicidin antimicrobial peptide (hCAP18) predicts increased infectious disease mortality in hemodialysis. Clinical Infectious Diseases, in press.

Uh, A., Nicholson, R.C., Gonzalez, G.V., Simmons, C.F., Gombart, A., Smith, R. and Equils, O. (2008) Lipopolysaccharide stimulation of trophoblasts induces corticotropin-releasing hormone expression through MyD88. American Journal of Obstetrics and Gynecology 199, 317.e1-317.e6.

Akagi, T., Saitoh, T., O'Kelly, J., Akira, S., Gombart, A.F. and Koeffler, H.P. (2008) Impaired response to GM-CSF and G-CSF, and enhanced apoptosis in C/EBPβ-deficient hematopoietic cells. Blood 111, 2999-3004.

Greenwood, J.

Sprague, C.R., Fraley, T.S., Jang, H.S., Lal, S. and Greenwood, J.A. (2008) Phosphoinositide binding to the substrate regulates susceptibility to proteolysis by calpain. J. Biol. Chem. 283, 9217-9223.

Gross, Michael

Pagliardini, S., Ren, J., Gray, P., VanDunk, C., Gross, M.K., Goulding, M. and Greer, J. (2008) Central Respiratory Rhythmogenesis is Abnormal in Lbx1 Deficient Mice. Journal of Neuroscience. (in press).

Kioussi, C. and Gross, M.K. (2008) How to Build Transcriptional Network Models of Mammalian Pattern Formation. PloS One 3, e2179.

Shih, H.P., Gross, M.K. and Kioussi, C. (2008) Muscle Development: Forming Head and Trunk Muscles. Acta Histochemica 110, 97-108.

Hagen, Tory

Dixon, B.M., Heath, S.-H., Suh, J.S. and Hagen, T.M. (2008) Assessment of endoplasmic reticulum glutathione redox stataus is confounded by extensive ex vivo oxidation. Antiox. Redox. Signal. 10, 963-972.

Smith, A.R., Visioli, F., Frei, B. and Hagen, T.M (2008) Lipoic acid significantly restores, in rats, the age-related decline in vasomotion. Br. J. Pharmacol. 153, 1615-1622. (Editor's pick and comment.)

Zhang, W-J., Bird, K.E., McMillen, T.S., LeBoeuf, R.C., Hagen, T.M. and Frei, B. (2008) Dietary α-lipoic acid supplementation inhibits atherosclerotic lesion development in ApoE-/- and ApoE/LDL receptor^-/- mice. Circulation 117, 421-428.

Petersen Shay, K. and Hagen, T.M. (2008) Age-associated impairment of Akt phosphorylation in primary rat hepatocytes is remediated by alpha-lipoic acid through PI3 kinase, PTEN, and PP2A. Biogerontology. in press.

Petersen Shay, K., Moreau, R.F., Smith, E.J. and Hagen, T.M. (2008) Is alpha-lipoic acid a scavenger of reactive oxygen species in vivo? Evidence for its initiation of stress signaling pathways that promote endogenous antioxidant capacity. IUBMB Life 60, 362-367.

Karplus, P. Andrew

Colussi, T., Parsonage, D., Boles, W., Matsuoka, T., Mallet, T.C., Karplus, P.A. and Claiborne, A. (2008) Structure of α-glycerophosphate oxidase from Streptococcus sp.: A template for the mitochondrial α-glycerophosphate dehydrogenase. Biochemistry 47, 965-977.

Manning, V., Hamilton, S.M., Karplus, P.A. and Ciuffetti, L.M. (2008) The Arg-Gly-Asp-containing, solvent-exposed loop of Ptr ToxA is required for internalization. Mol. Plant Microbe Int. 21, 315-325.

Karplus, P.A., Shapavalov, M.D., Dunbrack, R.S. Jr. and Berkholz, D.S. (2008) A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions. Acta Cryst. D. 64, 335-336.

Parsonage, D., Karplus, P.A. and Poole, L.B. (2008) Substrate Specificity and Redox Potential of AhpC, a Bacterial Peroxiredoxin. Proc. Nat. Acad. Sci. 105, 8209-8214.

Meek, L., Martin, R.C., Shan, X., Karplus, P.A., Mok, D.W.S. and Mok, M.C. (2008) Isolation of legume glycosyltransferases and active site mapping of the Phaseolus lunatus zeatin O-glucosyltransferase ZOG1. J. Plant Growth Regul. 27, 192-201.

Wallen, J.R., Paige, C., Mallett, T.C., Karplus, P.A. and Claiborne, A. (2008) Pyridine nucleotide complexes with Bacillus anthracis coenzyme A disulfide reductase: a structural analysis of dual NAD(P)H specificity. Biochemistry 47, 5182-5193.

Berkholz, D.S., Faber, H.R., Savvides, S.N. and Karplus, P.A. (2008) Catalytic cycle of human glutathione reductase near 1 Å resolution. J. Mol. Biol. 382, 371-384.

Benison, G., Chiodo, M., Karplus, P.A. and Barbar, E. (2008) Interplay of Ligand Binding and Phosphorylation in the Regulation of Dynein Light Chain LC8. J. Mol. Biol. 384, 954-966.

Simmons, C.R., Krishnamoorthy, K., Granett, S.L., David, J., Schuller, D.J., Dominey Jr., J.E., Begley, T.P., Stipanuk, M.H. and Karplus, P.A. (2008) A Putative Fe²⁺-bound Persulfenate Intermediate in Cysteine Dioxygenase. Biochemistry 47, 11390-11392.

Nelson, K.J., Parsonage, D., Hall, A., Karplus, P.A. and Poole, L.B. (2008) Cysteine pKa values for the bacterial peroxiredoxin AhpC. Biochemistry 47, 12860-12868.

Mathews, Chris

Mannava, S., Grachtchouk, V., Wheeler, L.J., Im, M., Zhuang, D., Slavina, E.G., Mathews, C.K., Shewach, D.S. and Nikiforov, M.A. (2008) Direct Role of Nucleotide Metabolism in C-Myc-dependent Control of Melanoma Cells Proliferation. Cell Cycle 7, 1-9.

Pursell, Z.F., MacDonald, J.T., Mathews, C.K. and Kunkel, T.A. (2008) Trace Amounts of 8-oxo-dGTP in Mitochondrial Pools Reduce DNA Polymerase γ Replication Fidelity. Nucl. Ac. Res. 36, 2174-2181.

Mathews, C.K. (2008) Academic Life—The Whole Package (Invited Reflections Article). J. Biol. Chem. 283, 20,613-20,620.

Mathews, C.K. and Wheeler, L.J. (2008) Measuring DNA Precursor Pools in Mitochondria. In J. Stuart (ed.) Mitochondrial DNA: Methods and Protocols, Second Edition. Methods in Molecular Biology Series, Humana Press, Totowa, NJ, in press.

Schimerlik, Michael

Simonich MT, McQuistan T, Jubert C, Pereira C, Hendricks JD, Schimerlik M, Zhu B, Dashwood RH, Williams DE, Bailey GS. (2008) Low-dose dietary chlorophyll inhibits multi-organ carcinogenesis in the rainbow trout. Food Chem Toxicol. 46, 1014-24.

van Holde, Ken

van Holde, K. (2008) Learning How to be a Scientist. J. Biol. Chem. 283, 4461.

