Recent publications

2021

Bhat, S. V., Price, J. D. W. and Dahms, T. E. S. AFM-based correlative microscopy illuminates human pathogens. Frontiers in Cellular and Infection Microbiology 2021, 11, 655501. doi: 10.3389/fcimb.2021.655501

El-Baz, A. M., Mosbah, R. A., Goda, R. M., Mansour, B., Sultana, T., Dahms, T. E. S. and El-Ganiny A. M. Back to Nature: Combating Candida albicans Biofilm, Phospholipase and Hemolysin Using Plant Essential Oils. Antibiotics 2021, 10(1), 81. doi: 10.3390/antibiotics10010081.

Mehla, J., Liechti, G., Morgenstein, R. M., Caufield, J. H., Hosseinnia, A., Gagarinova, A., Phanse, S., Goodacre, N., Brockett, M., Sakhawalkar, N., Babu, M., Xiao, R., Montelione, G. T., Vorobiev, S., Blaauwen, T. D., Hunt, J. F. and Uetz, P. ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis. J Biol Chem 2021, 100700.

Martinez-Matias, N., Chorna, N., Gonzalez-Crespo, S., Villanueva, L., Montes-Rodriguez, I., Melendez-Aponte, L. M., Roche-Lima, A., Carrasquillo-Carrion, K., Santiago-Cartagena, E., Rymond, B. C., Babu, M., Stagljar, I. and Rodriguez-Medina, J. R. Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis. Sci Rep 2021, 11 (1), 7411.

Aly, K. A., Moutaoufik, M. T., Phanse, S., Zhang, Q. and Babu, M., From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease. iScience 2021, 24 (2), 102030.

Rizzolo, K., Yu, A. Y. H., Ologbenla, A., Kim, S. R., Zhu, H., Ishimori, K., Thibault, G., Leung, E., Zhang, Y. W., Teng, M., Haniszewski, M., Miah, N., Phanse, S., Minic, Z., Lee, S., Caballero, J. D., Babu, M., Tsai, F. T. F., Saio, T. and Houry, W. A. Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex. Nat Commun 2021, 12 (1), 281.

 

2020

Rabbi, F., Renzaglia, K.S., Ashton, N.W., Suh, D.-Y. Reactive oxygen species are required for spore wall formation in Physcomitrella patens. Botany 2020, 98, 575–587.

Jun, D., Idem, U. and Dahms, T. E. S. Altered Envelope Structure and Nanomechanical Properties of a C-Terminal Protease A-Deficient Rhizobium leguminosarum. Microorganisms 2020, 8(9), 1421. doi: 10.3390/microorganisms8091421.

Sharma, K., Sultana, T., Dahms, T. E. S. and Dillon, J.-A. R. CcpN: a moonlighting protein regulating catabolite repression of gluconeogenic genes inBacillus subtilis also affects cell length and interacts with DivIVA. Canadian Journal of Microbiology 2020, 66(12), 723-732. doi: 10.1139/cjm-2020-0022.

Sharma, K., Sultana, T., Liao, M., Dahms, T. E. S. and Dillon, J.-A. R. EF1025, a hypothetical protein from Enterococcus faecalis, interacts with DivIVA and affects cell length and cell shape. Frontiers in Microbiology 2020, 11, 83.

Patel, D. H. and East, A. L. L. Semicontinuum (cluster-continuum) modeling of acid-catalyzed aqueous reactions: alkene hydration. J. Phys. Chem. A 2020, 124, 9088-9104.

Klapatiuk, D. O., Johnson, K. E. and East, A. L. L. Limited ionicity in protic ionic liquids: organic acid/trialkylamine mixtures. ECS Trans. 2020, 98(10), 149-159.

Patel, D. H., Marx, D. and East, A. L. L. Improving yield and rate of acid-catalyzed deconstruction of lignin by mechanochemical activation. Chem. Phys. Chem. 2020, 21, 2660-2666.

Mukadam, A. A.; Aravindakshan, N. P. and East, A. L. L. Comment on ‘Local, solvation pressures and conformational changes in ethylenediamine aqueous solutions probed using Raman spectroscopy’ by M. Caceres, A. Lobato, N. J. Mendoza, L. J. Bonales and V. G. Baonza, Phys. Chem. Chem. Phys., 2016, 18, 26192. Phys. Chem. Chem. Phys. 2020, 22, 7119-7125.

