2013 Biochemistry & Biophysics Publications

Ahern, Kevin

Ahern K. (2013) Fatty Acid Metabolism. Biochemistry and Molecular Biology Education. 41, 362. 

Ahern K. (2013) New Serine Protease Song. Biochemistry and Molecular Biology Education. 41, 209

Ahern K, Rajagopal I. (2013) Kevin and Indira's Guide to Getting Into Medical School.  Davinci Press (2013) ISBN 978-1-300-64751-5. 

Barbar, Elisar

Nyarko A, Song Y, Novácek J, Zídek L, Barbar E.* (2013)   Multiple Recognition Motifs in Nucleoporin Nup159 Provide a Stable and Rigid Nup159/Dyn2 Assembly. J. Biol. Chem. 288, 2614-22.

Dunker AK, Babu MM, Barbar E, et al. (2013) What's in a name: Why these proteins are intrinsically disordered? Intrinsically Disordered Proteins 1, 1-5.

 Kidane AI, Song Y, Nyarko A, Hall J, Hare M, Löhr F, Barbar E.* (2013) Structural features of LC8-induced self-association of Swallow.  Biochemistry 5, 6011-20 4.

 Barbar E,* Nyarko A.  (2013) NMR Characterization of Self-Association Domains Promoted by Interactions with LC8 Hub Protein. Computational and Structural Biotechnology Journal. Bio-NMR Special Issue

Frei, Balz

Michels, A.J., Hagen, T.M., and Frei, B. (2013) Human genetic variation influences vitamin C homeostasis by altering vitamin C transport and antioxidant enzyme function.  Annu. Rev. Nutr. 33, 45-70.

Rodriguez, K.J., Wong, H.K., Oddos, T., Southall, M., Frei, B. and Kaur, S. (2013) A purified Feverfew extract protects from oxidative damage by inducing DNA repair in skin cells via a PI3-kinase-dependent Nrf2/ARE pathway. J. Dermatol. Sci. 72, 304-310.

Michels, A.J., and Frei, B. (2013) Myths, artifacts, and fatal flaws: Identifying limitations and opportunities in vitamin C research. Nutrients 5:5161-5192.

Freitag, Michael

Connolly L R, Smith KM, Freitag, M.  (2013) The Fusarium graminearum Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters. PLOS Genetics9: e1003916. PMCID: in process.

Studt L, Schmidt FJ, Jahn L, Sieber CM, Connolly LR, Niehaus EM, Freitag M, Humpf HU, Tudzynski B. (2013) Two histone deacetylases, FfHda1 and FfHda2, are important for secondary metabolism and virulence in Fusarium fujikuroi. Appl Environ Microbiol. Oct 4. [Epub ahead of print] PMID: 24096420

Traeger S, Altegoer F, Freitag M, Gabaldon T, Kempken F, Kumar A, Marcet-Houben M, Pöggeler S, Stajich JE, Nowrousian M. (2013) The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution. PLoS Genet. 9: e1003820. doi: 10.1371/journal.pgen.1003820.  PMID: 24068976

Mourino-Perez RR, Linacre-Rojas LP, Roman-Gavilanes AI, Lew TK, Callejas-Negrete OA, Roberson RW, Freitag M. (2013) MTB-3, a Microtubule Plus-End Tracking Protein (+TIP) of Neurospora crassa. PLoS ONE 8:e 70655. doi: 10.1371/journal.pone.0070655. PMCID:PMC3741187.

Niehaus EM, Kleigrewe K, Wiemann P, Studt L, Sieber CM, Connolly LR, Freitag M, Guldener U, Tudzynski B, Humpf HU. (2013) Genetic Manipulation of the Fusarium fujikuroiFusarin Gene Cluster Yields Insight into the Complex Regulation and Fusarin Biosynthetic Pathway. Chem Biol. 20: 1055-66. doi: 10.1016/j.chembiol.2013.07.004. PMID: 23932525.