Ahern, Kevin

Columns

Ahern, K. "WebWatch", Biotechniques (2007) Vol. 42, 6 columns.

Ahern, K. "WebWatch", Biotechniques (2007) Vol. 43, 6 columns.

Ahern, K. "Best of the Web", Gen. Eng. News (2007) Vol. 27, 21 columns.

Educational Songs

Ahern, K. (2007) "Hemoglobin's Moving Around". Biochem. Mol. Biol. Educ. (2007) 35, page 478.

Ahern, K. (2007) "The Tao of Hormones". Biochem. Mol. Biol. Educ. (2007) 35, page 226.

Ahern, K. (2007) "When Acids Get Oxidized". Biochem. Mol. Biol. Educ. 35, page 78.

Anderson, Sonia

Roberts, B.R., Tainer, J.A., Getzoff, E.D., Malencik, D.A., Anderson, S.R., Bomben, V.C., Meyers, K.R., Karplus, P.A., Beckman, J.S. (2007) Structural Characterization of Zinc-deficient Human Superoxide Dismutase and Implications for ALS. J Mol Biol 373(4):877-90. Epub 2007 Aug 2.

Baird, William

Courter, L.A., Musafia-Jeknic, T., Fischer, K., Bildfell, R., Giovanni, J., Pereira, C. and Baird, W.M. (2007) Urban Dust Particulate Matter Alters PAH-Induced Carcinogenesis by Inhibition of CYP1A1 and CYP1B1. Toxicol Sci. Jan., 95(1), 63-73.

Courter, L.A., Pereira, C. and Baird, W.M. (2007) Diesel exhaust influences carcinogenic PAH-induced genotoxicity in human breast epithelial cells in culture. Mutation Research 625, 72-82.

Barbar, Elisar

Song, Y., Benison, G., Nyarko, A., Hays, T.S. and Barbar, E. (2007) Potential Role for Phosphorylation in Differential Regulation of the Assembly of Dynein Light Chains. J. Biol. Chem. 282, 17272-17279.

Benison, G., Karplus, P.A. and Barbar, E. (2007) Structure and Dynamics of LC8 Complexes with KXTQT-Motif Peptides: Swallow and Dynein Intermediate Chain Compete for a Common Site. J. Mol. Biol. 371, 457-468.

Benison, G., Berkholz, D., and Barbar, E. (2007) Protein Assignments Without Peak Lists Using Higher-Order Spectra. J. Magn. Reson. 190, 8-16.

Beckman, Joe

Pacher, P., Beckman, J.S., Liaudet, L. (2007) Nitric oxide and peroxynitrite in health and disease. Physiol Rev. 87, 315–424.

Ye, Y., Quijano, C., Robinson, K.M., Ricart, K.C., Strayer, A.L., Sahawneh, M.A., Shacka, J.J., Kirk, M., Barnes, S., Accavitti-Loper, M.A., Radi, R., Beckman, J.S., Estevez, A.G. (2007) Prevention of peroxynitrite-induced apoptosis of motor neurons and PC12 cells by tyrosine-containing peptides. J Biol Chem. 282, 6324–6337. Epub Jan 2.

Pehar, M., Vargas, M.R., Robinson, K.M., Cassina, P., Diaz-Amarilla, P.J., Hagen, T.M., Radi, R., Barbeito, L., Beckman, J.S. (2007) Mitochondrial superoxide production and nuclear factor erythroid 2-related factor 2 activation in p75 neurotrophin receptor-induced motor neuron apoptosis. J Neurosci. 27(29):7777-85.

Roberts, B.R., Tainer, J.A., Getzoff, E.D., Malencik, D.A., Anderson, S.R., Bomben, V.C., Meyers, K.R., Karplus, P.A., Beckman, J.S. (2007) Structural Characterization of Zinc-deficient Human Superoxide Dismutase and Implications for ALS. J Mol Biol 373(4):877-90. Epub 2007 Aug 2.

Pacher, P., Beckman, J.S, Liaudet, L. (2007) Nitric oxide and peroxynitrite in health and disease. Physiol Rev. 87(1):315-424. Review.

Frei, Balz

Zhu, B., Zhao, H.T., Kalyanaraman, B., Liu, J., Guo-Qiang Shan, G.Q., Du, Y.G. and Frei, B. (2007) Mechanism of metal-independent decomposition of organic hydroperoxides and formation of alkoxyl radicals by halogenated quinones. Proc. Natl. Acad. Sci. USA 104, 3698-3702.

Zhang, W., Wei, H., Hagen, T. and Frei, B. (2007) αAlpha-Lipoic acid attenuates LPS-induced inflammatory responses by activating the phosphoinositide 3-kinase/Akt signaling pathway. Proc. Natl. Acad. Sci. USA 104, 4077-4082.

Blumberg, J.B. and Frei, B. (2007) Why clinical trials of vitamin E and cardiovascular diseases may be fatally flawed. Commentary on "The Relationship between Dose of Vitamin E and Suppression of Oxidative Stress". Free Radic. Biol. Med. 43, 1374-1376.

Freitag, Michael

Riquelme, M., Bartnicki-Garcia, S., Gonzalez-Prieto, J.M., Sanchez-Leon, E., Verdin-Ramos, J.A., Beltran-Aguilar, A. and Freitag, M. (2007) Spitzenkorper localization and intracellular traffic of GFP-labeled CHS-3 and CHS-6 chitin synthases in living hyphae of Neurospora crassa. Eukaryot. Cell. 6, 1853-1864 (journal cover).

Connolly, L. and Freitag, M. (2007) Construction of genomic libraries from Neurospora crassa with an improved BigEasy™ 2.0 linear cloning system. eLucidations 7, 8-12. (not peer-reviewed)

Freitag, C., Freitag, M. and Morrell, J.J. (2007) Detecting fungal DNA in treated and non-treated wood. Proceedings of the International Research Group on Wood Preservation (paper prepared for the 38^th International Meeting in Jackson Hole, WY). (not peer-reviewed)

Perkins, D.D., Freitag, M., Shrode, L.A., Selker, E.U. and Ebbole, D.J. (2007) Recurrent locus-specific mutation resulting from a cryptic ectopic insertion in Neurospora. Genetics 175, 527-544.

Gross, Michael

Shih, H.P., Gross, M.K. and Kioussi C. (2007) Expression Pattern of the Homeodomain Transcription Factor Pitx2 during Muscle Development. Gene Expression Patterns 7(4), 441-51.

Shih, H.P., Gross, M.K. and Kioussi C. (2007) Cranial Muscle Defects of Pitx2 Mutants Result from Specification Defects in the First Branchial Arch. Proc Natl Acad Sci USA 104(14), 5907-5912.

Greenwood, J.

Full, S.J., Deinzer, M.L., Ho, P.S. and Greenwood, J.A. (2007) Phosphoinositide binding regulates □-actinin CH2 domain structure: analysis by hydrogen/deuterium exchange mass spectrometry. Protein Sci. 16, 2597-2604.

Hagen, Tory

Visioli, F, Hagen, TM. 2007) Nutritional strategies for healthy cardiovascular aging: focus on micronutrients. Pharmacol Res. 55, 199-206.

McMackin C.J., Widlansky M.E., Hamburg N.M., Huang A.L., Weller S., Holbrook M., Gokce N., Hagen T.M., Keaney J.F. Jr, Vita J.A. (2007) Effect of combined treatment with alpha-Lipoic acid and acetyl-L-carnitine on vascular function and blood pressure in patients with coronary artery disease. J Clin Hypertens. 9, 249-255.