Hooshyar, M., Jessulat, M., Burnside, D., Kluew, A., Babu, M and Golshani, A. Deletion of yeast TPK1 reduces the efficiency of non-homologous end joining DNA repair. Biochem Biophys Res Commun 2020, 533 (4), 899-904.

Zilocchi, M., Broderick, K., Phanse, S., Aly, K. A. and Babu, M. Mitochondria under the spotlight: On the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders. Comput Struct Biotechnol J 2020, 18, 2535-2546.

Hajikarimlou, M., Hunt, K., Kirby, G., Takallou, S., Jagadeesan, S. K., Omidi, K., Hooshyar, M., Burnside, D., Moteshareie, H., Babu, M., Smith, M., Holcik, M., Samanfar, B. and Golshani, A. Lithium Chloride Sensitivity in Yeast and Regulation of Translation. Int J Mol Sci 2020, 21 (16).

Hajikarimlou, M., Moteshareie, H., Omidi, K., Hooshyar, M., Shaikho, S., Kazmirchuk, T., Burnside, D., Takallou, S., Zare, N., Jagadeesan, S. K., Puchacz, N., Babu, M., Smith, M., Holcik, M., Samanfar, B. and Golshani, A. Sensitivity of yeast to lithium chloride connects the activity of YTA6 and YPR096C to translation of structured mRNAs. PLoS One 2020, 15 (7), e0235033.

Velez-Segarra, V., Gonzalez-Crespo, S., Santiago-Cartagena, E., Vazquez-Quinones, L. E., Martinez-Matias, N., Otero, Y., Zayas, J. J., Siaca, R., Del Rosario, J., Mejias, I., Aponte, J. J., Collazo, N. C., Lasso, F. J., Snider, J., Jessulat, M., Aoki, H., Rymond, B. C., Babu, M., Stagljar, I. and Rodriguez-Medina, J. R. Protein Interactions of the Mechanosensory Proteins Wsc2 and Wsc3 for Stress Resistance in Saccharomyces cerevisiae. G3 (Bethesda) 2020, 10 (9), 3121-3135.

Zilocchi, M., Colugnat, I., Lualdi, M., Meduri, M., Marini, F., Corasolla Carregari, V., Moutaoufik, M. T., Phanse, S., Pieroni, L., Babu, M., Garavaglia, B., Fasano, M. and Alberio, T. Exploring the Impact of PARK2 Mutations on the Total and Mitochondrial Proteome of Human Skin Fibroblasts. Front Cell Dev Biol 2020, 8, 423.

Pourhaghighi, R., Ash, P. E. A., Phanse, S., Goebels, F., Hu, L. Z. M., Chen, S., Zhang, Y., Wierbowski, S. D., Boudeau, S., Moutaoufik, M. T., Malty, R. H., Malolepsza, E., Tsafou, K., Nathan, A., Cromar, G., Guo, H., Abdullatif, A. A., Apicco, D. J., Becker, L. A., Gitler, A. D., Pulst, S. M., Youssef, A., Hekman, R., Havugimana, P. C., White, C. A., Blum, B. C., Ratti, A., Bryant, C. D., Parkinson, J., Lage, K., Babu, M., Yu, H., Bader, G. D., Wolozin, B. and Emili, A. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Syst 2020, 10 (4), 333-350 e14.

He, S., Moutaoufik, M. T., Islam, S., Persad, A., Wu, A., Aly, K. A., Fonge, H., Babu, M. and Cayabyab, F. S. HERG channel and cancer: A mechanistic review of carcinogenic processes and therapeutic potential. Biochim Biophys Acta Rev Cancer 2020, 1873 (2), 188355.

Zilocchi, M., Moutaoufik, M. T., Jessulat, M., Phanse, S., Aly, K. A. and Babu, M., Misconnecting the dots: altered mitochondrial protein-protein interactions and their role in neurodegenerative disorders. Expert Rev Proteomics 2020, 17 (2), 119-136.

El-Halfawy, O. M., Czarny, T. L., Flannagan, R. S., Day, J., Jr, J. C. B., Kuiack, R. C., Salim, A., Eckert, P., Epand, R. M., McGavin, M. J., Organ, M. G., Heinrichs, D. E. and Brown, E. D. Discovery of an antivirulence compound that reverses β-lactam resistance in MRSA. Nature Chemical Biology 2020, 16(2), 143-149.

