2012 Biochemistry & Biophysics Faculty Publications

Ahern, Kevin

Ahern, Kevin.  (2012) The Splendidest Ever Metabolic Melodies Songbook, DaVinci Press, ISBN 978-1-105-72994-2

Ahern, K. and Rajagopal, I.  (2012) Biochemistry Free and Easy, DaVinci Press.

Ahern, Kevin. (2012) “Henderson Hasselbalch” Biochemistry and Molecular Biology Education , 40, 405.

Ahern, Kevin. (2012) “Pentose Phosphate Pathway” Biochemistry and Molecular Biology Education (2012), 40, p. 288.

Ahern, Kevin. (2012) “Around the Nucleus” Biochemistry and Molecular Biology Education , 40, 216.

Ahern, Kevin. (2012) “Chromatin” Biochemistry and Molecular Biology Education, 40, 156.

Baird, William

Larkin A, Siddens LK, Krueger SK, Tilton SC, Waters KM, Williams DE, Baird WM.  (2012) Application of a fuzzy neural network model in predicting polycyclic aromatic hydrocarbon-mediated perturbations of the Cyp1b1 transcriptional regulatory network in mouse skin.  Toxicol Appl Pharmacol.  267(2):192-9.

Siddens LK, Larkin A, Krueger SK, Bradfield CA, Waters KM, Tilton SC, Pereira CB, Löhr CV, Arlt VM, Phillips DH, Williams DE, Baird WM.  (2012) Polycyclic aromatic hydrocarbons as skin carcinogens: comparison of benzo[a]pyrene, dibenzo[def,p]chrysene and three environmental mixtures in the FVB/N mouse.  Toxicol Appl Pharmacol.  264(3):377-86.

Shorey LE, Castro DJ, Baird WM, Siddens LK, Löhr CV, Matzke MM, Waters KM, Corley RA, Williams DE.  (2012) Transplacental carcinogenesis with dibenzo[def,p]chrysene (DBC): timing of maternal exposures determines target tissue response in offspring.  Cancer Lett.  317(1):49-55.

Barbar, Elisar

Nyarko A, Song Y, Nováček J, Žídek L, Barbar E. (2012) Multiple recognition motifs in nucleoporin Nup159 provide a stable and rigid Nup159-Dyn2 assembly.  J Biol Chem. 288(4):2614-22.

Barbar E. (2012) Native disorder mediates binding of dynein to NudE and dynactin.  Biochem Soc Trans. 40(5):1009-13.

Nyarko A, Song Y, Barbar E.  (2012) Intrinsic disorder in dynein intermediate chain modulates its interactions with NudE and dynactin.  J Biol Chem. 287(30):24884-93.

Powell JD, Barbar E, Dreher TW.  (2012) Turnip yellow mosaic virus forms infectious particles without the native beta-annulus structure and flexible coat protein N-terminus.  Virology. 422(2):165-73.


Beckman, Joseph

Drechsel DA, Estévez AG, Barbeito L, Beckman JS. (2012) Nitric oxide-mediated oxidative damage and the progressive demise of motor neurons in ALS.  Neurotox Res. 22(4):251-64.

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


Frei, Balz

Dixon BM, Barker T, McKinnon T, Cuomo J, Frei B, Borregaard N, Gombart AF.  (2012) Positive correlation between circulating cathelicidin antimicrobial peptide (hCAP18/LL-37) and 25-hydroxyvitamin D levels in healthy adults.  BMC Res Notes.  24;5:575.

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.

Frei B, Birlouez-Aragon I, Lykkesfeldt J.  (2012) Authors' perspective: What is the optimum intake of vitamin C in humans?  Crit Rev Food Sci Nutr. 52(9):815-29. Review.

Yilmazer-Musa M, Griffith AM, Michels AJ, Schneider E, Frei B.  (2012) Grape seed and tea extracts and catechin 3-gallates are potent inhibitors of α-amylase and α-glucosidase activity.  J Agric Food Chem. 60(36):8924-9.

Finlay LA, Michels AJ, Butler JA, Smith EJ, Monette JS, Moreau RF, Petersen SK, Frei B, Hagen TM.  (2012) 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.  302(5):R587-97.

Freitag, Michael

Pomraning KR, Smith KM, Bredeweg EL, Phatale PA, Connolly LR and Freitag M.1 (2012) Paired-end library preparation for rapid genome sequencing.  Methods Mol. Biol. 944: 1-22.

Smith KM,Galazka JM,Phatale PA,Connolly LR,Freitag M.  (2012) Centromeres of filamentous fungi.  Chromosome Research, 20: 635-656.

Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio L, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler T, Freitag M3, Geraldes A, El-Kassaby YA, Mansfield SD,Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA (2012) Genome Resequencing Reveals Multiscale Geographic Structure and Extensive Linkage Disequilibrium in the Forest Tree Populus trichocarpa.  New Phytologist 196: 713-725.