Zang, W-J, Wei, H., Hagen, T.M., Frei, B. (2007) α-Lipoic acid attenuates lipopolysaccharide-induced inflammatory responses in vitro and in vivo by activating the phosphoinositide 3-kinase/Akt signaling pathway. Proc. Natl. Acad. Sci. 104, 4077-4082.

Pehar, M., Vargas, M.R., Robinson K.M., Cassina, P., Diaz-Amarilla, P.J., Hagen, T.M., Radi, R., Barbeito, L., Beckman, J.S. (2007) Mitochondrial superoxide production and nuclear factor erythroid 2-related factor 2 activation in p75 neurotrophin receptor-induced motor neuron apoptosis. J Neurosci. 27, 7777-7785.

Milgram, N.W., Araujo, J.A., Hagen, T.M., Treadwell B.V., Ames, B, N. (2007) Acetyl-L-carnitine and alpha-lipoic acid supplementation of aged beagle dogs improves learning in two landmark discrimination tests. FASEB J. 21, 3756-3762.

Bogani P, Canavesi M, Hagen TM, Visioli F, Bellosta S. (2007) Thiol supplementation inhibits metalloproteinase activity independent of glutathione status. Biochem Biophys Res Commun. 363, 651-655.

Ho, P. Shing

Voth, A.R. and Ho, P.S. (2007) The role of halogen bonding in inhibitor recognition and binding by protein kinases. Curr. Top. Med. Chem. 7, 1336-1348.

Voth, A.R., Hays, F. A. and Ho, P.S. (2007) Directing Macromolecular Conformation through Halogen Bonds. Proc. Natl. Acad. Sci. USA 104, 6188-6193 (From the cover & In this Issue feature).

Khuu, P., Sandor, M., DeYoiung, J. and Ho, P.S. (2007) Phylogenomic analysis of the emergence of GC-rich transcription elements. Proc. Natl. Acad. Sci. USA 104, 16528-16533.

Daniels, M., Hart, L.P., Ho, P.S., Ballini, J.P., Vigny, P., Brochon, J.C. (2007) Intrinsic fluorescence of B and Z forms of poly d(G-m(5)C)·poly d(G-m(5)C), a synthetic double-stranded DNA: spectra and lifetimes by the maximum entropy method. Photochem. Photobiol. Sci. 6, 883-893.

Full, S.J., Deinzer, M.L., Ho, P.S. and Greenwood, J. (2007) Phosphoinositide binding regulates □-actinin CH2 domain structure: Analysis by hydrogen/deuterium exchange mass spectrometry. Protein Sci. 16, 2597-2604.

Hsu, Victor

de Vries, S.J., van Dijk, A.D.J., Krzeminski, M, van Dijk, M., Thureau, A., Hsu, V.L., Wassenaar, T., Bonvin, A.M.J.J. (2007) HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69, 726-733.

Karplus, P. Andrew

Li, Q., Nance, M.R., Kulikauskas, R., Nyberg, K., Fehon, R., Karplus, P.A., Bretscher, A.P. & Tesmer, J.J.G. (2007) Self-masking in intact ERM-merlin proteins: an active role for the enigmatic a-helical domain. J. Mol. Biol., 365, 1446-1459.

Benison, G., Karplus, P.A., & Barbar, E. (2007) Structure and Dynamics of LC8 Complexes with KXTQT-Motif Peptides: Swallow and Dynein Intermediate Chain Compete for a Common Site. J. Mol. Biol. 371, 457-468.

Roberts, B.R., Tainer, J.A., Getzoff, E.D., Malencik, D.A., Anderson, S.R., Bomben, V.C., Myers, K.R., Karplus, P.A. & Beckman, J.S. (2007) “Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS.” J. Mol. Biol. 373, 877-890.

Karplus, P.A. & Hall, A. (2007) “Structural Survey of the Peroxiredoxins” Subcell. Biochem. 44, 41-60. [or in Peroxiredoxin Systems: Structures and Functions (L. Flohe & J. R. Harris, eds.) Springer, pp. 41-60.]

Kioussi, Chrissa

Shih H.P., Gross, M.K. and Kioussi C. (2007) Expression Pattern of the Homeodomain Transcription Factor Pitx2 during Muscle Development. Gene Expression Patterns 7(4), 441-51.

Shih, H.P., Gross, M.K. and Kioussi C. (2007) Cranial Muscle Defects of Pitx2 Mutants Result from Specification Defects in the First Branchial Arch. Proc Natl Acad Sci USA 104(14), 5907-5912.

Kioussi, C., Appu M., Löhr, C.V., Fischer, K.A., Amparan,D., Bajaj, G. Yang, J., and . Ishmael, J.E. (2007) Co-expression of Myosin II Regulatory Light Chain and the NMDAR1 Subunit in Neonatal and Adult Mouse Brain. Brain Res. Bull. 74, 439-451.

Mathews, Chris

Mathews, C. K. (2007) The News of Science, a Colloquium-style Course Designed to Promote Broad Scientific Awareness. Biochem. Mol. Biol. Education 35, 101–104.

Marusyk, A., Wheeler, L.J., Mathews, C.K. and DeGregori, J. (2007) p53 Mediates Sencescence-like Arrest Induced by Chronic Replicative Stress. Mol. Cell Biol. Mol. Cell. Biol. 17, 5336-5351.

Mathews, C. K. and Song, S. (2007) Maintaining Precursor Pools for Mitochondrial DNA Replication. FASEB J. 21, 2294–2303.

Liskay, R.M., Wheeler, L.J., Mathews, C.K. and Erdeniz, R. (2007) Involvement of Deoxycytidylate Deaminase in the Response to S_n1-type Methylation Inhiibitors in Budding Yeast. Current Biology 17, R755-R757.

Merrill, Gary

Koc, A, and Merrill, G.F. (2007) Checkpoint deficient rad53-11 yeast cannot accumulate dNTPs in response to DNA damage. Biochem Biophys Res Commun. 2007 Feb 9, 353(2), 527-30.

Bondareva, A.A., Capececchi, M.R., Iverson, S.V., Li, Y., Lopez, N.I., Lucas, O., Merrill, G.F., Prigge, J.R., Siders, A.M., Wakamiya, M., Wallin, S.L. and Schmidt, E.E. (2007) Effects of thioredoxin reductase-1 deletion on embryogenesis and transcriptome. Free Radic. Biol. Med. 43, 911-923. doi:10.1016/j.freeradbiomed.2007.05.026.

Schimerlik, Michael

Yan, X., Perez, E., Leid, M., Schimerlik, M.I., de Lera, A., Deinzer, M.L. (2007) Deuterium exchange and mass spectrometry reveal the interaction difference of two synthetic modulators of RXRalpha LBD. Protein Science 16, 2491-2501.

Liu, D., Guo. J., Luo, Y., Broderick, D.J., Schimerlik, M.I., Pezzuto, J.M. & van Breemen, R.B. (2007) Screening for ligands of human retinoid X receptor-alpha using ultrafiltration mass spectrometry. Anal. Chem. 79, 9398-9402.

van Holde, Ken

van Holde K, Zlatanova J. (2007) Chromatin fiber structure: Where is the problem now? Semin Cell Dev Biol. 18, 651-658.

Ahern, Kevin

Columns

Ahern, K. "WebWatch", Biotechniques (2007) Vol. 42, 6 columns.

