Publications

 

The publications listed below were either authored or acknowledged by authors through work done at Dalhousie's Biological Mass Spectrometry Core Facility.
 

"TRPM8 as the rapid testosterone signaling receptor: Implications in the regulation of dimorphic sexual and social behaviors."
Mohandass A, Krishnan V, Gribkova ED, Asuthkar S, Baskaran P, Nersesyan Y, Hussain Z, Wise LM, George RE, Stokes N, Alexander BM, Cohen AM, Pavlov EV, Llano DA, Zhu MX, Thyagarajan B, Zakharian E
The FASEB Journal. 2020; 34: 10887 10906. https://doi.org/10.1096/fj.202000794R

"Exploring Epidermal Mucus Protease Activity as an Indicator of Stress in Atlantic Sturgeon (Acipenser oxyrinchus oxyrhinchus)"
Anna E. Murphy Michael J. W. Stokesbury and Russell H. Easy
Journal of Fish Biology, 12 August 2020 https://doi.org/10.1111/jfb.14489

"Protection of the transplant kidney during cold perfusion with doxycycline: proteomic analysis in a rat model"
Michael AJ Moser, Katherine Sawicka, Jolanta Sawicka, Aleksandra Franczak, Alejandro Cohen, Iwona Bil-Lula, Grzegorz Sawicki
Proteome Sci 18,3(2020). https://doi.org/10.118/s12953-020-00159-3

"Heat stress response in the closest algal relatives of land plants reveals conserved stress signaling circuits"
de Vries, Jan, de Vries, Sophie, Curtis, Bruce A., Zhou, Hong, Penny, Susanne, Feussner, Kirstin, Pinto, Devanand M., Steinert, Michael, Cohen, Alejandro M., von Schwartzenberg, Klaus, Archibald, John M.
The Plant Journal, 2020. doi:10.1111/tpj.14782

"Demonstration of beta-tropomyosin (Tpm2) and duplication of the alpha-slow tropomyosin gene (TPM3) in Atlantic salmon Salmo salar"
A. Madhushika M. Silva, Luke S. Kennedy, Stephanie C. Hasan, Alejandro M. Cohen, David H. Heeley
Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology. 2020 Volume 245, 110439

"Prediction and Consequences of Cofragmentation in Metaproteomics"
J. Scott P. McCain and Erin M. Bertrand
J. Proteome Res. 2019, 18, 10, 3555-3566

"Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators"
Miao Wu, J. Scott P. McCain, Elden Rowland, Rob Middag, Mats Sandgren, Andrew E. Allen & Erin M. Bertrand
Nature Communications, vol(10), Article Number: 3582 (2019)

"Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy"
J. Patrick Murphy, Youra Kim, Derek R. Clements,Prathyusha, Konda Heiko, Schuster Daniel J. Kowalewski, Joao A. Paulo, Alejandro M. Cohen, Stefan Stevanovic, Steven P. Gygi and Shashi Gujar
Journal of Proteome Research. 2019, 18(6):2666-2675

"The Influenza A Virus Endoribonuclease PA-X Usurps Host mRNA Processing Machinery to Limit Host Gene Expression"
Lea Gaucherand, Brittany K. Porter, Rachel E. Levene, Emma L. Price, Summer K. Schmaling, Chris H. Rycroft, Yuzo Kevorkian, Craig McCormick, Denys A. Khaperskyy, Marta M. Gaglia
Cell Reports, Volume 27, Issue 3, 2019, Pages 776-792.e7

"Inhibition of Pyruvate Dehydrogenase Kinase Enhances the Antitumor Efficacy of Oncolytic Reovirus"
Barry E. Kennedy, John Patrick Murphy, Derek R. Clements, Prathyusha Konda,  NamitHolay, Youra Kim, Gopal P. Pathak, Michael A. Giacomantonio, Yassine El Hiani and ShashiGujar
Cancer Research August 1 2019 (79) (15) 3824-3836

"Transcriptome and proteome analyses to investigate the molecular underpinnings of cold response in the Colorado potato beetle, Leptinotarsa decemlineata"
Louise Govaere, Mathieu D. Morin, Jacques J. Frigault, Sébastien Boquel, Alejandro Cohen, Simon G. Lamarre, Pier Jr. Morin
Cryobiology, Volume 88, 2019, Pages 54-63

