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PublicationsPublished or in press manuscripts:
157. Ahmed, N.; Francis, M. E.; Ahmed, N.; Kelvin, A. A.; Pezacki, J. P. "microRNA-185 Inhibits SARS-CoV-2 Infection through the Modulation of the Host’s Lipid Microenvironment" Viruses 2023, 15, 9, 1921. DOI: 10.3390/v15091921 156. Ahmed, N.; Ahmed, N.; Bilodeau, D. A.; Pezacki, J. P. "An unnatural enzyme with endonuclease activity towards small non-coding RNAs" Nat. Comm. 2023, 14, 1, 3777. DOI: 10.1038/s41467-023-39105-0 155. Strmiskova, M.; Josephson, J. D.; Toudic, C.; Pezacki, J. P. "Optimized Bioorthogonal Non-canonical Amino Acid Tagging to Identify Serotype-Specific Biomarkers in Verotoxigenic Escherichia coli" ACS Infect. Dis. 2023, 9, 4, 856-863. DOI: 10.1021/acsinfecdis.2c00548 154. Evers, P.; Pezacki, J. P. "Unraveling Complex MicroRNA Signaling Pathways with Activity‐Based Protein Profiling to Guide Therapeutic Discovery" Isr. J. Chem. 2023, 63, 3-4, e202200088. DOI: 10.1002/ijch.202200088 153. Pham, T.; Walden, E.; Huard, S.; Pezacki, J. P.; Fullerton, M. D.; Baetz K. "Fine-tuning acetyl-CoA carboxylase 1 activity through localization: functional genomics reveals a role for the lysine acetyltransferase NuA4 and sphingolipid metabolism in regulating Acc1 activity and localization" Genetics 2022, 221, 4, iyac086. DOI: 10.1093/genetics/iyac086 152. Desrochers, G. F.; Filip, R.; Bastianelli, M.; Stern, T.; Pezacki, J. P. "microRNA-27b regulates hepatic lipase enzyme LIPC and reduces triglyceride degradation during hepatitis C virus infection" J. Biol. Chem. 2022, 298, 6, 101983. DOI: 10.1016/j.jbc.2022.101983 151. Ahmed, N.; Ahmed, N.; Pezacki, J. P. "miR-383 regulates hepatic lipid homeostasis and response to dengue virus infection" ACS Infect. Dis. 2022, 8, 5, 928-941. DOI: 10.1021/acsinfecdis.1c00470 150. Labana, P.; Dornan, M. H.; Lafrenière, M.; Czarny, T. L.; Brown, E. D.; Pezacki, J. P.; Boddy, C. N. "Armeniaspirols inhibit the AAA+ proteases ClpXP and ClpYQ leading to cell division arrest in Gram-positive bacteria" Cell Chem. Bio. 2021, 28, 12, 1703-1715. DOI: 10.1016/j.chembiol.2021.07.001 149. Scinto, L. S.; Bilodeau, D. A.; Hincapie, R.; Lee, W.; Nguyen, S. S.; Xu, M.; Am Ende, C. W.; Finn, M. G.; Lang, K.; Lin, Q.; Pezacki, J. P.; Prescher, J. A.; Robillard, M. S.; Fox, J. M. "Bioorthogonal chemistry" Nat. Rev. Methods Primers 2021, 1, 1, 30. DOI: 10.1038/s43586-021-00028-z 148. Hum, C.; Loiselle, J.; Ahmed, N.; Shaw, T. A.; Toudic, C.; Pezacki, J. P. "MicroRNA mimics or inhibitors as antiviral therapeutic approaches against COVID-19" Drugs 2021, 81, 5, 517-531. DOI: 10.1007/s40265-021-01474-5 147. Filip, R.; Desrochers, G. F.; Lefebvre, D. M.; Reed, A.; Singaravelu, R.; Cravatt, B. F.; Pezacki, J. P. "Profiling of MicroRNA targets using activity-based protein profiling: Linking enzyme activity to MicroRNA-185 function" Cell Chem. Bio. 2021, 28, 2, 202-212. DOI: 10.1016/j.chembiol.2020.12.009 146. Bilodeau, D. A.; Margison, K. D.; Serhan, M.; Pezacki, J. P. "Bioorthogonal reactions utilizing nitrones as versatile dipoles in cycloaddition reactions" Chem. Rev. 2021, 121, 12, 6699-6717. DOI: 10.1021/acs.chemrev.0c00832 145. Ahmed, N.; Ahmed, N.; Filip, R.; Pezacki, J. P. "Nuclear Hormone Receptors and Host-Virus Interactions" Nuclear Receptors: The Art and Science of Modulator Design and Discovery 2021, 315-348. DOI: 10.1007/978-3-030-78315-0_13 (Book chapter) 144. Shaw, T. A.; Powdrill, M. H.; Sherratt, A. R.; Garland, K.; Li, B. J.; Beauchemin, A. M.; Pezacki, J. P. "Reactivity of N-acyl hydrazone probes with the mammalian proteome" RSC Med. Chem. 2021, 12, 5, 797-803. DOI: 10.1039/D1MD00027F 143. Wallace, H. L.; Wang, L.; Davidson, C.; Chelakkot, V.; Grant, M.; Pezacki, J. P.; Hirasawa, K.; Russell, R. S. "Knock Out of Cell Death Pathway Components Results in Differential Caspase Expression in Response to HCV Infection" Proceedings 2020, 50, 1, 144. DOI: 10.3390/proceedings2020050144 142. Shaw, T. A.; Ablenas, C. J.; Desrochers, G. F.; Powdrill, M. H.; Bilodeau, D. A.; Vincent-Rocan, J.