Farha, M. A., El-Halfawy, O. M., Gale, R. T., MacNair, C. R., Carfrae, L. A., Zhang, X., Jentsch, N. G., Magolan, J. and Brown, E. D. Uncovering the hidden antibiotic potential of Cannabis. ACS Infect Dis 2020, 6(3), 338-346.

 

2019

Aravindakshan, N.P., Johnson, K.E., and East, A.L.L. The origin of the conductivity maximum in molten salts. III. Zinc halides. J. Chem. Phys. 2019, 151, 034507 (10p).

Pill, M.F., East, A.L.L., Marx, D., Beyer, M.K., and Clausen-Schaumann, H. Mechanical activation drastically accelerates amide bond hydrolysis, matching enzyme activity. Angew. Chem. Int. Ed. 2019, 58, 9787-9790.

Sadraei, R., Murphy, R.S., Laurenti, E. and Magnacca, G. Characterization methodology to evaluate the activity of supported soybean peroxidase. Ind. Eng. Chem. Res. 2019, 58, 19802-19809.

Bittmann, S.F., Dsouza, R., Siddiqui, K.M., Hayes, S.A., Rossos, A., Corthey, G., Kochman, M., Prokhorenko, V.I., Murphy, R.S., Schwoerer, H. and Miller, R.J.D. Ultrafast ring-opening and solvent-dependent product relaxation of photochromic spironaphthopyran. Phys. Chem. Chem. Phys. 2019, DOI: 10.1039/c9cp02950h.

Sang, M.S.J., Cai, J., Kandasamy, Y.S. and Murphy, R.S. Synthesis of amphiphilic asymmetrical dithienylethenes with aryl groups at the reactive carbons. Can. J. Chem. 2019, 97, 398-405.

King, R.C., Nilewar, S. and Sterenberg, B.T. Phosphorus-carbon Bond Forming Reactions of Iron Tetracarbonyl-Coordinated Phosphenium Ions. J. Organomet. Chem. 2019, 880, 68-74.

Xin X., Huang G., An C., Raina-Fulton R., and Weger H. Insights into Long-​Term Toxicity of Triclosan to Freshwater Green Algae in Lake Erie. Env. Sci. Tech. 2019, 53, 2189-2198.

Kumar A., Hosseinnia A., Gagarinova A., Phanse S., Kim S., Aly K., Zilles S., and Babu M. A Gaussian process-​based definition reveals new and bona fide genetic interactions com-​pared to a multiplicative model in the Gram-​negative Escherichia coli. Bioinformatics (Oxford, England) 2019, published online Aug. 27.

Wu Z., Malty R., Moutaoufik M.T., Zhang Q., Jessulat M., and Babu M. A Tag-​Based Affinity Purification Mass Spectrometry Workflow for Systematic Isolation of the Human Mitochondrial Protein Complexes. Adv. Exp. Med. Biol. 2019, 1158, 83-100.

Santiago-Cartagena E., González-Crespo S., Vélez V., Martínez N., Snider J., Jessulat M., Aoki H., Minic Z., Akamine P., Mejías I., Pérez L.M., Rymond B.C., Babu M., Stagljar I., and Rodríguez-Medina J.R. Identification and Functional Testing of Novel Interacting Protein Partners for the Stress Sensors Wsc1p and Mid2p of Saccharomyces cerevisiae. G3 (Bethesda, Md.) 2019, 9, 1085-1102.

Carlson M.L., Stacey R.G., Young J.W., Wason I.S., Zhao Z., Rattray D.G., Scott N., Kerr C.H., Babu M., Foster L.J., and Duong Van Hoa F. Profiling the Escherichia coli membrane protein interactome captured in Peptidisc libraries. eLife 2019, 8, e48615 (26p).

Bakir, G., Girouard, B. E., Johns, R. W., Findlay, C. R.-J., Bechtel, H. A., Eisele, M., Kaminskyj, S. G. W., Dahms, T. E. S. and Gough, K. M. Ultrastructural and SINS analysis of the cell wall integrity response of Aspergillus nidulans to the absence of galactofuranose The Analyst 2019, 144, 928-934.