Ahern, K. "WebWatch", Biotechniques (2007) Vol. 43, 6 columns.

Ahern, K. "Best of the Web", Gen. Eng. News (2007) Vol. 27, 21 columns.

Educational Songs

Ahern, K. (2007) "Hemoglobin's Moving Around". Biochem. Mol. Biol. Educ. (2007) 35, page 478. Ahern, K. (2007) "The Tao of Hormones". Biochem. Mol. Biol. Educ. (2007) 35, page 226.

Ahern, K. (2007) "When Acids Get Oxidized". Biochem. Mol. Biol. Educ. 35, page 78.

Anderson, Sonia

Roberts, B.R., Tainer, J.A., Getzoff, E.D., Malencik, D.A., Anderson, S.R., Bomben, V.C., Meyers, K.R., Karplus, P.A., Beckman, J.S. (2007) Structural Characterization of Zinc-deficient Human Superoxide Dismutase and Implications for ALS. J Mol Biol 373(4):877-90. Epub 2007 Aug 2.

Baird, William

Courter, L.A., Musafia-Jeknic, T., Fischer, K., Bildfell, R., Giovanni, J., Pereira, C. and Baird, W.M. (2007) Urban Dust Particulate Matter Alters PAH-Induced Carcinogenesis by Inhibition of CYP1A1 and CYP1B1. Toxicol Sci. Jan., 95(1), 63-73.

Courter, L.A., Pereira, C. and Baird, W.M. (2007) Diesel exhaust influences carcinogenic PAH-induced genotoxicity in human breast epithelial cells in culture. Mutation Research 625, 72-82.

Barbar, Elisar

Song, Y., Benison, G., Nyarko, A., Hays, T.S. and Barbar, E. (2007) Potential Role for Phosphorylation in Differential Regulation of the Assembly of Dynein Light Chains. J. Biol. Chem. 282, 17272-17279.

Benison, G., Karplus, P.A. and Barbar, E. (2007) Structure and Dynamics of LC8 Complexes with KXTQT-Motif Peptides: Swallow and Dynein Intermediate Chain Compete for a Common Site. J. Mol. Biol. 371, 457-468.

Benison, G., Berkholz, D., and Barbar, E. (2007) Protein Assignments Without Peak Lists Using Higher-Order Spectra. J. Magn. Reson. 190, 8-16.

Beckman, Joe

Pacher, P., Beckman, J.S., Liaudet, L. (2007) Nitric oxide and peroxynitrite in health and disease. Physiol Rev. 87, 315–424.

Ye, Y., Quijano, C., Robinson, K.M., Ricart, K.C., Strayer, A.L., Sahawneh, M.A., Shacka, J.J., Kirk, M., Barnes, S., Accavitti-Loper, M.A., Radi, R., Beckman, J.S., Estevez, A.G. (2007) Prevention of peroxynitrite-induced apoptosis of motor neurons and PC12 cells by tyrosine-containing peptides. J Biol Chem. 282, 6324–6337. Epub Jan 2.

Pehar, M., Vargas, M.R., Robinson, K.M., Cassina, P., Diaz-Amarilla, P.J., Hagen, T.M., Radi, R., Barbeito, L., Beckman, J.S. (2007) Mitochondrial superoxide production and nuclear factor erythroid 2-related factor 2 activation in p75 neurotrophin receptor-induced motor neuron apoptosis. J Neurosci. 27(29):7777-85.

Roberts, B.R., Tainer, J.A., Getzoff, E.D., Malencik, D.A., Anderson, S.R., Bomben, V.C., Meyers, K.R., Karplus, P.A., Beckman, J.S. (2007) Structural Characterization of Zinc-deficient Human Superoxide Dismutase and Implications for ALS. J Mol Biol 373(4):877-90. Epub 2007 Aug 2.

Pacher, P., Beckman, J.S, Liaudet, L. (2007) Nitric oxide and peroxynitrite in health and disease. Physiol Rev. 87(1):315-424. Review.

Frei, Balz

Zhu, B., Zhao, H.T., Kalyanaraman, B., Liu, J., Guo-Qiang Shan, G.Q., Du, Y.G. and Frei, B. (2007) Mechanism of metal-independent decomposition of organic hydroperoxides and formation of alkoxyl radicals by halogenated quinones. Proc. Natl. Acad. Sci. USA 104, 3698-3702.

Zhang, W., Wei, H., Hagen, T. and Frei, B. (2007) αAlpha-Lipoic acid attenuates LPS-induced inflammatory responses by activating the phosphoinositide 3-kinase/Akt signaling pathway. Proc. Natl. Acad. Sci. USA 104, 4077-4082.

Blumberg, J.B. and Frei, B. (2007) Why clinical trials of vitamin E and cardiovascular diseases may be fatally flawed. Commentary on "The Relationship between Dose of Vitamin E and Suppression of Oxidative Stress". Free Radic. Biol. Med. 43, 1374-1376.

Freitag, Michael

Riquelme, M., Bartnicki-Garcia, S., Gonzalez-Prieto, J.M., Sanchez-Leon, E., Verdin-Ramos, J.A., Beltran-Aguilar, A. and Freitag, M. (2007) Spitzenkorper localization and intracellular traffic of GFP-labeled CHS-3 and CHS-6 chitin synthases in living hyphae of Neurospora crassa. Eukaryot. Cell. 6, 1853-1864 (journal cover).

Connolly, L. and Freitag, M. (2007) Construction of genomic libraries from Neurospora crassa with an improved BigEasy™ 2.0 linear cloning system. eLucidations 7, 8-12. (not peer-reviewed)

Freitag, C., Freitag, M. and Morrell, J.J. (2007) Detecting fungal DNA in treated and non-treated wood. Proceedings of the International Research Group on Wood Preservation (paper prepared for the 38^th International Meeting in Jackson Hole, WY). (not peer-reviewed)

Perkins, D.D., Freitag, M., Shrode, L.A., Selker, E.U. and Ebbole, D.J. (2007) Recurrent locus-specific mutation resulting from a cryptic ectopic insertion in Neurospora. Genetics 175, 527-544.

Gross, Michael

Shih, H.P., Gross, M.K. and Kioussi C. (2007) Expression Pattern of the Homeodomain Transcription Factor Pitx2 during Muscle Development. Gene Expression Patterns 7(4), 441-51.

Shih, H.P., Gross, M.K. and Kioussi C. (2007) Cranial Muscle Defects of Pitx2 Mutants Result from Specification Defects in the First Branchial Arch. Proc Natl Acad Sci USA 104(14), 5907-5912.

Greenwood, J.

Full, S.J., Deinzer, M.L., Ho, P.S. and Greenwood, J.A. (2007) Phosphoinositide binding regulates □-actinin CH2 domain structure: analysis by hydrogen/deuterium exchange mass spectrometry. Protein Sci. 16, 2597-2604.

Hagen, Tory

Visioli, F, Hagen, TM. 2007) Nutritional strategies for healthy cardiovascular aging: focus on micronutrients. Pharmacol Res. 55, 199-206.

McMackin C.J., Widlansky M.E., Hamburg N.M., Huang A.L., Weller S., Holbrook M., Gokce N., Hagen T.M., Keaney J.F. Jr, Vita J.A. (2007) Effect of combined treatment with alpha-Lipoic acid and acetyl-L-carnitine on vascular function and blood pressure in patients with coronary artery disease. J Clin Hypertens. 9, 249-255.