-F.; Niu, M.; Monette, A.; Mouland, A. J.; Beauchemin, A. M.; Pezacki, J.P. “A bifunctional nucleoside probe for the inhibition of the human immunodeficiency virus-type 1 reverse transcriptase” Bioconj. Chem. 2020, 31, 5, 1537-1544. DOI: 10.1021/acs.bioconjchem.0c00191 141. Margison, KD; Bilodeau, DA; Mahmoudi, F; Pezacki, J.P. “Cycloadditions of Trans-Cyclooctenes and Nitrones as Tools for Bioorthogonal Labelling” ChemBioChem 2020, 21, 948-951. DOI: 10.1002/cbic.201900627 140. Nakajima, M.; Bilodeau, D.A.; Pezacki, J.P. "Predicting reactivity for bioorthogonal cycloadditions involving nitrones" RSC Adv. 2020, 10, 29306-29310. DOI: 10.1039/D0RA05092J 139. Bilodeau, DA; Margison, KD; Ahmed, N; Strmiskova, M; Sherratt, AR; Pezacki, J.P. “Optimized aqueous Kinugasa reactions for bioorthogonal chemistry applications” Chem. Commun. 2020, 56, 1988-1991. 138. Gobeil Odai, K.; O'Dwyer, C.; Steenbergen, R.; Shaw, T. A.; Renner, T. M.; Ghorbani, P.; Rezaaifar, M.; Han, S.; Langlois, M.-A.; Crawley, A. M.; Russell, R. S.; Pezacki, J. P.; Tyrrell, D. L.; Fullerton, Morgan D. “In Vitro Hepatitis C Virus Infection and Hepatic Choline Metabolism.” Viruses 2020, 12, 1, DOI:10.3390/v12010108 137. Farzam, A., Chohan, K., Strmiskova, M., Hewitt, S.J., Park, D.S., Pezacki, J.P., Özcelik, D. “A functionalized hydroxydopamine quinone links thiol modification to neuronal cell death” Redox Biol. 2020, 28, U1010377. doi.org/10.1016/j.redox.2019.101377 136. Singaravelu, R., Ahmed, N., Quan, C., Srinivasan, P., Ablenas, C.J., Roy, D.G., Pezacki, J.P. “Conserved miRNA-183 cluster regulates the innate antiviral response” J. Biol. Chem. 2019, 294, 19785–19794. 135. Ablenas, C., Gidi, Y., Powdrill, M., Ahmed, N., Shaw T., Mesko, M., Gotte, M., Cosa, G., Pezacki, J.P. “Hepatitis C virus helicase binding and activity monitored through site-specific labeling using an expanded genetic code.” ACS Infect. Dis. 2019, 5, 2118−2126. 134. Özcelik, D., Pezacki, J.P. “Small Molecule Inhibition of Protein Disulfide Isomerase in Neuroblastoma Cells Induces an Oxidative Stress Response and Apoptosis Pathways.” ACS Chem. Neurosci. 2019, 10, 4068-4075. 133. Ahmed, N.; Foss, D.V.; Powdrill, M.H.; Pezacki JP “Site-specific crosslinking of a p19 viral suppressor of RNA silencing protein and its RNA targets using an expanded genetic code” Biochemistry 2019, 58, 3520-3526. 132. Filip, R.; Shaw, T. A.; Nishida, A.; Pezacki, J.P. “Fungal natural alkaloid schizocommunin activates the aryl hydrocarbon receptor pathway” MedChemComm 2019, 10, 985 - 990. 131. Danielson DC, Schirle, NS, MacRae IJ, Pezacki JP “Structural examination of p19 mutants with high affinity for small RNAs” FEBS Open Bio 2019, 9, 1042-1051. DOI: 10.1002/2211-5463.12644. (Cover article) 130. Strmiskova M., Bilodeau D. A., Chigrinova M., Pezacki, J.P. “Phenanthridine-based nitrones as substrates for strain-promoted alkyne-nitrone cycloadditions” Can. J. Chem. 2019, 97, 1-6. 129. Desrochers, G. F., Pezacki, J. P. “ABPP and Host-Virus Interactions.” Curr. Topics Microbiol. Immunol. 2019, 420:131 154, DOI:10.1007/82_2018_139. (Book Chapter) 128. Özcelik D, Seto A, Rakic B, Farzam A, Supek F, Pezacki JP "Gene expression profiling of endoplasmic reticulum stress in hepatitis C virus-containing cells treated with an inhibitor of protein disulfide isomerases " ACS Omega. 2018, 3, 17227-17235. 127. Shaw TA, Singaravelu R, Powdrill MH, Nhan J, Ahmed N, Özcelik D, Pezacki JP "MicroRNA-124 regulates fatty acid and triglyceride homeostasis" iScience. 2018, 10, 149-157. 126. Ahmed N, De Graaf JF, Ahmed N, Foss DV, Delcorde J, Schultz PG, Pezacki JP "Visualization of the delivery and release of small RNAs using genetic code expansion and unnatural RNA-binding proteins " ACS Bioconjug. Chem. 2018, 29(12), 3982-3986. 125. Desrochers GF, Cornacchia C, McKay CS, Pezacki JP "Activity-Based PIK Probes Detect Changes to Protein-Protein Interactions During Hepatitis C Virus Replication" ACS Infect. Dis. 2018, 4(5), 752-757. 124. Singaravelu R, Quan C, Powdrill MH, Shaw TA, Srinivasan P, Lyn RK, Alonzi RC, Jones DM, Filip R, Russell RS, Pezacki JP "MicroRNA-7 mediates cross-talk between metabolic signaling pathways in the liver" Sci. Rep. 2018, 8:361 123. Lafrenière MA, Desrochers GF, Mekbib K, Pezacki JP "An affinity-based probe for methyltransferase enzyme based on sinefungin" Can. J. Chem. 2017, 95; 1059-1063 122. Sherratt AR, Rouleau Y, Luebbert C, Strmiskova M, Veres T, Bidawid S, Corneau N, Pezacki JP. "Rapid Screening and Identification of Living Pathogenic Organisms via Optimized Bioorthogonal Non-canonical Amino Acid Tagging" Cell Chem Biol. 2017, 17; 24(8):1048-1055 121. Ouimet M, Ediriweera H, Afonso MS, Ramkhelawon B, Singaravelu R, Liao X, Bandler RC, Rahman K, Fisher EA, Rayner KJ, Pezacki JP, Tabas I, Moore KJ. "microRNA-33 Regulates Macrophage Autophagy in Atherosclerosis" Arterioscler Thromb Vasc Biol. 2017; 37(6): 1058-1067 120. Lafreniere MA, Powdrill MH, Singaravelu R, Pezacki JP "6-Hydroxydopamine inhibits the hepatitis C virus through alkylation of host and viral proteins and the induction of oxidative stress" ACS Infect. Dis. 2016, 2 (11), 863-871. 