 

2018

Rossos, A., Katsiaflaka, M., Cai, J., Myers, S.M., Koenig, E., Bücker, R., Keskin, S., Kassier, G., Gengler, R.Y.N., Miller, R.J.D., and Murphy, R.S. Photochromism of amphiphilic dithienylethenes as Langmuir–Schaefer films. Langmuir 2018, 34, 10905-10912.

Nilewar, S., Jayaraman, A. and Sterenberg, B.T. Alkyne Insertion into P-C(sp2) Bonds as a Route to Fused Phospholes: Transition-metal like Reactivity at Phosphorus. Organometallics 2018, 37, 4699–4710.
Minic Z., Dahms T.E.S., and Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-​protein interactions and protein phosphorylation. J. Chromatography B 2018, 1102-1103, 96-108.

Shahina Z., El-Ganiny A.M., Minion J., Whiteway M., Sultana T., and Dahms T.E.S. Cinnamomum zeylanicum bark essential oil induces cell wall remodelling and spindle defects in Candida albicans. Fungal Biol. Biotechnol. 2018, 5, 3.

Bhat S.V., Sultana T., Koernig A., McGrath S., Shahina Z., and Dahms T.E.S. Correlative atomic force microscopy quantitative imaging-​laser scanning confocal microscopy quantifies the impact of stressors on live cells in real-​time. Sci. Reports 2018, 8, 8305.

Bhat S.V., Kamencic B., Koernig A., Shahina Z., and Dahms T.E.S. Exposure to Sub-​lethal 2,​4-​Dichlorophenoxyacetic Acid Arrests Cell Division and Alters Cell Surface Properties in Escherichia coli. Front. Microbiol. 2018, 9, 44.

Li L., Aslam M., Rabii F., Vanderwel M.C., Ashton N.W., and Suh D.Y. PpORS, an ancient type III polyketide synthase, is required for integrity of leaf cuticle and resistance to dehydration in the moss, Physcomitrella patens. Planta 2018, 247, 527-541.

Raina-Fulton, R. and Mohamad, A.A. Pressurized Solvent Extraction with Ethyl Acetate and Liquid Chromatography-​Tandem Mass Spectrometry for the Analysis of Selected Conazole Fungicides in Matcha. Toxics 2018, 6, 64 (13p).

Babu, M., Bundalovic-Torma, C., Calmettes, C., Phanse, S., Zhang, Q., Jiang, Y., Minic, Z., Kim, S., Mehla, J., Gagarinova, A., Rodionova, I., Kumar, A., Guo, H., Kagan, O., Pogoutse, O., Aoki, H., Deineko, V., Caufield, J.H., Holtzapple E., Zhang Z., Vastermark A., Pandya Y., Lai C.C., El Bakkouri M., Hooda Y., Shah M., Burnside D., Hooshyar, M., Vlasblom, J., Rajagopala, S.V., Golshani, A., Wuchty, S., F Greenblatt, J., Saier, M., Uetz, P., F Moraes, T., Parkinson, J., and Emili, A. Global landscape of cell envelope protein complexes in Escherichia coli. Nat Biotechnol. 2018, 36, 103-112.

Rodionova, I.A., Goodacre, N., Babu, M., Emili, A., Uetz, P., and Saier, M.H. Jr. The Nitrogen Regulatory PII Protein (GlnB) and N-Acetylglucosamine 6-Phosphate Epimerase (NanE) Allosterically Activate Glucosamine 6-Phosphate Deaminase (NagB) in Escherichia coli. J Bacteriol. 2018, 200, e00691-17 (13p).

Galván Márquez, I., Ghiyasvand, M., Massarsky, A., Babu, M., Samanfar, B., Omidi, K., Moon, T.W., Smith, M.L., and Golshani, A. Zinc oxide and silver nanoparticles toxicity in the baker's yeast, Saccharomyces cerevisiae. PLoS One 2018, 13, e0193111 (19p).

2017

Jayaraman, A., Nilewar, S., Jacob, T.V., and Sterenberg, B.T. Sequential Electrophilic Substitution Reactions of Tungsten-coordinated Phosphenium Ions and Phosphine Triflates. ACS Omega 2017, 2, 7849-7861.

Hubick, S., Jayaraman, A., McKeen, A., Reid, S. Alcorn, J., Stavrinides, J., Sterenberg, B.T. A potent synthetic inorganic antibiotic with activity against drug-resistant pathogens. Scientific Reports 2017, 17,
41999.