Zang, W-J, Wei, H., Hagen, T.M., Frei, B. (2007) α-Lipoic acid attenuates lipopolysaccharide-induced inflammatory responses in vitro and in vivo by activating the phosphoinositide 3-kinase/Akt signaling pathway. Proc. Natl. Acad. Sci. 104, 4077-4082.

Pehar, M., Vargas, M.R., Robinson K.M., Cassina, P., Diaz-Amarilla, P.J., Hagen, T.M., Radi, R., Barbeito, L., Beckman, J.S. (2007) Mitochondrial superoxide production and nuclear factor erythroid 2-related factor 2 activation in p75 neurotrophin receptor-induced motor neuron apoptosis. J Neurosci. 27, 7777-7785.

Milgram, N.W., Araujo, J.A., Hagen, T.M., Treadwell B.V., Ames, B, N. (2007) Acetyl-L-carnitine and alpha-lipoic acid supplementation of aged beagle dogs improves learning in two landmark discrimination tests. FASEB J. 21, 3756-3762.

Bogani P, Canavesi M, Hagen TM, Visioli F, Bellosta S. (2007) Thiol supplementation inhibits metalloproteinase activity independent of glutathione status. Biochem Biophys Res Commun. 363, 651-655.

Ho, P. Shing

Voth, A.R. and Ho, P.S. (2007) The role of halogen bonding in inhibitor recognition and binding by protein kinases. Curr. Top. Med. Chem. 7, 1336-1348.

Voth, A.R., Hays, F. A. and Ho, P.S. (2007) Directing Macromolecular Conformation through Halogen Bonds. Proc. Natl. Acad. Sci. USA 104, 6188-6193 (From the cover & In this Issue feature).

Khuu, P., Sandor, M., DeYoiung, J. and Ho, P.S. (2007) Phylogenomic analysis of the emergence of GC-rich transcription elements. Proc. Natl. Acad. Sci. USA 104, 16528-16533.

Daniels, M., Hart, L.P., Ho, P.S., Ballini, J.P., Vigny, P., Brochon, J.C. (2007) Intrinsic fluorescence of B and Z forms of poly d(G-m(5)C)·poly d(G-m(5)C), a synthetic double-stranded DNA: spectra and lifetimes by the maximum entropy method. Photochem. Photobiol. Sci. 6, 883-893.

Full, S.J., Deinzer, M.L., Ho, P.S. and Greenwood, J. (2007) Phosphoinositide binding regulates □-actinin CH2 domain structure: Analysis by hydrogen/deuterium exchange mass spectrometry. Protein Sci. 16, 2597-2604.

Hsu, Victor

de Vries, S.J., van Dijk, A.D.J., Krzeminski, M, van Dijk, M., Thureau, A., Hsu, V.L., Wassenaar, T., Bonvin, A.M.J.J. (2007) HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69, 726-733.

Karplus, P. Andrew

Li, Q., Nance, M.R., Kulikauskas, R., Nyberg, K., Fehon, R., Karplus, P.A., Bretscher, A.P. & Tesmer, J.J.G. (2007) Self-masking in intact ERM-merlin proteins: an active role for the enigmatic a-helical domain. J. Mol. Biol., 365, 1446-1459.

Benison, G., Karplus, P.A., & Barbar, E. (2007) Structure and Dynamics of LC8 Complexes with KXTQT-Motif Peptides: Swallow and Dynein Intermediate Chain Compete for a Common Site. J. Mol. Biol. 371, 457-468.

Roberts, B.R., Tainer, J.A., Getzoff, E.D., Malencik, D.A., Anderson, S.R., Bomben, V.C., Myers, K.R., Karplus, P.A. & Beckman, J.S. (2007) “Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS.” J. Mol. Biol. 373, 877-890.

Karplus, P.A. & Hall, A. (2007) “Structural Survey of the Peroxiredoxins” Subcell. Biochem. 44, 41-60. [or in Peroxiredoxin Systems: Structures and Functions (L. Flohe & J. R. Harris, eds.) Springer, pp. 41-60.]

Kioussi, Chrissa

Shih H.P., Gross, M.K. and Kioussi C. (2007) Expression Pattern of the Homeodomain Transcription Factor Pitx2 during Muscle Development. Gene Expression Patterns 7(4), 441-51.

Shih, H.P., Gross, M.K. and Kioussi C. (2007) Cranial Muscle Defects of Pitx2 Mutants Result from Specification Defects in the First Branchial Arch. Proc Natl Acad Sci USA 104(14), 5907-5912.

Kioussi, C., Appu M., Löhr, C.V., Fischer, K.A., Amparan,D., Bajaj, G. Yang, J., and . Ishmael, J.E. (2007) Co-expression of Myosin II Regulatory Light Chain and the NMDAR1 Subunit in Neonatal and Adult Mouse Brain. Brain Res. Bull. 74, 439-451.

Mathews, Chris

Mathews, C. K. (2007) The News of Science, a Colloquium-style Course Designed to Promote Broad Scientific Awareness. Biochem. Mol. Biol. Education 35, 101–104.

Marusyk, A., Wheeler, L.J., Mathews, C.K. and DeGregori, J. (2007) p53 Mediates Sencescence-like Arrest Induced by Chronic Replicative Stress. Mol. Cell Biol. Mol. Cell. Biol. 17, 5336-5351.

Mathews, C. K. and Song, S. (2007) Maintaining Precursor Pools for Mitochondrial DNA Replication. FASEB J. 21, 2294–2303.

Liskay, R.M., Wheeler, L.J., Mathews, C.K. and Erdeniz, R. (2007) Involvement of Deoxycytidylate Deaminase in the Response to S_n1-type Methylation Inhiibitors in Budding Yeast. Current Biology 17, R755-R757.

Merrill, Gary

Koc, A, and Merrill, G.F. (2007) Checkpoint deficient rad53-11 yeast cannot accumulate dNTPs in response to DNA damage. Biochem Biophys Res Commun. 2007 Feb 9, 353(2), 527-30.

Bondareva, A.A., Capececchi, M.R., Iverson, S.V., Li, Y., Lopez, N.I., Lucas, O., Merrill, G.F., Prigge, J.R., Siders, A.M., Wakamiya, M., Wallin, S.L. and Schmidt, E.E. (2007) Effects of thioredoxin reductase-1 deletion on embryogenesis and transcriptome. Free Radic. Biol. Med. 43, 911-923. doi:10.1016/j.freeradbiomed.2007.05.026.

Schimerlik, Michael

Yan, X., Perez, E., Leid, M., Schimerlik, M.I., de Lera, A., Deinzer, M.L. (2007) Deuterium exchange and mass spectrometry reveal the interaction difference of two synthetic modulators of RXRalpha LBD. Protein Science 16, 2491-2501.

Liu, D., Guo. J., Luo, Y., Broderick, D.J., Schimerlik, M.I., Pezzuto, J.M. & van Breemen, R.B. (2007) Screening for ligands of human retinoid X receptor-alpha using ultrafiltration mass spectrometry. Anal. Chem. 79, 9398-9402.

van Holde, Ken

van Holde K, Zlatanova J. (2007) Chromatin fiber structure: Where is the problem now? Semin Cell Dev Biol. 18, 651-658.

Ahern, Kevin

Columns

Ahern, K. "WebWatch", BioTechniques (2005) Vol. 38, 6 columns.