119. Strmiskova M, Desrochers GF, Powdrill MH, Shaw T, Lafreniere MA, Pezacki JP “Chemical Methods for Probing Virus-Host Proteomic Interactions”ACS Infect. Dis. 2016, 2 (11), 773-786. 118. Powdrill MH, Desrochers GF, Singaravelu R, Pezacki JP “The role of microRNAs in metabolic interactions between viruses and their hosts” Curr. Opin. Virol. 2016, 19, 71-76. (invited review) 117. Sherratt AR, Chigrinova M, MacKenzie DA, Rastogi NK, Ouattara MTM, Pezacki AT, Pezacki JP “Dual strain-promoted alkyne-nitrone cycloadditions for simultaneous labeling of bacterial peptidoglycans.”, Bioconj. Chem. 2016, 27, 1222−1226. 116. Danielson DC, Sachrajda N, Wang W, Filip R, Pezacki JP “A novel p19 fusion protein as a delivery agent for short-interfering RNAs”, Mol. Ther. Nucleic Acids 2016, 5, e303. 115. Singaravelu R, O'Hara S, Jones DM, Chen R, Taylor NG, Srinivasan P, Quan C, Roy DG, Steenbergen RH, Kumar A, Lyn RK, Özcelik D, Rouleau Y, Nguyen MA, Rayner KJ, Hobman TC, Tyrrell DL, Russell RS, Pezacki JP “MicroRNAs regulate the immunometabolic response to viral infection in the liver”, Nat. Chem. Biol. 2015, 11, 988-993. 114. Nasheri N, Ning Z, Figeys D, Goto NK, Yao S, Pezacki JP “Activity-based profiling of the proteasome pathway during hepatitis C virus infection”, Proteomics. 2015, 15, 3815-3825. 113. Desrochers GF, Sherratt AR, Blais DR, Nasheri N, Ning Z, Figeys D, Goto NK Pezacki JP “Profiling protein kinase activity during hepatitis C virus replication using a Wortmannin-based probe”, ACS Inf. Dis. 2015, 1, 443-452. 112. Mackenzie DA, Sherratt AR, Chigrinova M, Kell AJ, Pezacki JP “Bioorthogonal labelling of living bacteria using unnatural amino acids containing nitrones and a nitrone derivative of vancomycin”, Chem. Commun. 2015, 51, 12501-12504. 111. Karunakaran D, Thrush AB, Geoffrion M, Ramphos E, Singaravelu R, Nguygen M-A, Shangari P, Pezacki JP, Harper M-E, Moore KJ, Rayner KJ ” Macrophage mitochondrial energy status regulates cholesterol efflux and is enhanced by anti-miR33 in atherosclerosis”, Circ. Res. 2015, 117, 266-278. 110. Singaravelu R, Srinivasan P, Pezacki JP “Armand-Frappier Outstanding Student Award: The emerging role of 25-hydroxycholesterol in innate immunity”, Can. J. Microbiol. 2015, 61, 521-530. 109. Danielson DC, Powdrill MH, Filip R, Parekh V, Pezacki JP “Inhibiting the RNA silencing pathway with the p19 protein and small molecules.” Biochem. Biophys. Res. Commun. 2015, 463, 1135-1140. 108. Chigrinova M, Mackenzie DA, Sherratt AR, Cheung LLW, Pezacki JP “Kinugasa Reactions in Water: from Green Chemistry to Bioorthogonal Labelling”, Molecules 2015, 20, 6959-6969. 107. Singaravelu R, Desrochers GF, Srinivasan P, O’Hara S, Jones DM, Lyn RK, Muller R, Russell RS, and Pezacki JP “Soraphen A: a probe for investigating the role of de novo lipogenesis during viral infection”, ACS Inf. Dis. 2015, 3, 130–134 (cover article). 106. Sherratt AR, Chigrinova M, McKay CS, Beaulieu LPB, Rouleau Y, Pezacki JP “Copper-catalyzed cycloaddition reactions of nitrones and alkynes for bioorthogonal labeling of living cells”, RCS Advances 2014, 4, 46966-46969. 105. Nasheri N, McKay CS, Fulton K, Twine S, Powdrill MH, Sherratt AR, Pezacki JP “Hydrophobic triaryl-substituted β-lactams as activity-based probes for profiling eukaryotic enzymes and host-pathogen interactions” ChemBioChem 2014, 15, 2195-2200 (cover article). 104. Singaravelu R, Delcorde J, Lyn RK, Jones DM, Russell RS, Pezacki JP “Investigating the Antiviral Role of Cell Death-Inducing DFF45-like Effector B (CIDEB) in HCV Replication” FEBS J. 2014, 281, 3751-3765. 103. MacKenzie DA, Chigrinova M, Cheung LLW, Sherratt AR, Pezacki JP “Strain-promoted cycloadditions involving nitrones and alkynes - rapid tunable reactions for bioorthogonal labeling” Curr. Opin. Chem. Biol. 2014, 21, 81–88. (Downloaded more than 500 times in the first 3 months according to the journal) 102. Sherratt AR, McKay CS, O’Hara S, Nasheri N, Hunt A, Ning Z, Figeys D, Goto NK, Pezacki JP “An activity-based probe for phosphatidyl inositol kinases” ChemBioChem 2014, 15, 1253-1256. 