Puckett S, Reese KA, Mitev GM, Mullen V, Johnson RC, Pomraning KR, Mellbye BL, Tilley LD, Iversen PL, Freitag M3, Geller BL (2012) Bacterial Resistance to Antisense Peptide-Phosphorodiamidate Morpholino Oligomers.  Antimicrobial Agents and Chemotherapy. Antimicrob Agents Chemother.   56(12):6147-53.

Seiboth B, Karmi-Aghcheh R,  Phatale PA,  Linke R,  Sauer DG, Smith KM, Baker SE, Freitag M3 and Kubicek CP (2012) The putative protein methyltransferase LAE1 controls 1 cellulase gene expression in Trichoderma reesei.  Mol. Microbiol. 84: 1150-1164.

Lepesant JM, Boissier C, Cosseau C, Freitag M3, Portela J, Climent D, Perrin C, Neto AZ, Grunau C (2012) Sex-specific sequences of Schistosoma mansoni: a possible link between recombination repression, chromatin structure and repeat transcription.  Genome Biol. 13: R14.

Vining KV, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler T, Freitag M3, Strauss S (2012) Dynamic DNA Cytosine Methylation in the Populus trichocarpa Genome: Tissue-level Variation and Relationship to Gene Expression.  BMC Genomics 13: 27

Ishikawa FH, Souza EA, Shoji J, Connolly LR, Freitag M3, Read ND, Roca MG (2012) The heterokaryon incompatibility response is suppressed following cell fusion by conidial anastomosis tubes in the plant pathogen.  Colletotrichum lindemuthianum. PLoS ONE 7:e31175.

Gombart, Adrian F

Dixon BM, Barker T, McKinnon T, Cuomo J, Frei B, Borregaard N, Gombart AF.  (2012) Positive correlation between circulating cathelicidin antimicrobial peptide (hCAP18/LL-37) and 25-hydroxyvitamin D levels in healthy adults.  BMC Res Notes. 24;5:575.

Kyme P, Thoennissen NH, Tseng CW, Thoennissen GB, Wolf AJ, Shimada K, Krug UO, Lee K, Müller-Tidow C, Berdel WE, Hardy WD, Gombart AF, Koeffler HP, Liu GY. (2012) C/EBPε mediates nicotinamide-enhanced clearance of Staphylococcus aureus in mice.  J Clin Invest. 4;122(9):3316-29.  Epub 2012 Aug 27. Erratum in: J Clin Invest. 122(11):4301.

Guo C, Rosoha E, Lowry MB, Borregaard N, Gombart AF.  (2012) Curcumin induces human cathelicidin antimicrobial peptide gene expression through a vitamin D receptor-independent pathway.  J Nutr Biochem.  25. [Epub ahead of print]

Campbell Y, Fantacone ML, Gombart AF.  (2012) Regulation of antimicrobial peptide gene expression by nutrients and by-products of microbial metabolism.  Eur J Nutr. 51(8):899-907.

Sun G, Li H, Wu X, Covarrubias M, Scherer L, Meinking K, Luk B, Chomchan P, Alluin J, Gombart AF, Rossi JJ.  (2012) Interplay between HIV-1 infection and host microRNAs.  Nucleic Acids Res. 40(5):2181-96.

Greenwood, Juliet

Lal S, La Du J, Tanguay RL, Greenwood JA.  (2012) Calpain 2 is required for the invasion of glioblastoma cells in the zebrafish brain microenvironment.  J Neurosci Res. 90(4):769-81.  

Wang, R., Lohr, C.V., Fischer, K.A., Dashwood, W.M., Greenwood, J.A., Ho, E., Williams, D.E., Ashktorab, H., Dashwood, M.R., and Dashwood, R.H. (2012) Epigenetic inactivation of endothelin-2 and ET-3 in colon cancer.  Int. J. Cancer, 132, 1004-12.  

Smith, M., Boenzli, M., Hindagolla, V., Ding, J., Miller, J., Hutchison, J., Greenwood, J.A., Abeliovich, H., and Bakalinsky, A. (2012) Identification of gold nanoparticle-resistant mutants of Saccharomyces cerevisiae suggests a role for respiratory metabolism in mediating toxicity.  Appl. Environ. Microbiol.,  79, 728-33.

Hagen, Tory

Keith DJ, Butler JA, Bemer B, Dixon B, Johnson S, Garrard M, Sudakin DL, Christensen JM, Pereira C, Hagen TM. (2012) Age and gender dependent bioavailability of R- and R,S-α-lipoic acid: a pilot study.  Pharmacol Res.  66(3):199-206.

Shay KP, Michels AJ, Li W, Kong AN, Hagen TM.  (2012) Cap-independent Nrf2 translation is part of a lipoic acid-stimulated detoxification stress response.  Biochem Biophys Acta. 1823(6):1102-9.                                                 

Gómez LA, Hagen TM.  (2012) Age-related decline in mitochondrial bioenergetics: does supercomplex destabilization determine lower oxidative capacity and higher superoxide production?  Semin Cell Dev Biol.  23(7):758-67.