Ahern, K. "WebWatch", BioTechniques (2005) Vol. 39, 6 columns. Ahern, K. "On the Web", Gen. Eng. News (2005) Vol. 25, 21 columns. Technical Articles

Ahern, K. “Molecular Biology Software 2005” Gen. Eng. News, Mary Ann Liebert, Inc., Publishers (2005), Vol. 25, #16, p. 31-37.

Anderson, Sonia

McCullar, J.S., Malencik, D.A., Vogel, W.K., Crofoot, K.M., Anderson, S.R. and Filtz, T.M. (2006) Calmodulin potentiates G-protein activation of phospholipase C-3. Biochem. Pharmacol. 73 (2), 270-278.

Baird, William

Mahadevan, B., Marston, C., Dashwood, W., Li, Y., Pereira, C. and Baird, W.M. (2005) Effect of a standardized complex mixture derived from coal tar on the metabolic activation of carcinogenic polycyclic aromatic hydrocarbons in human cells in culture. Chem. Res.Toxicol. 18(2), 224-31.

Mahadevan, B., Keshava, S., Musafia-Jeknic, T., Pecaj, A., Weston, A. and Baird, W.M. (2005) Altered gene expression patterns in MCF-7 cells induced by the urban dust particulate complex mixture SRM 1649a. Cancer Research 65(4), 1257-58.

Reliene, R., Hlavacova, A., Mahadevan, B., Baird, W.M. and Schiestl, R.H. (2005) Diesel exhaust particles cause increased levels of DNA deletions after transplacental exposure in mice. Mutat. Res. 570(2), 245-252.

Hooven, L.A., Mahadevan, B., Keshava, C., Johns, C., Pereira, C., Desai, D., Amin, S., Weston, A. and Baird, W.M. (2005) Effects of Suberoylanilide hydroxamic acid and Trichostatin A on Induction of Cytochrome P450 enzymes and benzo[a]pyrene DNA adduct formation in human cells. Bioorg. Med. Chem. Lett. 15(15), 1283-1287.

Baird, W.M., Hooven, L.A. and Mahadevan, B. (2005) Carcinogenic polycyclic aromatic hydrocarbon-DNA adducts and mechanism of action. Environ. Mol. Mutagen. 45, 106-114.

Musafia-Jeknic, T., Luch, A., Seidel, A., Johns, C., Pereira, C. and Baird, W.M. (2005) Effect Of Nucleotide Sequence on the Binding of (-)-Anti-Dibenzo-[a,l]Pyrene-11,12-Diol 13,14-Epoxide to Short Oligodeoxyriboneucleotides. Polycyclic Aromatic Hydrocarbons 25, 103-111.

Mahadevan, B., Mata, J.E., Albershardt, D.J., Stevens, J.F., Pereira, C.B., Rodriguez-Proteau, R. and Baird, W.M. (2005) The effects of red raspberry extract on PAH transport across Calu-3 cell monolayer, an in vitro cell model. Int. J. Cancer Prev. 2, 129–141.

Mahadevan, B., Luch, A., Bravo, C.F., Atkin, J., Steppan, L.B., Pereira, C., Kerkvliet, N.I. and Baird, W.M. (2005) Dibenzo[a,l]pyrene induced systemic DNA adduct formation in lung tissue in vivo. Cancer Letters 227, 25-32.

Musafia-Jeknic, T., Mahadevan, B., Pereira, C. and Baird, W.M. (2005) Long Term Effects of a Standardized Complex Mixture of Urban Dust Particulate on the Metabolic Activation of Carcinogenic Polycyclic Aromatic Hydrocarbons in Human Cells. Toxicological Sciences 88(2), 358-366.

Reliene, R., Hlavacova, A., Mahadevan, B., Baird, W.M. and Schiestl, R.H. (2005) Diesel exhaust particles cause increased levels of DNA deletions after transplacental exposure in mice. Mutat Res. 570(2), 245-52.

Barbar, Elisar

Nyarko A, Cochrun L, Norwood S, Pursifull N, Voth A and Barbar, E. (2005) Ionization of His 55 at the dimer interface of dynein light-chain LC8 is coupled to dimer dissociation. Biochemistry. 44, 14248–14255.

Beckman, Joe

Cassina, P., Pehar, M., Vargas, M.R., Castellanos, R., Barbeito, A.G., Estévez, A.G., Thompson, J.A., Beckman, J.S., Barbeito, L. (2005) Astrocyte activation by fibroblast growth factor-1 and motor neuron apoptosis: Implications for amyotrophic lateral sclerosis. J. Neurochem. 93, 38–46.

Ermilova, I.P., Ermilov, V.B., Levy, M., Ho, E., Pereira, C., Beckman, J.S. (2005) Protection by dietary zinc in ALS mutant G93A SOD transgenic mice. Neurosci. Lett. 379, 42–46.

Pehar, M., Vargas, M.R., Cassina, P., Barbeito, A.G., Beckman, J.S., Barbeito, L. (2005) Complexity of astrocyte-motor neuron interactions in amyotrophic lateral sclerosis. Neurodegener Dis. 2, 139–46. Review.

Robinson, K.M. and Beckman, J.S. (2005) Synthesis of peroxynitrite from nitrite and hydrogen peroxide. In Methods Enzymol. 396, 207–214.

Vargas, M.R., Pehar, M., Cassina, P., Martinez-Palma, L., Thompson, J.A., Beckman, J.S., Barbeito, L. (2005) Fibroblast growth factor-1 induces heme oxygenase-1 via nuclear factor erythroid 2-related factor 2 (Nrf2) in spinal cord astrocytes: consequences for motor neuron survival. J Biol Chem. 280, 25571–25579.

Frei, Balz

Higdon, J.V., and Frei, B. (2005) Is there a gender difference in the effect of antioxidants on cancer risk? Br. J. Nutr. 93, 139-40.

Hathcock, J.N., Frei, B., Lawson, S., and Johnston, C. (2005) Reply to L Massey. Am. J. Clin. Nutr. 82, 489.

Hathcock, J.N., Azzi, A., Blumberg, J., Dickinson, A., Frei, B., Traber, M.G., Johnston, C.S., Kraemer, K., Parthasarathy, S. and Packer, L. (2005) Reply to H Hemilä. Am. J. Clin. Nutr. 82, 1142-1143.

Widlansky, M.E., Duffy, S.J., Hamburg, N.M., Gokce, N., Warden, B.A., Wiseman, S., Keaney, J.F., Jr., Frei, B. and Vita, J.A. (2005) Effects of black tea consumption on plasma catechins and markers of

oxidative stress and inflammation in patients with coronary artery disease. Free Radic. Biol. Med. 38, 499-506.

Hathcock, J.N., Azzi, A., Blumberg, J., Bray, T., Dickinson, A., Frei, B., Jialal, I., Johnston, C.S., Kelly, F.J., Kraemer, K., Packer, L., Parthasarathy, S., Sies, H. and Traber, M.G. (2005) Vitamins E and C are safe across a broad range of intakes. Am. J. Clin. Nutr. 81, 736-745.

Stone, P.H., Lloyd-Jones, D.M., Kinlay, S., Frei, B., Carlson, W., Rubenstein, J., Andrews, T.C., Johnstone, M., Sopko, G., Cole, H., Orav, J., Selwyn, A.P., Creager, M.A., Vascular Basis Study Group (2005) Effect of intensive lipid lowering, with or without antioxidant vitamins, compared with moderate lipid lowering on myocardial ischemia in patients with stable coronary artery disease: the Vascular Basis for the Treatment of Myocardial Ischemia Study. Circulation 111, 1747-1755.