101. Singaravelu R, Russell RS, Tyrrell DL, Pezacki JP “Hepatitis C virus and human microRNAs: miRed in a host of possibilities” Curr. Opin. Virol. 2014, 7, 1-10. 100. Lyn RK, Singaravelu R, Kargman S, O’Hara S, Chan H, Oballa R, Huang Z, Partridge AW, Pezacki JP “Stearoyl-CoA desaturase inhibition blocks formation of hepatitis Cm virus-induced specialized membranes” Sci. Reports (Nature Publishing Group) 2014, 4, 4549. DOI: 10.1038/srep04549. (Merck collaboration) 99. MacKenzie DA, Pezacki JP “Kinetics studies of rapid strain-promoted [3+2] cycloadditions of nitrones with bicyclo[6.1.0]nonyne” Can. J. Chem. 2014, 92, 337–340. 98. Singaravelu R, Chen R, Lyn RK, Jones DM, Rouleau Y, O’Hara S, Cheng J, Srinivasan P, Nasheri N, Russell RS, Tyrrell DL, Pezacki JP “Hepatitis C virus induced up-regulation of miR-27 expression promotes triglyceride accumulation” Hepatology 2014, 59, 98-108 (Cover article, Web of Science highly cited article – ‘As of July/August 2014, this highly cited paper received enough citations to place it in the top 1% of its academic field based on a highly cited threshold for the field and publication year.’). 97. Singaravelu R, Lyn RK, Srinivasan P, Delcorde J, Steenbergen R, Tyrrell DL, Pezacki JP “Human serum stimulates CIDEB-mediated lipid droplet enlargement in hepatoma cells” Biochem. Biophys. Res. Commun. 2013, 441, 447–452. 96. Lyn RK, Hope G, Sherratt AR, McLauchlan J, Pezacki JP “Bidirectional lipid droplet velocities are controlled by differential binding strengths of HCV core DII protein” PLoS One 2013, 8, e78065. 95. Mazumder N, Lyn RK, Singaravelu R, Ridsdale A, Moffatt DJ, Hu C-W, Tsai H-R, McLauchlan J, Stolow A, Kao F-J, Pezacki JP “Fluorescence lifetime imaging of alterations to cellular metabolism by domain 2 of the hepatitis C virus core protein” PLoS One 2013, 8, e66738. 94. Chigrinova M, McKay CS, Beaulieu LPB, Udachin KA, Beauchemin AM, Pezacki JP “Rearrangements and addition reactions of biarylazacyclooctynones and the implications to copper-free click chemistry” Org. Biomol. Chem. 2013, 11, 3436-3441. 93. Nasheri N, Joyce M, Rouleau Y, Yang P, Yao S, Tyrrell DL, Pezacki JP “Modulation of Fatty Acid Synthase Enzyme Activity and Expression during Hepatitis C Virus Replication” Chem. Biol. 2013, 20, 570-582 (Cover article). 92. Danielson DC, Pezacki JP “Studying the RNA silencing pathway with the p19 protein” FEBS Letters 2013, 587, 1198–1205. 91. Labib M, Khan N, Ghobadloo, S, Cheng J, Pezacki JP, Berezovski M “Three-Mode Electrochemical Sensing of Ultra-Low MicroRNA Levels” J. Am. Chem. Soc. 2013, 135, 3027-3038. (First example of miRNA detection in blood samples via electrochemical sensing using p19) 90. Sherratt A, Blais DR, Ghasriani H, Pezacki JP, Goto NK “Activity-based protein profiling of the E. coli GlpG rhomboid protein delineates the catalytic core.” Biochemistry 2012, 51, 7794−7803. 89. Singaravelu R, Nasheri N, Sherratt A, Pezacki JP “Systems biology methods help develop a better understanding of HCV-induced liver injury” Hepatology 2012, 56, 1-4. 88. Legault MCB, McKay CS, Moran J,Lafreniere M, Pezacki JP “Novel intramolecular cyclization and subsequent rearrangments of alkyne-tethered N-heterocyclic carbenes” Tet. Let. 2012, 53, 5663-5666. 87. McKay CS, Chigrinova M, Blake JA, Pezacki JP “Kinetics studies of metal-free [3+2]-cycloadditions of nitrones with biarylazacyclooctynones” Org. Biomol. Chem. 2012, 10, 3066-3070. 86. Hoop KA, Kennedy DC, Mishki T, Lopinski G, Pezacki JP “Silicon Surface Modification using NHC and Thiamine Catalyzed Benzoin Condensations” Can. J. Chem. 2012, 90, 262-270. 85. Clime L, Brassard D, Pezacki JP, Veres T “Self-priming of liquids in capillary autonomous microfluidic systems” Microfluid Nanofluid 2012, 12, 371-382. 84. Blais DR, Nasheri N, McKay CS, Legault MCB, Pezacki JP “Activity-based protein profiling of host-virus interactions” Trends Biotechnol 2012, 30, 89-99. 83. Kennedy DC, McKay CS, Legault MCB, Danielson D, Pegoraro AF, Stolow A, Mester Z, Pezacki JP “Cellular Consequences of Copper Complexes used to Catalyze Click Reactions” J. Am. Chem. Soc. 2011, 133, 17993-18001. (Highly cited paper detailing the reasons for copper toxicity) 82. Cheng J, Danielson D, Nasheri, N, Singaravelu R, Pezacki JP ”Enhanced specificity of the viral suppressor of RNA silencing protein p19 towards sequestering of human microRNA-122” Biochemistry 2011, 50, 7745-55. 