"Marine Bacteria, A Source for Alginolytic Enzyme to Disrupt Pseudomonas aeruginosa Biofilms"
Said M. Daboor, Renee Raudonis, Alejandro Cohen , John R. Rohde and Zhenyu Cheng
Mar. Drugs 2019, 17(5), 307

"Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin"
J. Patrick MurphyQijia YuPrathyusha KondaJoao A. PauloMark P. JedrychowskiDaniel J. KowalewskiHeiko SchusterYoura KimDerek ClementsAditya JainStefan StevanovicSteven P. GygiJoseph D. Mancias and Shashi Gujar
Analytical Chemistry 2019, 91(8): 5106-5115

"Knockdown of the small heat-shock protein p26 by RNA interference modifies the diapause proteome of Artemia franciscana"
Hajer Salem Malitan, Alejandro M. Cohen, Thomas H. MacRae
Biochemistry and Cell Biology, 2019, 97(4): 471-479

"The NAD+ Salvage Pathway Supports PHGDH-Driven Serine Biosynthesis"
J. Patrick Murphy, Michael A. Giacomantonio, Joao A. Paulo, Robert A. Everley, Barry E. Kennedy, Gopal P. Pathak, Derek R. Clements, Youra Kim, Cathleen Dai, Tanveer Sharif, Steven P. Gygi, Shashi Gujar.
Cell Reports, Volume 24, Issue 9, 2018, Pages 2381-2391.e5

"Tandem tyrosine phosphosites in the Enteropathogenic Escherichia coli chaperone CesT are required for differential type III effector translocation and virulence."
Runte, C. S., Jain, U. , Getz, L. J., Secord, S. , Kuwae, A. , Abe, A. , LeBlanc, J. J., Stadnyk, A. W., Kaper, J. B., Hansen, A. and Thomas, N. A.
Molecular Microbiology, 108: 536-550 (2018). doi:10.1111/mmi.13948

"Regulation of cell surface protease receptor S100A10 by retinoic acid therapy in acute promyelocytic leukemia (APL)"
Holloway, Ryan W., Thomas, Margaret L., Cohen, Alejandro M., Bharadwaj, Alamelu G., Rahman, Mushfiqur, Marcato, Paola, Marignani, Paola A. and Waisman, David M
Cell Death & Disease, Volume 9, Article number: 920 (2018).

"Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis"
Courtney W Stairs, Laura Eme, Sergio A Muñoz-Gómez, Alejandro Cohen, Graham Dellaire, Jennifer N Shepherd, James P Fawcett, Andrew J Roger
Elife, 2018. April, Vol (7), Page:e34292

"RTN4 Knockdown Dysregulates the AKT Pathway, Destabilizes the Cytoskeleton, and Enhances Paclitaxel-Induced Cytotoxicity in Cancers"
Gopal P. Pathak, Rashmi Shah, Barry E. Kennedy, J. Patrick Murphy, Derek Clements, Prathyusha Konda, Michael Giacomantonio, Zhaolin Xu, Isabel R. Schlaepfer, Shashi Gujar
Molecular Therapy, Volume 26, Issue 8, 2018, Pages 2019-2033,

"Membrane‐Based SDS Depletion Ahead of Peptide and Protein Analysis by Mass Spectrometry"
Proteomics 25 March 2018. https://doi.org/10.1002/pmic.201700025
Nicole Unterlander and Alan A. Doucette

"Oxytocin Modulates Nociception as an Agonist of Pain-Sensing TRPV1"
Cell Reports 21(6):1681-1691 · November 2017
Yelena Nersesyan, Lusine Demirkhanyan, Deny Cabezas-Bratesco, Victoria Oakes, Ricardo Kusuda, Tyler Dawson, Xiaohui Sun, Chike Cao, Alejandro Martin Cohen, Bharath Chelluboina, Krishna Kumar Veeravalli, Katharina Zimmermann, Carmen Domene, Sebastian Brauchi, Eleonora Zakharian

"Quantitative Temporal in Vivo Proteomics Deciphers the Transition of Virus-Driven Myeloid Cells into M2 Macrophages"
Derek R. Clements, John Patrick Murphy, Andra Sterea, Barry E. Kennedy, Youra Kim, Erin Helson, Shekoufeh Almasi, Namit Holay, Prathyusha Konda, Joao A. Paulo, Tanveer Sharif, Patrick W. Lee, Michael P. Weekes, Steven P. Gygi, and Shashi Gujar
Journal of Proteome Research 2017 16 (9), 3391-3406

