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July 2015

Pharmacology and Molecular Sciences Archives

1. Cox PM and Bumpus NN. Structure-activity studies reveal the oxazinone ring is a determinant of cytochrome P450 2B6 activity toward efavirenz. ACS Med Chem Lett. 2014 Sep 4;5(10):1156-1161.
Key words: cytochromes P450; drug metabolism; mass spectrometry; efavirenz; structure-activity

2. Lu Y, Fuchs EJ, Hendrix CW, Bumpus NN. CYP3A5 Genotype Impacts Maraviroc Concentrations in Healthy Volunteers. Drug Metab Dispos. 2014 Nov;42(11):1796-802.
Key words: Pharmacogenetics, maraviroc, HIV, drug metabolism and pharmacokinetics

3. Prendergast J, Umanah GK, Yoo SW, Lagerlöf O, Motari MG, Cole RN, Huganir RL, Dawson TM, Dawson VL, Schnaar RL. Ganglioside regulation of AMPA receptor trafficking. J Neurosci. 2014 Sep 24;34(39):13246-58.
Key words: AMPA receptor, ganglioside, GluR2, N-ethylmaleimide-sensitive factor, Nicalin; Thorase

1. Cieniewicz AM, Moreland L, Ringel AE, Mackintosh SG, Raman A, Gilbert TM, Wolberger C, Tackett AJ, Taverna SD. The bromodomain of Gcn5 regulates site-specificity of lysine acetylation on histone H3. Molecular and Cellular Proteomics. 2014 Aug 8. pii: mcp.M114.038174. [Epub ahead of print]
Key words: Gcn5, histone, acetylation, bromodomain, chromatin


2. Gilbert TM, McDaniel SL, Byrum SD, Cades JA, Dancy BCR, Wade H, Tackett AJ, Strahl BD, Taverna SD. An H3K36me3 binding PWWP protein targets the NuA3 acetyltransferase complex to coordinate transcriptional elongation at coding regions. Molecular and Cellular Proteomics. 2014 Aug 6. pii: mcp.M114.038224. [Epub ahead of print]
Key words: Histone, transcription, acetylation, methylation, chromatin

3. Papazyan R, Voronina E, Chapman JR, Luperchio TR, Gilbert TM, Meier E, Mackintosh SG, Shabanowitz J, Tackett AJ, Reddy KL, Coyne RS, Hunt DF, Liu Y, Taverna SD. Methylation of histone H3K23 blocks DNA damage in pericentric heterochromatin during meiosis.
eLife. 2014 Aug 26;3:e02996. doi: 10.7554/eLife.02996
Key words: Histone, DNA damage, methylation, meiosis, genome integrity

4. Waldrip ZJ, Byrum SD, Storey A, Gao J, Byrd AK, Mackintosh SG, Wahls WP, Taverna SD, Raney KD, Tackett AJ. A CRISPR-based approach for proteomic analysis of a single genomic locus. Epigenetics. 2014; 9(9). [Epub ahead of print]
Key words: Transcription, histone post-translational modifications, epigenetics, CRISPR, mass spectrometry

1. Mehta S, Aye-Han NN, Ganesan A, Oldach L, Gorshkov K, Zhang J. Calmodulin-controlled spatial decoding of oscillatory Ca2+ signals by calcineurin. Elife. 2014 Jul 23:e03765. doi: 10.7554/eLife.03765. [Epub ahead of print]
Key words: calcium; oscillation; FRET; biosensor; live-cell imaging

1. Brammer Basta LA, Patel H, Kakalis L, Jordan F, Freel Meyers CL. Defining critical residues for substrate binding to 1-deoxy-d-xylulose 5-phosphate synthase - active site substitutions stabilize the predecarboxylation intermediate C2?-lactylthiamin diphosphate. FEBS J. 2014 June;281(12):2820-37.
Key words: CD; DXP synthase; enzymology; protein fluorescence; thiamin