81. McKay CS, Blake JA, Cheng J, Danielson D, Pezacki JP “Strain-promoted alkyne-nitrone cycloadditions for labeling human cancer cells” Chem. Commun. 2011, 47, 10040-10042. (First labeling of cancer cells via SPANC) 80. Khan N, Cheng J, Pezacki JP, Berezovski MV “Quantitative Analysis of microRNA in Blood Serum with Protein-Facilitated Affinity Capillary Electrophoresis” Anal. Chem. 2011, 83, 6196-6201. 79. Tian R, Hoa XD, Lambert J-P, Pezacki JP, Veres T, Figeys D “The development of a multiplexed microfluidic proteomic reactor and its application for studying protein-protein interactions” Anal. Chem. 2011, 83, 4095-4102. 78. Faragher RJ, McKay CS, Hoa XD, Prikrylova B, Lopinski GP, Figeys D, Veres T, Pezacki JP “Functionalizing cyclic olefin polymers using copper catalyzed azide-alkyne “click” reactions” Can. J. Chem. 2011, 89, 608-615. 77. Nasheri N, Cheng J, Singaravelu R, Wu P, McDermott MT, Pezacki JP “An enzyme-linked assay for the rapid quantification of miRNAs based on the viral suppressor of RNA silencing protein p19” Anal. Biochem. 2011, 412, 164-172. 76. Kennedy DC, McKay CS, Tay LL, Rouleau Y, Pezacki JP “Carbon-bonded silver nanoparticles: alkyne-functionalized ligands for SERS imaging of mammalian cells” Chem. Commun. 2011, 47, 3156-8. 75. Pezacki JP, Blake JA, Danielson D, Kennedy DC, Lyn RK, Singaravelu R “Chemical contrast for imaging living systems: molecular vibrations drive CARS microscopy” Nature Chem. Biol. 2011, 7, 137-45. (Web of Science highly cited article – As of July/August 2014, is in the top 1% of its academic field based on a high threshold for the field and publication year.) 74. A. D. Slepkov, A. Ridsdale, H.-N. Wan, M.-H. Wang, A. F. Pegoraro, D. J. Moffatt, J. P. Pezacki, F.-J. Kao, and A. Stolow “Forward-collected fluorescence lifetime imaging coherent anti-Stokes Raman scattering microscopy” J. Biomed. Opt. 2011, 16, 021103. 73. Nasheri N, Singaravelu R, Goodmurphy M, Lyn RK, Pezacki JP “Competing roles of microRNA-122 recognition elements in hepatitis C Virus RNA” Virology 2011, 410, 336-344. 72. Moran J, McKay CS, Pezacki JP “Strain-promoted 1,3-dipolar cycloadditions of diazo compounds with cyclooctynes” Can. J. Chem. 2011, 89, 148-151. 71. Lyn RL, Kennedy DC, Stolow A, Ridsdale A, Pezacki JP “Dynamics of lipid droplets induced by the hepatitis C virus core protein” Biochem. Biophys. Res. Commun. 2010, 399, 518-24. 70. Pegoraro AF, Slepkov AD, Ridsdale A, Pezacki JP, Stolow A. “Single laser source for multimodal coherent anti-Stokes Raman scattering microscopy” Appl. Opt. 2010, 49, F10-17. 69. Blais DR, Lyn RK, Joyce M, Rouleau Y, Steenbergen R, Barsby N, Zhu lF, Pegoraro AF, Stolow A, Tyrrell DL, Pezacki JP “Activity-based protein profiling identifies a host enzyme, carboxylesterase 1, which is differentially active during hepatitis C virus replication“ J. Biol. Chem. 2010, 285, 25602-25612. (Important example of a host-virus interaction involving a host enzyme during HCV infection that was identified by ABPP) 68. Kennedy DC, Hoop KA, Tay LL, Pezacki JP “Development of Nanoparticle Probes for Multiplex SERS Imaging Applications” Nanoscale 2010, 2, 1413-1416. 67. Sagan SM, Nasheri N, Luebbert C, Pezacki JP “The efficacy of siRNAs against Hepatitis C virus is strongly influenced by the structure and target site accessibility” Chem. Biol. 2010, 17, 515-527. 66. Tay LL, Hulse, J, Kennedy, DC, Pezacki, JP “Surface Enhanced Raman and Resonant Rayleigh Scatterings From Adsorbate Saturated Nanoparticles” J. Phys. Chem. C. 2010, 114, 7356–7363. 65. Pezacki, JP, Singaravelu, R, Lyn, RK “Host-virus interactions during hepatitis C virus infection: A complex and dynamic molecular biosystem” Mol. Biosys. 2010, 6, 1131-1142. 64. Singaravelu, R, Blais, DR, McKay, CS, Pezacki JP ”Activity-based protein profiling of the hepatitis C virus replication in Huh7 hepatoma cells using a non-directed active site probe” Proteome Science 2010, 8, 5. 63. Blais DR, Brulotte M, Qian Y, Belanger S, Yao SQ, Pezacki JP "Activity-based proteome profiling of hepatoma cells during hepatitis C virus replication using protease substrate probes" J. Proteome Res. 2010, 9, 912–923. (One of the first applications of activity-based protein profiling to host-virus interactions for HCV) 62. McKay CS, Moran J, Pezacki JP “Nitrones as Dipoles for Rapid Strain-Promoted 1,3-Dipolar Cycloadditions with Cyclooctynes” Chem. Commun. 