Wiemann P, Sieber CM, von Bargen KW, Studt L, Niehaus EM, Espino JJ, Huß K, Michielse CB, Albermann S, Wagner D, Bergner SV, Connolly LR, Fischer A, Reuter G, Kleigrewe K, Bald T, Wingfield BD, Ophir R, Freeman S, Hippler M, Smith KM, Brown DW, Proctor RH, Munsterkotter M, Freitag M, Humpf HU, Guldener U, Tudzynski B. (2013) Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog. 9: e1003475. doi: 10.1371/journal.ppat.1003475. PMCID: PMC3694855.

Vining K, Pomraning KR, Wilhelm LJ, Ma C, Pellegrini M, Di Y, Mockler TC, Freitag M, Strauss SH. (2013) Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa. BMC Plant Biol. 13: 92. doi: 10.1186/1471-2229-13-92. PMCID: PMC3728041.

Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon BG, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ, Ciuffetti LM. (2013) Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 (Bethesda) 3: 41-63. doi: 10.1534/g3.112.004044. PMCID: PMC3538342.

Vidal-Dupiol J, Zoccola D, Tambutté E, Grunau C, Cosseau C, Smith KM, Freitag M, Dheilly NM, Allemand D, Tambutté S. (2013) Genes Related to Ion-Transport and Energy Production Are Upregulated in Response to CO2-Driven pH Decrease in Corals: New Insights from Transcriptome Analysis. PLoS ONE 8: e58652. doi: 10.1371/journal.pone.0058652. PMID: 23544045

R. Zhu, Shevchenko O, Ma C, Maury S, Freitag M, Strauss SH. (2013) Poplars with a PtDDM1-RNAi transgene have reduced DNA methylation and show aberrant post-dormancy morphology. Planta Feb 28. [Epub ahead of print] PMID: 23455459

Karimi-Aghcheh R, Bok JW, Phatale PA, Smith KM, Baker SE, Lichius A, Omann M,  Zeilinger S, Seiboth B, Rhee C, Keller NP, Freitag M,  Kubicek CP. (2013) Functional analyses of Trichoderma reesei LAE1 reveal conserved and contrasting roles of this regulator. G3 (Bethesda) 3: 369-78. doi: 10.1534/g3.112.005140. PMID: 23390613

Pomraning KR, Connolly LR,Whalen JP, Smith KM, Freitag M. (2013) Repeat-Induced Point mutation, DNA methylation and heterochromatin in Gibberella zeae (anamorph: Fusarium graminearum). In: “Fusarium genomics and molecular and cellular biology” D. Brown and R. Proctor (Eds.), Horizon Scientific Press.

Gombart, Adrian

Guo C, Sinnott B, Niu B, Lowry MB, Fantacone ML, Gombart AF. (2013) Synergistic induction of human cathelicidin antimicrobial peptide gene expression by vitamin D and stilbenoids. Mol Nutr Food Res.  Sep 14. doi: 10.1002/mnfr.201300266. [Epub ahead of print] PubMed PMID: 24039193.

Wickramasekara SI, Zandkarimi F, Morré J, Kirkwood J, Legette L, Jiang Y, Gombart AF, Stevens JF, Maier CS. (2013) Electrospray Quadrupole Travelling Wave Ion Mobility Time-of-Flight Mass Spectrometry for the Detection of Plasma Metabolome Changes Caused by Xanthohumol in Obese Zucker (fa/fa) Rats. Metabolites3(3):701-717.

Greenwood, Juliet 

Wang R, Löhr CV, Fischer KA, Dashwood WM, Greenwood JA, Ho E, Williams DE, Ashktorab H, Dashwood MR, Dashwood RH. (2013) Epigenetic inactivation of endothelin-2 and ET-3 in colon cancer Int. J. Cancer, 132, 1004-12.  PMID: 22865632

Smith M, Boenzli M, Hindagolla V, Ding J, Miller J, Hutchison J, Greenwood JA, Abeliovich H, Bakalinsky A. (2013) Identification of gold nanoparticle-resistant mutants of Saccharomyces cerevisiae suggests a role for respiratory metabolism in mediating toxicity.  Appl. Environ. Microbiol., 79, 728-33.  PMID: 23144132 

Hau AM, Greenwood JA, Löhr CV, Serrill JD, Proteau P, Ganley IG, McPhail KL,  Ishmael JE. (2013) Coibamide A Induces mTOR-Independent Autophagy and Cell Death in Human Glioblastoma Cells.  PLOS ONE, e65250.  PMID: 23762328

Hagen, Tory M

Michels AJ, Hagen TM, Frei B. Human genetic variation influences vitamin C homeostasis by altering vitamin C transport and antioxidant enzyme function.  Annu Rev Nutr. 2013;33:45-70. 