Doulias, P.T., Nousis, L., Zhu, B.Z., Frei, B. and Galaris, D. (2005) Protection by tropolones against H₂O₂-induced DNA damage and apoptosis in cultured Jurkat cells. Free Radic. Res. 39, 125-135.

Back, S.A., Luo, N.L., Mallinson, R.A., O'Malley, J.P., Wallen, L.D., Frei, B., Morrow, J.D., Petito, C.K., Roberts, C.T. and Murdoch, G.H. and Montine, T.J. (2005) Selective vulnerability of preterm white matter to oxidative damage defined by F₂-isoprostanes. Ann. Neurol. 58, 108-120.

Sowell, J., Conway, H.M., Bruno, R.S., Traber, M.G., Frei, B. and Stevens, J.F. (2005) Ascorbylated 4-hydroxy-2-nonenal as a potential biomarker of oxidative stress response. J. Chromatogr B 15, 139-145.

Greenwood, J.

Fraley, T.S., Pereira, C.B., Tran, T.C., Singleton, C., and Greenwood, J.A. (2005) Phosphoinositide binding regulates D-actinin dynamics: mechanism for modulating cytoskeletal remodeling. J. Biol. Chem. 280, 15479-15482.

Tran, T.C., Singleton, C., Fraley, T.S., and Greenwood, J.A. (2005) Cysteine-rich protein 1 (CRP1) regulates actin filament bundling. BMC Cell Biology, 6 (December), 45.

Hagen, Tory

Judge, S, Jang, Y.M, Smith, A.R., Selman, C., Phillips, T., Speakman, J., Hagen, T.M. and Leeuwenburgh, C. (2005) Lifelong voluntary wheel running reduces subsarcolemmal and interfibrillar mitochondrial hydrogen peroxide production in heart: a possible mechanism for the increase in mean lifespan observed with exercise. FASEB J. 10, 1096/fj.04-2622fje.

Moreau R, Nguyen BT, Doneanu CE, Hagen TM. (2005) Reversal by aminoguanidine of the age-related increase in glycoxidation and lipoxidation in the cardiovascular system of Fischer 344 rats. Biochem Pharmacol. 69, 29-40.

Suh, J.H., Moreau, R., Heath, S-H. and Hagen, T.M. (2005) Dietary supplementation with (R)-a-lipoic acid reverses the age-related accumulation of iron and depletion of antioxidant status in the brain. Redox Report. 10, 52-60.

Marley K, Mooney DT, Clark-Scannell G, Tong TT, Watson J, Hagen TM, Stevens JF, Maier CS. (2005 ) Mass tagging approach for mitochondrial thiol proteins. J Proteome Res. 4, 1403-1412.

Ho, P. Shing

Mok, M.C., Martin, R.C., Dobrev, P.I., Vanková, R., Ho, P.S., Yonekura-Sakakibara, K., Sakakibara, H. and Mok, D.W.S. (2005) Topolinsand hydroxylated thidiazuron derivatives are substrates of cytokinin O-glucosyltransferase with position specificity related to receptor recognition. Plant Physiology 137, 1057-1066.

Hays, F. A., Teegarden, A., Jones, Z.J.R., Harms, M., Raup, D., Watson, J., Cavaliere, E. and Ho, P.S. (2005) How sequence defines structure: A crystallographic map of DNA structure and conformation. Proc. Natl. Acad. Sci. USA 102, 7157-7162.

Karplus, P. Andrew

Sarma, G.N., Nickel, C., Rahlfs, S., Fischer, M., Becker, K., and Karplus, P.A. (2005) Crystal structure of a novel Plasmodium falciparum 1-cys peroxiredoxin. J. Mol. Biol. 346, 1021-1034.

Parsonage, D., Youngblood, D.S., Sarma, G.N., Wood, Z.A., Karplus, P.A. and Poole, L.B. (2005) Analysis of the link between enzymatic activity and oligomeric state in AhpC, a bacterial peroxiredoxin. Biochemistry, 44, 10583-10592.

Roberts, B.R., Wood, Z.A., Jönsson, T.J., Poole, L.B. and Karplus, P.A. (2005) Oxidized and synchrotron cleaved structures of the disulfide redox center in the N-terminal domain of Salmonella typhimurium AhpF. Prot. Sci. 14, 2414-20.

Sarma, G.N., Manning, V., Ciuffetti, L. and Karplus. P.A. (2005) Crystal structure of an RGD-containing host-selective toxin: Pyrenophora tritici-repentis Ptr ToxA.. The Plant Cell 17, 3190-3202.

Poole, L.B., Roberts, B.R., Wood, Z.A., Jönsson, T.J., Reynolds, C.M. and Karplus, P.A. (2005) The AhpC-reducing, thioredoxin-like N-terminal domain of AhpF. In Flavins and Flavoproteins (T. Nishino, R. Miura, M. Tanokura, K. Fukui eds.) pp. 353-357, ArchiTect Inc. Tokyo, Japan.

Mathews, Chris

Kim, J., L. J. Wheeler, R. Shen, and C. K. Mathews (2005) Protein-DNA Interactions in the T4 dNTP Synthetase Complex Dependent upon Gene 32 Single-strand DNA-binding Protein. Mol. Microbiol. 55, 1502–1513.

Song, S., Z. F. Pursell, W. C. Copeland, M. J. Longley, T. A. Kunkel, and C. K. Mathews (2005) DNA Precursor Asymmetries in Mammalian Tissue Mitochondria and Possible Contribution to Mutagenesis via Reduced Replication Fidelity. Proc. Natl. Acad. Sci. USA 102, 4990–4995.

Kim, J., M. C. Olcott, I. Rajagopal, and C. K. Mathews (2005) Adenylate Kinase of Escherichia coli, an Integral Component of the Phage T4 dNTP Synthetase Complex. J. Biol. Chem. 280, 28221–28229.

Wheeler, L. J., I. Rajagopal, and C. K. Mathews (2005) Stimulation of Mutagenesis by Proportional Deoxyribonucleoside Triphosphate Accumulation in Escherichia coli. DNA Repair 4, 1450–1456.

Mathews, C.K. (2005) Bacteriophage T4. In Encyclopedia of Life Sciences, Second Edition. John Wiley & Sons, 1-9.

van Holde, Ken

Tomschik, M., Zheng, H., van Holde, K., Zlatanova, J. and Leuba, S. (2005) Fast, long-range reversible conformation fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer. PNAS 102, 3278-3283.

Ahern, Kevin

Columns

Ahern, K. "WebWatch", BioTechniques (2004) Vol. 36, 6 columns.

Ahern, K. "WebWatch", BioTechniques (2004) Vol. 37, 6 columns. Ahern, K. "On the Web", Gen. Eng. News (2004) Vol. 24, 21 columns. Technical Articles

Ahern, K. Gen. Eng. News (2004) Vol. 24, 2 columns.

Anderson, Sonia

Bauman, A.T., Malencik, D.A., Barofsky, D.F., Barofsky, E., Anderson, S.R. and Whanger, P.D. (2004) Selective production of rat mutant selenoprotein W with and without bound glutathione. Biochem. Biophys. Res. Comm. 313, 308-313.