"Observing enzyme ternary transition state analogue complexes by 19F NMR spectroscopy"
Chemical Science · October 2017. DOI: 10.1039/C7SC04204C
Anna Ampaw, Madison Carroll, Jill von Velsen, Debabrata Bhattasali, Alejandro Cohen, Matthew W. Bowlerb  and  David L. Jakeman

"Proteomic Analysis of Perfusate from Machine Cold Perfusion of Transplant Kidneys: Insights Into Protection from Injury"
Annals of Transplantation, 2017; 22: DOI: 10.12659/AOT.905347
Michael A. J. Moser, Katherine Sawicka, Steven Arcand,Preston O’Brien, Patrick Luke, Gavin Beck, Jolanta Sawicka, Alejandro Cohen and Grzegorz Sawicki.  

"Anti-nociceptive action of peripheral mu-opioid receptors by G-beta-gamma protein-mediated inhibition of TRPM3 channels".
eLIFE Neuroscience. eLife 2017;6:e26280 DOI: 10.7554/eLife.26280
Sandeep Dembla, Marc Behrendt, Florian Mohr, Christian Goecke, Julia Sondermann, Franziska M Schneider, Marlene Schmidt, Julia Stab, Raissa Enzeroth, Michael G Leitner, Paulina Nuñez-Badinez, Jochen Schwenk, Bernd Nürnberg, Alejandro Cohen, Stephan E Philipp, Wolfgang Greffrath ,Moritz Bünemann, Dominik Oliver, Eleonora Zakharian, Manuela Schmidt and Johannes Oberwinkler

"Analysis of 17β-estradiol, estriol and estrone in American eel (Anguilla rostrata) tissue samples using liquid chromatography coupled to electrospray-differential ion mobility tandem mass spectrometry: Analysis of 17β-estradiol, estriol and estrone by LC-ESI-DMS-MSMS."
Rapid Communications in Mass Spectrometry 03/2017;, DOI:10.1002
Alejandro Cohen, Neil W. Ross, Paul M. Smith, James P. Fawcett

"MHC-I ligand discovery using targeted database searches of mass spectrometry data: Implications for T cell immunotherapies."
Journal of Proteome Research 02/2017;, DOI:10.1021
John Patrick Murphy, Prathyusha Konda, Daniel J. Kowalewski, Heiko Schuster, Derek Clements, Youra Kim, Alejandro Martin Cohen, Tanveer Sharif, Morten Nielsen, Stefan Stevanović, Patrick W. Lee, Shashi Gujar

"High-throughput proteome analysis reveals targeted TRPM8 degradation in prostate cancer"
Oncotarget, 2017, Vol. 8, (No. 8), pp: 12877-12890
Swapna Asuthkar, Lusine Demirkhanyan, Samuel Robert Mueting, Alejandro Cohen, Eleonora Zakharian

"Mass Spectrometry of Intact Proteins Reveals +98 u Chemical Artifacts Following Precipitation in Acetone."
J Proteome Res. 2017 Feb 3;16(2):889-897
Güray MZ, Zheng S, Doucette AA

"Adipocyte-secreted chemerin is processed to a variety of isoforms and influences MMP3 and chemokine secretion through an NFkB-dependent mechanism."
Molecular and Cellular Endocrinology. Volume 436, 15 November 2016, Pages 114–129
Helen J. Dranse, Shanmugam Muruganandaa, James P. Fawcett, Christopher J. Sinal

"Competing fragmentation processes of β-substituted propanoate
ions upon collision-induced dissociation"
Rapid Commun. Mass Spectrom. 2016, 30, 2133–2144
Luc M. LeBlanc, Sean W. Powers, J. Stuart Grossert and Robert L. White

"Determination of Flow Rates in Capillary Liquid Chromatography Coupled to a Nanoelectrospray Source using Droplet Image Analysis Software"
Analytical Chemistry. 2016 Aug 2;88(15):7476-80
Alejandro M. Cohen, Axel J. Soto and James P. Fawcett