1. Tullman JA, Harmon M-E, Delannoy M, Gibson W. Recovery of an HMWP/hmwBP (pUL48/pUL47) complex from virions of human cytomegalovirus: subunit interactions, oligomers composition, deubiquitylase activity. J Virology. 2014 May 14. pii: JVI.00971-14. [Epub ahead of print.]
Key words: Cytomegalovirus, herpesvirus, protein-protein interactions, ubiquitin, deubiquitylase, virus structure

1. Calcaterra NE, Barrow JC. Classics in Chemical Neuroscience: Diazepam (Valium). ACS Chem. Neurosci. 2014 Apr 16;5(4):253-60.
Key words: Diazepam, Valium, benzodiazepine, GABA, anxiety, hypnotic, sedative

1. Hersman EM, Bumpus NN. A targeted proteomics approach for profiling murine cytochrome P450 expression. J Pharmacol Exp Ther. 2014 May;349(2):221-8.
Key words: cytochrome P450; mass spectrometry; drug metabolism

1. Webster MR, Kamat C, Connis N, Zhao M, Weeraratna AT, Rudek MA, Hann CL, Freel Meyers CL. Bisphosphonamidate clodronate prodrug exhibits selective cytototxic activity against melanoma cell lines. Mol Cancer Ther. 2014 Feb;13(2):297-306.
Key words: prodrug, bisphosphonate, melanoma, clodronate

1. Kiwamoto T, Brummet ME, Wu F, Motari MG, Smith DF, Schnaar RL, Zhu Z, Bochner BS. Mice deficient in the St3gal3 gene product ?2,3 sialyltransferase (ST3Gal-III) exhibit enhanced allergic eosinophilic airway inflammation. J Allergy Clin Immunol. 2014 Jan;133(1):240-247.
Key words: asthma, airway, inflammation, eosinophil, lung

1. Avery LB and Bumpus NN. Valproic acid is a novel activator of AMP-activated protein kinase and decreases liver mass, hepatic fat accumulation, and serum glucose in obese mice. Molecular Pharmacology. 2014 Jan;85(1):1-10.
Key words: Valproic Acid; AMP-activated Protein Kinase; Metabolomics; Mass Spectrometry; Cytochrome P450

2. Teng X, Dayhoff-Brannigan M, Cheng WC, Gilbert CE, Sing CN, Diny NL, Wheelan SJ, Dunham MJ, Boeke JD, Pineda FJ, Hardwick JM. Genome-wide consequences of deleting any single gene. Mol Cell. 2013 Nov 21;52(4):485-94.
Key words: genome evolution, yeast, cancer, amino acid-sensing, cell death

1. Byrum SD, Taverna SD, and Tackett AJ. (2013) Purification of a specific native genomic locus for proteomic analysis. Nucleic Acids Res. 2013 Nov 1;41(20), e195, doi:10.1093/nar/gkt822
Key words: Epigenetics, Transcription, Histone post-translational modifications, Acetylation, Mass spectromery

2. Hu S, Wan J, Su Y, Song Q, Zeng Y, Nguyen HN, Shin J, Cox E, Rho H-S, Woodard C, Xia S, Liu S, Lu H, Ming G, Wade H, Song H, Qian J, Zhu H. DNA methylation presents distinct binding sites for human transcription factors. eLife. 2013; 2:e00726.
Key words: DNA methylation, transcription, protein microarrays, KLF4, CpG

3. Lade JM, Avery LB, Bumpus NN. 2013. Human biotransformation of the non-nucleoside reverse transcriptase inhibitor rilpivirine and a cross species metabolism comparison. Antimicrobial Agents and Chemotherapy. 2013 Oct; 57(10):5067-5079.
Key words: cytochrome P450; HIV; antiretroviral; mass spectrometry; drug metabolism