Walker, M.K., Farkas, D.F., Anderson, S.R. and Meunier-Goddik, L. (2004) Effects of High Pressure Processing at Low Temperature on the Molecular Structure and Surface Properties of a-Lactoglobulin. Journal of Food Science and Agricultural Chemistry 52, 8230-8235.

Baird, William

Baird, W.M. and Mahadevan, B. (2004) The uses of carcinogen-DNA adduct measurement in establishing mechanisms of mutagenesis and in chemoprevention. Mutation Research 547, 1-4.

Mahadevan, B., Parsons, H., Musafia, T., Sharma, A., Amin, S., Pereira, C. and Baird, W.M. (2004) Effect of artificial mixtures of environmental polycyclic aromatic hydrocarbons present in coal tar, urban dust and diesel exhaust particulates on MCF-7 cells in culture. Environmental and Molecular Mutagenesis 44(2), 99-107.

Baird, W.M. and Mahadevan, B. (2004) The uses of carcinogen-DNA adduct measurement in establishing mechanisms of mutagenesis and in chemoprevention. Mutation Research 547, 1-4.

Barbar, Elisar

Barbar, E. and Hare, M. (2004) Characterization of the cargo attachment complex of cytoplasmic dynein using NMR and mass spectrometry. In: Methods in Enzymology—Energetics of Biological Macromolecules, Part E (J.M. Holt, M.L. Johnson, and G.K. Ackers, eds.), Vol. 380, pp. 219–241. Elsevier, Inc.

Makokha, M., Huang, Y.-J., Montelione, G., Edison, A.S. and Barbar, E. (2004) The solution structure of the pH-induced monomer of dynein light-chain LC8 from Drosophila. Protein Sci. 3, 727–734.

Nyarko, A., Hare, M., Hays, T.S. and Barbar, E. (2004). The intermediate chain of cytoplasmic dynein is partially disordered and gains structure upon binding to light-chain LC8. Biochemistry 43, 15595–15603.

Wang, L., Hare, M., Hays, T.S. and Barbar, E. (2004) Dynein light chain LC8 promotes assembly of the coiled-coil domain of swallow protein. Biochemistry 43, 4611–4620.

Beckman, Joe

Daiber, A., Bachschmid, M., Beckman, J.S., Munzel, T., Ullrich, V. (2004) The impact of metal catalysis on protein tyrosine nitration by peroxynitrite. Biochem. Biophys. Res. Commun. 317, 873–881.

Leinweber, B., Barofskym E,, Barofsky, D., Ermilov, V., Nylin, K., Beckman, J.S. (2004) Aggregation of ALS mutant superoxide dismutase expressed in Escherichia coli. Free Radic. Biol. Med. 36, 911–918.

Pehar, M., Cassina, P., Vargas, M.R., Castellanos, R., Viera, L., Beckman, J.S., Estevez, A.G., Barbeito, L. (2004) Astrocytic production of nerve growth factor in motor neuron apoptosis: Implications for amyotrophic lateral sclerosis. J. Neurochem. 89, 464–473.

Robinson, K.M., Morré, J., Beckman, J.S. (2004). Triuret: A novel product of peroxynitrite-mediated oxidation of urate. Arch. Biochem. Biophys. 423, 213–217.

Vargas, M.R., Pehar, M., Cassina, P., Estevez, A.G., Beckman, J.S., Barbeito, L. (2004) Stimulation of nerve growth factor expression in astrocytes by peroxynitrite. In Vivo. 18, 269–274.

Frei, Balz

Lotito, S.B. and Frei, B. (2004) Relevance of apple polyphenols as antioxidants in human plasma: contrasting in vitro and in vivo effects. Free Radic. Biol. Med. 36, 201-211.

Polidori, M.C., Mecocci, P., Levine, M. and Frei, B. (2004) Short-term and long-term vitamin C supplementation in humans dose-dependently increases the resistance of plasma to ex vivo lipid peroxidation. Arch. Biochem. Biophys. 423, 109-115.

Suh, J.H., Zhu, B.Z., deSzoeke, E., Frei, B. and Hagen, T.M. (2004) Dihydrolipoic acid lowers the redox activity of transition metal ions but does not remove them from the active site of enzymes. Redox Report 9, 57-61.

Mastaloudis, A., Yu, D., O'Donnell, R.P., Frei, B., Dashwood, R.H. and Traber, M. (2004) Endurance exercise results in DNA damage as detected by the comet assay. Free Radic. Biol. Med. 36, 966-975.

Lin, Y.P., Zhu, B.Z., Yang, M.C., Frei, B., Pan, M.H., Lin, J.K. and Wang, Y.J. (2004) Bcl-2 overexpression inhibits tetrachlorohydroquinone-induced apoptosis in NIH3T3 cells: a possible mechanism for tumor promotion. Mol. Carcinog. 40, 24-33.

Stone, P.H., Lloyd-Jones, D.M., Johnstone, M., Carlson, W., Rubenstein, J., Creager, M., Frei, B., Sopko, G., Clark, M.E., MacCallum, G., Kinlay, S., Orav, J. and Selwyn, A. (2004) Vascular basis for the treatment of myocardial ischemia study: trial design and baseline characteristics. Am. Heart J. 147, 875-882.

Lotito, S.B. and Frei, B. (2004) The increase in human plasma antioxidant capacity following apple consumption is due to the metabolic effect of fructose on urate, not apple-derived antioxidant flavonoids. Free Radic. Biol. Med. 37, 251-258.

Sowell, J., Frei, B. and Stevens, J.F. (2004) Vitamin C conjugates of genotoxic lipid peroxidation products: Structural characterization and detection in human plasma. Proc. Natl. Acad. Sci. USA 101, 17964-17969; see also: Sowell, J., Frei, B. and Stevens, J.F. (2007) Retraction for Sowell et al., Vitamin C conjugates of genotoxic lipid peroxidation products: Structural characterization and detection of human plasma. Proc. Natl. Acad. Sci. USA 104, 14543.

Lawson, S., Higdon, J.V. and Frei, B. (2004) The optimum intake of vitamin C: history and controversy. In: Vitamin C: Functions and Biochemistry in Animals and Plants (Asard, H., May, J.M. and Smirnoff, N., eds), pp. 1-6, Garland Science/BIOS Scientific Publishers, Oxon, UK.

Higdon, J.V. and Frei, B. (2004) Vitamin C as a cancer chemopreventive agent. In: Cancer Chemoprevention, Volume 1: Promising Cancer Chemopreventive Agents (Kelloff, G.J., Hawk, E.T. and Sigman, C.C., eds), pp. 485-510, The Humana Press, Totawa, NJ.

Higdon, J. and Frei, B. (2004) Vitamin C, vitamin E, and β-carotene in cancer chemoprevention. In: Phytopharmaceuticals in Cancer Chemoprevention Bagchi, D. and Preuss, H.G., eds), CRC Press, Boca Raton, FL.

Frei, B. (2004) Efficacy of dietary antioxidants to prevent oxidative damage and inhibit chronic disease. J. Nutr. 134, 3196S-3198S.

Lotito, S. and Frei, B. (2004) Apples and plasma antioxidant capacity in humans: the roles of fructose and urate. In: Medimond International Proceedings (Puntarulo, S. and Boveris, A., eds), pp. 41-48, Monduzzi, Bologna, Italy.

Greenwood, J.

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