"Breast cancer subtype dictates DNA methylation and ALDH1A3-mediated expression of tumor suppressor RARRES1"
Oncotarget. 2016 Jul 12; 7(28): 44096–44112
Krysta M. Coyle, J. Patrick Murphy, Dejan Vidovic, Ahmad Vaghar-Kashani, Cheryl A. Dean, Mohammad Sultan, Derek Clements, Melissa Wallace, Margaret L. Thomas, Amos Hundert, Carman A. Giacomantonio, Lucy Helyer, Shashi A. Gujar, Patrick W.K. Lee, Ian C.G. Weaver and Paola Marcato

"Oxysterol-binding Protein Activation at Endoplasmic Reticulum-Golgi Contact Sites Reorganizes Phosphatidylinositol 4-Phosphate Pools"
The Journal of Biological Chemistry. 2016 VoL. 291.
Asako Goto, Mark Charman, and Neale D. Ridgway

"Motoneurons Derived from Induced Pluripotent Stem Cells Develop Mature Phenotypes Typical of Endogenous Spinal Motoneurons"
The Journal of Neuroscience, 2015, January 21, 35(3):1291–1306
Jeremy S. Toma, Basavaraj C. Shettar, Peter H. Chipman, Devanand M. Pinto, Joanna P. Borowska, Justin K. Ichida, James P. Fawcett, Ying Zhang, Kevin Eggan and Victor F. Rafuse

"Stimulation-dependent gating of TRPM3 channel in planar lipid bilayers"
The FASEB Journal, 2015
Kunitoshi Uchida, Lusine Demirkhanyan, Swapna Asuthkar, Alejandro Cohen, Makoto Tominaga, Eleonora Zakharian

"The disulfide oxidoreductase SdbA is active in Streptococcus gordonii using a single C‐terminal cysteine of the CXXC motif"
Molecular Microbiology, 2015. doi:10.1111/mmi.13227
Davey, L., Cohen, A., LeBlanc, J., Halperin, S. A. and Lee, S. F.

"Activation of the Mitochondrial Permeability Transition Pore Leads to the Increase in Amount of C-Subunit of ATP Synthase Associated with Channel-Forming Complex of Polyhydroxybutyrate and Inorganic Polyphosphate"
Biophysical Journal, 2015 Volume 108, Issue 2, Supplement 1, p608a.
Pia A. Elustondo, Alexander Negoda, Alejandro M. Cohen, Evgeny Pavlov

"Genomic and Proteomic Analyses Indicate that Banchine and Campoplegine Polydnaviruses Have Similar, if Not Identical, Viral Ancestors"
Journal of Virology. September 2015 vol. 89 no. 17 8909-8921
Catherine Béliveau, Alejandro Cohen, Don Stewart, Georges Periquet, Abdelmadjid Djoumad, Lisa Kuhn, Don Stoltz, Brian Boyle, Anne-Nathalie Volkoff, Elisabeth A Herniou, Jean-Michel Drezen, Michel Cusson

"Inactivation of Mandelate Racemase by 3-Hydroxypyruvate Reveals a Potential Mechanistic Link between Enzyme Superfamilies"
Biochemistry. 2015, 54 (17), pp 2747–2757
Mitesh Nagar, Brittney N. Wyatt, Martin St. Maurice and Stephen L. Bearne

"A two-stage spin cartridge for integrated protein precipitation, digestion and SDS removal in a comparative bottom-up proteomics workflow"
Journal of Proteomics, 2015. Volume 118, 6 April 2015, Pages 140–150
Andrew M.J. Crowell, Dawn L. MacLellan and Alan A. Doucette

"The unexpected formation of [M − H]+ species during MALDI and dopant-free APPI MS analysis of novel antineoplastic curcumin analogues"
Journal of Mass Spectrometry, 2014 Volume 49, Issue 11, pages 1139–1147, November 2014
H Awad, MJ Stoudemayer, L Usher, IJ Amster, A Cohen, U Das, RM Whittal, J Dimmock, A El‐Aneed

"A viral aphrodisiac in the cricket Gryllus texensis"
The Journal of Experimental Biology, 2014 (217), 1970-1976 doi:10.1242/jeb.103408
Shelley A. Adamo, Ilya Kovalko, Russell H. Easy and Don Stoltz

"The progeny of Legionella pneumophila in human macrophages shows unique developmental traits"
FEMS Microbiology Letters, 2013-99-107 First published online: 1 December
Hany Abdelhady and Rafael A. Garduño

“Polyester modification of the mammalian TRPM8 channel protein: Implications for structure and function.”
Cell Reports. 2013 July 25; 4(2): 302–315.
Chike Cao, Yevgen Yudin, Yann Bikard, Wei Chen, Tong Liu, Hong Li, Dieter Jendrossek, Alejandro Cohen, Evgeny Pavlov, Tibor Rohacs, and Eleonora Zakharian.