4. To EE, Hendrix CW, Bumpus NN. 2013. Dissimilarities in the metabolism of antiretroviral drugs used in HIV pre-exposure prophylaxis in colon and vagina tissues. Biochemical Pharmacology. 2013 Oct 1; 86(7):979-990.
Key words: cytochrome P450; HIV; antiretroviral; mass spectrometry; drug metabolism

1. Hu S, Feng Y, Henson B, Wang B, Huang X, Li M, Desai P, Zhu H. VirD - A virion display array for profiling functional membrane proteins. Anal Chem. 2013 Sep 3;85(17):8046?8054.
Key words: VirD; multi-pass membrane proteins, virions, protein microarrays, GPCR

2. Woodard CL, Goodwin CR, Wan J, Xia S, Hu J, Newman RH, Zhang J, Hayward SD, Qian J, Laterra J, Zhu H. Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PLoS One 2013 Sept 2; 8(9):e72671.
Key words: Phosphorylation, lysate, protein microarrays, c-Met, signal transduction

1. Morris F, Vierling R, Boucher L, Bosch J, Freel Meyers C.L. DXP synthase-catalyzed C-N bond formation: nitroso substrate specificity studies guide selective inhibitor design. ChemBioChem. 2013 Jul 22;14(11):1309-1315.
Key words: isoprenoid biosynthesis, selective enzyme inhibitors, thiamin diphosphate


1. Smith J, Vierling RJ, Freel Meyers CL. Selective inhibition of E. coli 1-deoxy-D-xylulose-5-phosphate synthase by acetylphosphonates. MedChemComm. 2012; 3(1): 65-67.
Key words: isoprenoid biosynthesis, DXP synthase, anti-infectives, acetylphosphonate

1. Patel H, Nemeria N, Brammer L, Freel Meyers C, Jordan F. Observation of thiamin-bound intermediates and microscopic rate constants for their interconversion on 1-deoxy-D-xylulose 5-phosphate synthase: 600-fold rate acceleration of pyruvate decarboxylation by D-glyceraldehyde-3-phosphate. J Am Chem Soc 2012;134:18374-79.
Key words: thiamin diphosphate, isoprenoid biosynthesis, anti-infectives

1. Mountney A, Zahner MR, Sturgill ER, Riley CJ, Aston JW, Oudega M, Schramm LP, Hurtado A, Schnaar RL. Sialidase, chondroitinase ABC and combination therapy after spinal cord contusion injury. J Neurotrauma. 2012 Aug 31. [Epub ahead of print]
Key words: Spinal cord injury; axon regeneration; ganglioside; motor behavior; serotonergic axons

2. Shim JS, Rao R, Beebe K, Neckers L, Han I, Nahta R, Liu JO. Selective inhibition of HER2-positive breast cancer cells by the HIV protease inhibitor nelfinavir. J Natl Cancer Inst. 2012 Oct 5. [Epub ahead of print]
Key words include: Nelfinavir, Johns Hopkins Drug Library, Her2, breast cancer, and drug resistance

3. Sturgill ER, Aoki K, Lopez PH, Colacurcio D, Vajn K, Lorenzini I, Majic S, Yang WH, Heffer M, Tiemeyer M, Marth JD, Schnaar RL. Biosynthesis of the major brain gangliosides GD1a and GT1b. Glycobiology. 2012 Oct;22(10):1289-301. Epub 2012 Jun 26.
Key words: Brain, ganglioside, myelin, sialic acid, sialyltransferase

1. Byrum SD, Raman A, Taverna SD, Tackett AJ. ChAP-MS: A method for identification of proteins and histone posttranslational modifications at a single genomic locus. Cell Reports. 2012 July 26;2(1):198-205.
Key words: Histone, chromatin, affinity purification, transcription, mass spectrometry