Johnson, Colin P

Marty NJ, Holman CL, Abdullah N, Johnson CP. (2013) The C2 domains of otoferlin, dysferlin, and myoferlin alter the packing of lipid bilayers.  Biochemistry. Aug 20;52(33):5585-92. 

Karplus, Andy

Diederichs K & Karplus PA. (2013) Better models by discarding data? Acta Cryst D, 69, 1215-22.

Driggers CM, Cooley RB, Sankaran B, Hirschberger LL, Stipanuk MH & Karplus PA. (2013)  Cysteine dioxygenase structures from pH 4 to 9: consistent Cys-persulfenate formation at intermediate pH and a Cys-bound enzyme at higher pH.  J. Mol. Biol. 425, 3121-3136.

Gretes M & Karplus PA. (2013)  Observed octameric assembly of a Plasmodium yoelii peroxiredoxin can be explained by the replacement of native ‘ball-and-socket’ interacting residues by an affinity tag. Protein Sci, 22, 1445-1452.

Perkins A, Nelson KJ, Williams J, Parsonage D, Poole, LB & Karplus PA. (2013) The Sensitive Balance Between the Fully Folded and Locally Unfolded Conformations of a Model Peroxiredoxin. Biochemistry, 52, 8708-8721.

Poole LB, Nelson KJ & Karplus PA (2013) “Sulfenic Acids and Peroxiredoxins in Oxidant Defense and Signaling” in Oxidative Stress and Redox Regulations. (U. Jacob, D. Reichmann, Eds.) Springer, NY, pp. 85-118.

Nelson KJ, Parsonage DP, Karplus PA & Poole LB. (2013) Evaluating peroxiredoxin sensitivity towards inactivation by peroxide substrates. Meth. Enzymol. 527, 21-40.

Mathews, Chris

Mannava S, Moparthy KC, Wheeler LJ, Natarajan V, Zucker SN, Fink EE, Im M,  Flanagan S, Shewach DS, Burhans WC, Mathews CK, Nikiforov MA. (2013) Depletion of Deoxyribonucleotide Pools is a Source of DNA Damage in Cells Undergoing Oncogene-Induced Senescence. Am. J. Pathol. 182: 142–151.

Schaaper RM and Mathews CK. (2013) Mutational Consequences of dNTP Pool Imbalances in E. coli. DNA Repair 12:73–79.

Chimploy K, Song S, Wheeler LJ, Mathews CK. (2013) Ribonucleotide Reductase Association with Mammalian Tissue Mitochondria. J. Biol. Chem. 288:13145–13155.

Mehl, Ryan

Speight LC, Muthusamy AK, Goldberg JM, Warner JB, Wissner RF, Willi TS, Woodman BF, Mehl RA, Petersson. (2013) EJ. Efficient Synthesis and In Vivo Incorporation of Acridon-2-ylalanine, a Fluorescent Amino Acid for Lifetime and Forster Resonance Energy Transfer/Luminescence Resonance Energy Transfer Studies. J. Am. Chem Soc.  135(50):18806-18814.

Horowitz S, Dirk LM, Yesselman JD, Nimtz JS, Adhikari U, Mehl RA, Scheiner S, Houtz RL, Al-Hashimi HM, Trievel RC. (2013) Conservation and Functional Importance of Carbon-Oxygen Hydrogen Bonding in AdoMet-Dependent Methyltransferases. J. Am. Chem Soc. Oct 16;135(41):15536-48.

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.