Gómez LA, Heath SH, Hagen TM.   (2012) Acetyl-L-carnitine supplementation reverses the age-related decline in carnitine palmitoyltransferase 1 (CPT1) activity in interfibrillar mitochondria without changing the L-carnitine content in the rat heart.  Mech Ageing Dev. 133(2-3):99-106.

Johnson, Colin

Golubovskaya VM, Figel S, Ho BT, Johnson CP, Yemma M, Huang G, Zheng M, Nyberg C, Magis A, Ostrov DA, Gelman IH, Cance WG.   (2012) A small molecule focal adhesion kinase (FAK) inhibitor, targeting Y397 site: 1-(2-hydroxyethyl)-3, 5, 7-triaza-1-azoniatricyclo [,7)]decane; bromide effectively inhibits FAK autophosphorylation activity and decreases cancer cell viability, clonogenicity and tumor growth in vivo.  Carcinogenesis.  33(5):1004-13.  Epub 2012 Mar 7.

Karplus, P. Andrew

Perkins A, Gretes MC, Nelson KJ, Poole LB, Karplus PA. (2012) Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes.  Biochemistry.  51(38):7638-50. Epub 2012 Sep 14.

Karplus PA, Diederichs K. (2012) Linking crystallographic model and data quality.  Science. 336(6084):1030-3.

Sher I, Hanemann CO, Karplus PA, Bretscher A. (2012) The tumor suppressor merlin controls growth in its open state, and phosphorylation converts it to a less-active more-closed state.  Dev Cell.  22(4):703-5.

Karplus PA, Poole LB.  (2012) Peroxiredoxins as molecular triage agents, sacrificing themselves to enhance cell survival during a peroxide attack.  Mol Cell.  45(3):275-8.

Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL Jr, Karplus PA. (2012) Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites.  Proc Natl Acad Sci U S A.  109(2):449-53.

Hollingsworth SA, Lewis MC, Berkholz DS, Wong WK, Karplus PA. (2012) (φ,ψ)₂ motifs: a purely conformation-based fine-grained enumeration of protein parts at the two-residue level.  J Mol Biol. 10;416(1):78-93.

Gretes MC, Poole LB, Karplus PA. (2012) Peroxiredoxins in parasites.  Antioxid Redox Signal. 15;17(4):608-33.  Epub 2012 Jan 25. Review.

Mathews, Christopher

Mathews C K, van Holde KE, Appling D, Anthony-Cahill S.  (2012) Biochemistry, Fourth Edition Pearson Education Canada, Toronto (1342 pages).

Mathews, C. K. (2012) Milestone Review. DNA Synthesis as a Therapeutic Target: The First 65 Years.   FASEB J, 26, 2331-2338.

Saldivar, J. C., S. Miuma, J. Bene, S. A. Hosseini, H. Shibata, J. Sun, L. J. Wheeler, C. K. Mathews, and K.Huebner (2012)Inhibition of genome instability and preneoplastic processes through loss of Fhit expression, PLoS Genetics 8:e1003077.

Wheeler, L. J., and C. K. Mathews (2012) Yeast POS5 NADH Kinase: Effects of a Mitochondrial Mutator Mutation on Mitochndrial Nucleotides. J. Biol. Chem. 287:31218-31222.

Mannava S., K. C. Moparthy , L. J. Wheeler, K. I. Leonova, J. A. Wawrzyniak, A. Bianchi-Smiraglia, A. E. Berman, S.  Flanagan, D. S. Shewach, N. C. Zeitouni, A. V. Gudkov, C.K. Mathews, and M A. Nikiforov (2012).  Ribonucleotide reductase and thymidylate synthase or exogenous deoxyribonucleosides reduce DNA damage and senescence caused by C-MYC depletion. Aging 12:917-22.

Mehl, Ryan

Mehl RA.  (2012) Engineered unnatural animals: tools for multicellular biochemistry.  Chembiochem.  13(2):186-8. No abstract available.

Seitchik JL, Peeler JC, Taylor MT, Blackman ML, Rhoads TW, Cooley RB, Refakis C, Fox JM, Mehl RA.  (2012) Genetically encoded tetrazine amino acid directs rapid site-specific in vivo bioorthogonal ligation with trans-cyclooctenes.   J Am Chem Soc. 134(6):2898-901. Epub 2012 Feb 1.

Averick SE, Paredes E, Grahacharya D, Woodman BF, Miyake-Stoner SJ, Mehl RA, Matyjaszewski K, Das SR.  (2012) A protein-polymer hybrid mediated by DNA.  Langmuir. 28(4):1954-8.  Epub 2012 Jan 12.

Libby RD, Mehl RA. (2012) Characterization of covalent Ene adduct intermediates in "hydride equivalent" transfers in a dihydropyridine model for NADH reduction reactions.  Bioorg Chem. 40(1):57-66.  Epub 2011 Oct 20.

Peeler JC, Mehl RA.  (2012) Site-specific incorporation of unnatural amino acids as probes for protein conformational changes.  Methods Mol Biol. 794:125-34.

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

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.