2010, 46, 931–933. (First report of nitrones used in strain-promoted cycloadditions with cyclooctynes) 61. Kennedy DC, Duguay DR, Tay LL, Richeson DS, Pezacki JP “SERS detection and boron delivery to cancer cells using carborane labelled nanoparticles” Chem. Commun. 2009, 6750-6752. 60. Pegoraro, AF, Ridsdale, A, Moffatt, DJ, Pezacki, JP, Thomas, BK, Fu, L, Dong, L, Fermann, ME Stolow, A “All-fiber CARS microscopy of live cells” Optics Express 2009, 17, 2984-2996. 59. Lyn RK, Kennedy DC, Sagan SM, Blais DR, Rouleau Y, Pegoraro AF, Xie XS, Stolow A, Pezacki JP “Direct imaging of the disruption replication complexes of the hepatitis C virus by inhibitors of lipid metabolism” Virology 2009, 394, 130–142. (Cover article) 58. Kennedy DC, Tay LL, Lyn RK, Rouleau Y, Hulse J, Pezacki JP. “Nanoscale aggregation of cellular b2-adrenergic receptors seen by plasmonic interactions of functionalized nanoparticles.” ACS Nano 2009, 3, 2329-2339. 57. van der Wiel IM, Cheng J, Koukiekolo R, Lyn RK, Stevens N, Oconnor N, Turro N, Pezacki JP “FLEth RNA Intercalating Probe is a Convenient Reporter for Small Interfering RNAs” J. Am. Chem. Soc. 2009, 131, 9872–9873. (Novel screening approach for p19-RNA interactions described using FLEth intercalating probe) 56. Koukiekolo R, Jakubek ZJ, Cheng J, Sagan SM, Pezacki JP. “Studies of a viral suppressor of RNA silencing p19-CFP fusion protein: A FRET-based probe for sensing double stranded fluorophore tagged small RNAs” Biophys. Chem. 2009, 143,166-9. 55. Cheng J, Koukiekolo R, Kieliszievicz K, Sagan SM, Pezacki JP .“Cysteine residues of Carnation Italian ringspot virus p19 suppressor of RNA silencing help maintain global structural integrity and stability for siRNA binding.” BBA- Proteins and Proteomics 2009, 1794,1197-1203. 54. McKay CS, Kennedy DC, Pezacki JP. “Studies of multicomponent Kinugasa reactions in aqueous media” Tetrahedron Lett. 2009, 50, 1893–1896. 53. Kennedy DC, Lyn RK, Pezacki JP. “Cellular Lipid Metabolism Is Influenced by the Coordination Environment of Copper.” J. Am. Chem. Soc. 2009, 131, 2444–2445. (One of the first investigations of the influence of copper coordination on its effects on cellular metabolism) 52. Pegoraro AF, Ridsdale A, Moffatt DJ, Jia Y, Pezacki JP, Stolow A. “Optimally chirped multimodal CARS microscopy based on a single Ti:sapphire oscillator” Optics Express 2009, 17, 2984. 51. Pezacki JP, Sagan SM, Tonary AM, Rouleau Y, Supekova L, Su AI. “Transcriptional profiling of the effects of 25-hydroxycholesterol on human hepatocyte metabolism and the antiviral state it conveys against the hepatitis C virus.” BMC Chem. Biol. 2009 9, 2. 50. Vobornik D, Rouleau Y, Haley J, Bani-Yaghoub M, Taylor R, Johnston L, Pezacki JP. “Nanoscale Organization of β2-Adrenergic Receptor-Venus Fusion Protein Domains on the Surface of Mammalian Cells.” Biochem. Biophys. Res. Commun. 2009, 382, 85-90. 49. Davis M, Sagan SM, Pezacki JP, Evans DJ, and Simmonds P. “Bioinformatic and Physical Characterisation of Genome-Scale Ordered RNA Structure (GORS) in Mammalian RNA Viruses.” J. Virology 2008, 82, 11824-36. 48. Lorello GR, Legault MCB, Rakić B, Bisgaard K, Pezacki JP. “Synthesis and bioorthogonal coupling chemistry of a novel cyclopentenone-containing unnatural tyrosine analogue.” Bioorg. Chem. 2008 36,105-11. 47. Cheng J, Sagan SM, Jakubek Z, Pezacki JP. “Studies of the interaction of the viral suppressor of RNA silencing protein p19 with small RNAs using fluorescence polarization.” Biochemistry 2008, 47, 8130–8138. 46. Supekova L, Supek F, Lee J, Chen S, Gray N, Pezacki JP, Schlapbach A, Schultz PG. “Identification of human kinases involved in hepatitis C virus replication by small interference RNA library screening.” J. Biol. Chem. 2008, 283, 29-36. 45. Blais DR, Alvarez-Puebla RA, Bravo-Vasquez JP, Fenniri H, Pezacki JP. “A multiplexed pathogen detection immunoassay based on spatially addressable microarrays of barcoded resins.” Biotech. J. 2008, 3, 948-53. 44. Cheng J, Sagan SM, Assem N, Koukiekolo R, Goto NK, Pezacki JP. “Stabilized recombinant suppressors of RNA silencing: Functional effects of linking monomers of CIRV p19.” BBA Proteins and Proteomics 2007, 1774, 1528-35. 43. Koukiekolo R, Sagan SM, Pezacki JP. “Effects of pH and salt concentration on the siRNA binding activity of the RNA silencing suppressor protein p19.” FEBS Lett. 2007, 581, 3051-6. 