2. Jung KO, Khan AM, Tan BY, Hu Y, Simon GG, Nascimento EJ, Lemonnier F, Brusic V, Miotto O, Tan TW, Marques ET, Dhalia R, Salmon J, August JT. West nile virus T-cell ligand sequences shared with other flaviviruses: a multitude of variant sequences as potential altered Peptide ligands. J Virol. 2012 July; 86(14):7616-7624.
Key words: West Nile virus, T-cell ligand, flaviviruses, altered peptide ligands, immune cross-reactivity

1. Barrow, JC. Inhibitors of catechol-o-methyltransferase. CNS Neurol Disord Drug Targets, 2012 May;11(3):324-332.
Key words: Catechol-O-methyltransferase; COMT; dopamine; L-DOPA; Parkinson's disease

2. Calabrese V, Cornelius C, Dinkova-Kostova AT, Iavicoli I, Di Paola R, Koverech A, Cuzzocrea S, Rizzarelli E, Calabrese EJ. Cellular stress responses, hormetic phytochemicals and vitagenes in aging and longevity. Biochim Biophys Acta. 2012 May;1822(5):753-83.
Key words: Nrf2, Keap1, stress, sulforaphane, hormesis

3. Dedecker P, Mo GCH, Dertinger T, Zhang J. A widely accessible method for superresolution fluorescence imaging of living systems. Proc. Natl. Acad. Sci. USA. 2012 Jul 3;109(27):10909-10914. [Epub ahead of print]
Key words: subdiffraction-limit, two-color imaging, membrane rafts

4. Dinkova-Kostova AT, Kostov R. Glucosinolates and isothiocyanates in health and disease. Trends Mol Med. 2012 Jun;18(6):337-47.
Key words: NQO1, sulforaphane, phenethylisothiocyanate, cancer, neurodegenerative disease

5. Ibbotson SH, Dawe RS, Dinkova-Kostova AT, Weidlich S, Farr PM, Ferguson J, Wolf CR, Smith G. Glutathione S-transferase genotype is associated with sensitivity to psoralen-UVA (PUVA) photochemotherapy. Br J Dermatol. 2012; 166: 380-388.
Key words: GST, psoralen, UVA, 8-MOP, photochemotherapy

6. Kalra S, Knatko EV, Zhang Y, Honda T, Yamamoto M, Dinkova-Kostova AT. Highly potent activation of Nrf2 by topical tricyclic bis(cyano enone): Implications for protection against UV radiation during thiopurine therapy. Cancer Prev Res (Phila). 2012 Jul;5(7):973-81.
Key words: cyanoenone, Nrf2, NQO1, skin cancer, ultraviolet radiation

7. Zheng S, Laxmi Y R S, David E, Dinkova-Kostova AT, Shiavoni KH, Ren Y, Zheng Y, Trevino I, Bumeister R, Ojima I, Wigley WC, Bliska J, Mierke DF, Honda T. Synthesis, chemical reactivity as Michael acceptors, and biological potency of monocyclic cyanoenones, novel and highly potent anti-inflammatory and cytoprotective agents. J Med Chem. 2012 May 24; 55(10): 4837-4846.
Key words: Keap1, Michael acceptor, NQO1, iNOS, cyanoenone

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July 2015 articles:
Prospective Reimbursement Analysis
Johns Hopkins Clinical Research Network
Visit Animal Care and Use Committee Website
Current Classes
"Interinstitutional Assurance" Agreement (between Johns Hopkins and a company receiving an NIH research award)
Giovanni Armenise - Harvard Foundation Career Development Award
Free to Breathe Accelerate Clinical Trials Grant
2016 Searle Scholars Program
Otolaryngology Head & Neck Cancer SPORE - Career Development Projects
HHMI Gates Simons Faculty Scholars Program
Damon Runyon Cancer Research Foundation Accepting Applications for Early Career Fellowship Awards
Fondation Leducq Transatlantic Networks of Excellence Program
ALS Therapy Alliance
New Biosketch Format for NIH and AHRQ Applications
NIH Policy: Foreign Components Added to a Grant to a Domestic or Foreign Organization

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