"A proteomic investigation of apple fruit during ripening and in response to ethylene treatment"
Journal of Proteomics, Volume 93, 20 November 2013, Pages 276–294
Qifa Zheng, Jun Song,Leslie Campbell-Palmer, Kristen Thompson,Li Li, Brad Walker, Yunsong Cui and Xihong Li

"Differential chromatin proteomics of the MMS-induced DNA damage response in yeast"
Proteome Science 2011, 9:62
Dong Ryoung Kim, Rohan D Gidvani, Brian P Ingalls, Bernard P Duncker and Brendan J McConkey

"Exploring the Mechanism of Acyl Carrier Protein Interactions and Acyl Transfer"
FASEB Journal 2011 25 (Meeting Abstract Supplement) 928.9
Peter W Murphy, Gerrit Volkman, Elden E Rowland, Xiang-Qin Liu and David M Byers

"Oxidative stress response in the opportunistic oral pathogen Fusobacterium nucleatum"
Proteomics, 2011 Volume 11, Issue 10 Pages 2027–2037
Craig H. Steeves, Joanna Potrykus, David A. Barnett and Stephen L. Bearne

"Intein-mediated Cyclization of Bacterial Acyl Carrier Protein Stabilizes Its Folded Conformation but Does Not Abolish Function"
The Journal of Biological Chemistry, 2010, (285), 8605-8614.
Gerrit Volkmann, Peter W. Murphy, Elden E. Rowland, John E. Cronan, Jr., Xiang-Qin Liu, Christian Blouin and David M. Byers

"Intein-mediated creation of a cyclic acyl carrier protein"
FASEB Journal.l 2009 23 (Meeting Abstract Supplement) 850.8
Gerrit Volkmann, Peter W. Murphy, Elden E. Rowland, Xiang-Qin Liu and David M. Byers

"Triptolide: An inhibitor of a disintegrin and metalloproteinase 10 (ADAM10) in cancer cells"
Cancer Biology & Therapy, 2009, Volume 8, Issue 21.
Ramani Soundararajan, Ria Sayat, George S. Robertson & Paola A. Marignani

"Immune Response and Alveolar Bone Resorption in a Mouse Model of Treponema denticola Infection"
Infection and Immunity. 2009 vol. 77 no. 2 694-698
Song F. Lee, Elisoa Andrian, Elden Rowland and Ignacio Christian Marquez

"Proteomic investigation of amino acid catabolism in the indigenous gut anaerobe Fusobacterium varium"
Proteomics 2008, 8, 2691–270
Joanna Potrykus, Robert L. White and Stephen L. Bearn

"Electrospray Ionization Mass Spectra of Acyl Carrier Protein are Insensitive to Its Solution Phase Conformation"
Journal of the American Society for Mass Spectrometry, 2007 Volume 18, Issue 8, August, Pages 1525–1532
Peter W. Murphy, Elden E. Rowland and David M. Byers

"Proteomic investigation of glucose metabolism in thebutyrate-producing gut anaerobe Fusobacterium varium"
Proteomics 2007, 7, 1839–185
Joanna Potrykus, Brandi Mahaney, Robert L. White and Stephen L. Bearne

"Exploiting Nucleotidylyltransferases To Prepare Sugar Nucleotides"
Organic Letters,  2007 Vol. 9, No. 5 857-860
Shannon C. Timmons, Roy H. Mosher, Sheryl A. Knowles and David L. Jakeman

"Qualitative and Quantitative Evaluation of Protein Extraction Protocols for Apple and Strawberry Fruit Suitable for Two-Dimensional Electrophoresis and Mass Spectrometry Analysis"
Journal of Agricultural and Food Chemistry. 2007, 55, 1663−1673
Qifa Zheng, Jun Song, Kristen Doncaster, Elden Rowland and David M. Byers

A simple protocol for protein extraction of recalcitrant fruit tissues suitable for 2-DE and MS analysis"
Electrophoresis 2006, 27, 3144–3151
Jun Song, Gordon Braun, Eric Bevis and Kristen Doncaster