42. Noestheden M, Hu Q, Tay LL, Tonary AM, Pezacki JP. “Labeling Strategies for Live Cell Tracking of HCV Viral RNA Using Raman and Coherent Anti-Stokes Raman Scattering Microscopies” Org. Biomol. Chem. 2007, 5, 2380–2389. 41. Raez J, Blais DR, Zhang Y, Alvarez-Puebla RA, Bravo-Vasquez JP, Pezacki JP, Fenniri H. “Spectroscopically Encoded Microspheres for Antigen Biosensing.” Langmuir 2007, 23, 6482-5. 40. Noestheden M, Hu Q, Tay LL, Tonary AM, Stolow A, MacKenzie R, Tanha J, Pezacki JP. “Synthesis and characterization of CN-modified protein analogues as potential vibrational contrast agents.” Bioorg. Chem. 2007, 35, 284–293. 39. Jackman J, Noestheden M, Moffat D, Pezacki JP, Findlay S, Ben RN. “Assessing antifreeze activity of AFGP 8 using domain recognition software.” Biochem. Biophys. Res. Commun. 2007, 354, 340-4. 38. Hu Q, Tay LL, Noestheden M, Pezacki JP. “Mammalian Cell Surface Imaging with Nitrile-Functionalized Nanoprobes: Biophysical Characterization of Aggregation and Polarization Anisotropy in SERS Imaging.” J. Am. Chem. Soc. 2007, 129, 14-15. (One of the first demonstrations of SERS imaging of cell surface proteins on human cells) 37. Sagan SM, Koukiekolo R, Rodgers E, Goto NK, Pezacki JP. “Cysteine alkylation blocks siRNA binding to a p19 viral suppressor of RNA silencing.” Angew. Chem. Int. Ed. 2007, 46, 2005 –2009. 36. Diaz-Quijada GA, Farrahi S, Clarke J, Tonary AM, Pezacki JP. “Picoliter Wells from Selective Growth of HEK293 Cells on Chemically Modified PDMS Surfaces.” J. Biomat. Appl. 2007, 21, 235-249. 35. Rakić B, Brûlotte M, Rouleau Y, Bélanger S, Pezacki JP. “Bleomycin: A Potent Small-Molecule Probe for Hepatitis C Virus Replication.” ChemBioChem 2006, 7, 1330 – 1333. (One of the first mechanistic links established between hepatitis C virus replication and PPAR signaling) 34. Tonary AM, Pezacki JP. “Simultaneous quantitative measurement of luciferase reporter activity and cell number in two- and three-dimensional cultures of hepatitis C virus replicons.” Anal. Biochem. 2006, 350, 239-248. 33. Rakic B, Clarke J, Tremblay TL, Nelson K, Abrams SR, Pezacki JP. “A Small Molecule Probe for Hepatitis C Virus Replication That Blocks Protein Folding.” Chem. Biol. 2006, 13, 1051–1060. 32. Nan X, Tonary AM, Stolow A, Xie XS, Pezacki JP. “Intracellular imaging of HCV RNA and cellular lipids using simultaneous two-photon fluorescence and coherent anti-Stokes Raman scattering microscopies.” ChemBioChem 2006, 7, 1895 – 1897. 31. Rakic B, Sagan SM, Noestheden M, Bélanger S, Nan X, Evans CL, Xie XS, Pezacki JP. “Peroxisome Proliferator-activated Receptor α Antagonism Inhibits Hepatitis C Virus Replication.” Chem. Biol. 2006, 13, 23-30. 30. Sagan S, Rouleau Y, Leggiadro C, Supekova L, Schultz PG, Su AI, Pezacki JP. “The Influence of Cholesterol and Lipid Metabolism on Host Cell Structure and Hepatitis C Virus Replication.” Biochem. Cell Biol. 2006, 84, 67-79. 29. Ianoul A, Grant DD, Rouleau Y, Bani-Yaghoub M, Johnston LJ, Pezacki JP. “Imaging nanometer domains of b-adrenergic receptor complexes on the surface of cardiac myocytes.” Nature Chem. Biol. 2005, 1, 196-202 (Cover article, first nanoscale study of b-adrenergic receptors on mammalian cells). 28. Ianoul A, Street M, Grant D, Pezacki JP, Taylor RS, Johnston LJ. “Near-field scanning optical microscopy fluorescence study of ion channel localization on a cell membrane.” Biophys. J. 2004, 87, 3525-3535. 27. Su AI*, Pezacki JP*, Wodicka L, Brideau A, Supekova L, Thimme R, Wieland S, Purcell RH, Bukh J, Schultz PG, Chisari FV. “Gene Expression Profiling in Chimpanzees with Different Outcomes to Hepatitis C Virus Infection.” Proc. Natl. Acad. Sci. USA 2002, 99, 15669. 26. Supekova L*, Pezacki JP*, Su AI, Loweth CJ, Riedl R, Geierstanger B, Schultz PG, Wemmer DE. “Genomic Effects of Polyamide/DNA Interactions on mRNA Expression.” Chem. Biol. 2002, 9, 821. 25. Su AI, Guidiotti L, Pezacki JP, Chisari FV, Schultz PG. “Gene Expression During the Priming Phase of Liver Regeneration After Partial Hepatectomy in Mice.” Proc. Natl. Acad. Sci. USA 2002, 99, 11181. 24. Ship NJ, Pezacki JP, Kluger R. “Rates of release of nitric oxide from HbSNO and internal electron transfer.” Bioorg. Chem. 2003, 31, 3. 23. Pezacki JP, Ship NJ, Kluger R. “Release of Nitric Oxide from S-Nitrosohemoglobin. Electron Transfer as a Response to Deoxygenation.” J. Am. Chem. Soc. 2001, 123, 4615. 22. Pezacki JP, Pelling A, Kluger R. “S‑Nitrosylation of Cross-Linked Hemoglobins at b-Cysteine-93. Stabilized Hemoglobins as Nitric Oxide Sources.” J. Am. Chem. Soc. 2000, 122, 10734. 21. Chaulk S, Pezacki JP, MacMillan A. “Studies of RNA Cleavage by Photolysis of N-Hydroxypyridine-2(1H)-thione. A New Photochemical Footprinting Method.” Biochemistry 2000, 39, 10448. 20. Pezacki JP, Loncke PG, Ross JP, Warkentin J, Gadosy TA. “Silicon Migration from Oxygen to Carbon and Decarbonylation in Methoxytriphenylsiloxycarbene.” Org. Lett. 2000, 2, 2733. 19. Pezacki JP, Shukla D, Lusztyk J, Warkentin J. “Cyclohexadienyl Cations as Kinetic Probes for Cation Reactivity.” J. Am. Chem. Soc. 1999, 121, 6589. 18. Dunn JA*, Pezacki JP*. McGlinchey MJ, Warkentin J “Reactions of Dimethoxycarbene with Cyclic Perchlorinated Olefins and Ketones.” J. Org. Chem. 1999, 64, 4344. 17. Pezacki JP, Couture P, Dunn JA, Warkentin J, Wood PD, Lusztyk J, Chen T, Ford F, Toscano J, Platz MS. “Rates of 1,2-Hydrogen Migration in Cyclohexylidene and Substituted Cyclohexylcarbenes.” J. Org. Chem. 1999, 64, 4456. 16. Pezacki JP. “Normal Acid/Base Behaviour in Proton Transfer Reactions to Alkoxy Substituted Carbenes: Estimates for Intrinsic Barriers to Reaction and pKa Values.” Can. J. Chem. 1999, 77, 1230. 15. Tae EL, Zhu Z, Platz MS, Pezacki JP, Warkentin J. “Chemistry and Kinetics of Dipropylcarbene in Solution.” J. Phys. Chem. A 1999, 103, 5336. 14. Pezacki JP, Wood PD, Gadosy TA, Lusztyk J, Warkentin J. “Laser Flash Photolysis Studies of Oxygen and Sulfur Atom Transfer Reactions from Oxiranes and Thiiranes to Singlet Carbenes.” J. Am. Chem. Soc. 1998, 120, 8681. 13. Pezacki JP, Warkentin J, Wood PD, Lusztyk J, Yuzawa T, Gudmundsdöttir A, Morgan S, Platz MS. “Laser Flash Photolysis of 2-adamantane-2,3’-[3H]-diazirine: a reinvestigation.” J. Photochem. Photobiol. Chem. A. 1998, 116, 1. 12. Muchall HM, Werstiuk NH, Choudhury B, Ma J, Warkentin J, Pezacki JP. “Thermolysis of 2,2-dimethoxy-5,5-dimethyl-Δ3-1,3,4-oxadiazoline studied with photoelectron spectroscopy. He(I) photoelectron spectrum of dimethoxycarbene.” Can. J. Chem. 1998, 76, 238. 11. Pezacki JP, Pole DL, Warkentin J, Chen T, Ford F, Toscano J, Fell J, Platz MS. “Laser Flash and Dual Wavelength Photolysis of 3,4-Diaza-2,2-dimethoxy-1-oxa[4.3]spirooct-3- ene. Migration of Hydrogen and Carbon in Cyclobutylidene and in the Excited State of its Precursor.” J. Am. Chem. Soc. 1997, 119, 3191. 10. Pezacki JP, Wagner BD, Lew CSQ, Warkentin J, Lusztyk J. “D3-1,3,4-Oxadiazolines: Photochemical Precursors to Diazoalkanes and Sec-Alkanediazonium Ions in Acidic Solution.” J. Am. Chem. Soc. 1997, 119, 1789. 9. Kluger R, Lam JF, Pezacki JP, Yang C-M. “Diverting Thiamin from Catalysis to Destruction. Mechanism of Fragmentation of N1’-Methyl-2-(1-hydroxybenzyl)thiamin.” J. Am. Chem. Soc. 1995, 117, 11383. Manuscripts in Non-Refereed Journals: 8. Clarke JL, Pezacki JP, Letourneau H. “High Throughput Screening: Focusing on Assays in Drug Discovery.” Laboratory Focus. 9 (3): May 2005. 7. A. Pegoraro, A. Ridsdale, R.K. Lyn, J.P. Pezacki & A. Stolow “Simple High Performance Multi-modal Coherent Anti-Stokes Raman Scattering (CARS) Microscopy Based on a Two-Photon Microscope” Microsc. Microanal. 14 (Supplement S2), 758 (2008). 6. Pegoraro AF, Ridsdale A, Moffatt DJ, Pezacki JP, Stolow A. “CARS Microscopy Made Simple” Photons 7 (1):Spring 2009, pgs 50-52. 5. Pegoraro AF, Stolow A,Ridsdale A, Moffatt DJ, Pezacki JP, Jia Y. “CARS Microscopy Made Simple” Biophotonics International: October 2009, pgs 36-38. Book chapters: 4. Nasheri, N.; Pezacki, J.P., Sagan, S. M. “Design and screening of siRNAs against highly structured RNA targets” Methods. Mol. Biol. (Clifton, N.J.) 2013, Vol: 942 Pgs: 69-86 DOI: 10.1007/978-1-62703-119-6_4. Patents: 3. Pezacki J, Kluger R. “New cross-linked nitrosylated hemoglobin, useful for delivering oxygen to organs, comprises thio-nitrosyl groups on cysteine residues of its globin chains and chemical cross-links between its sub-units.” Patent Number CA2309236-A1. Derwent Primary Accession Number: 2002-383834 [31]. International Patent Classification: A61K-038/42; C07K-014/805. 2. Sherratt A, Rouleau Y, Pezacki JP. Detection, isolation and identification of microorganisms. (12431-0 SpecUSProvisional). Full patent submitted Friday Nov. 21, 2014. 1. Singaravelu R, Pezacki JP. MicroRNA cluster for boosting immunity and combatting infectious agents. Filed through uOttawa Nov, 2017. |