OMAL-Publications

2021

Smith CE, Tsai Y.C., Liang Y.H., Khago D., Mariano J., Li J., Tarasov S.G., Gergel E., Tsai B., Villaneuva M., Clapp M.E., Magidson V., Chari R., Byrd R.A., Ji X., Weissman A.M. (2021). A structurally conserved site in AUP1 binds the E2 enzyme UBE2G2 and is essential for ER-associated degradation. PLoS Biol. Dec 8;19(12). https://doi.org/10.1371/journal.pbio.3001474

Trofka, A., Huang, B.-L., Zhu, J., Heinz, W. F., Magidson, V., Shibata, Y., Shi, Y.-B., Tarchini, B., Stadler, H. S., Kabangu, M., Al Haj Baddar, N. W., Voss, S. R., & Mackem, S. (2021). Genetic basis for an evolutionary shift from ancestral preaxial to postaxial limb polarity in non-urodele vertebrates. Current Biology, 1–12. https://doi.org/10.1016/j.cub.2021.09.010

Ramakrishnan, S., Stagno, J. R., Heinz, W. F., Zuo, X., Yu, P., & Wang, Y.-X. (2021). The mechanism driving a solid–solid phase transition in a biomacromolecular crystal. IUCrJ, 8(4), 655–664. https://doi.org/10.1107/s2052252521004826

Ramakrishnan, S., Stagno, J. R., Magidson, V., Heinz, W. F., & Wang, Y.-X. (2021). Dependence of phase transition uniformity on crystal sizes characterized using birefringence. Structural Dynamics, 8(3), 034301. https://doi.org/10.1063/4.0000098

McGinity, C. L., Palmieri, E. M., Somasundaram, V., Bhattacharyya, D. D., Ridnour, L. A., Cheng, R. Y. S., Ryan, A. E., Glynn, S. A., Thomas, D. D., Miranda, K. M., Anderson, S. K., Lockett, S. J., McVicar, D. W., & Wink, D. A. (2021). Nitric oxide modulates metabolic processes in the tumor immune microenvironment. International Journal of Molecular Sciences, 22(13). https://doi.org/10.3390/ijms22137068

Ramakrishnan, S., Stagno, J. R., Magidson, V., Heinz, W. F., & Wang, Y.-X. (2021). A combined approach to characterize ligand-induced solid–solid phase transitions in biomacromolecular crystals. Journal of Applied Crystallography, 54(3), 787–796. https://doi.org/10.1107/s1600576721003137

Sjoberg, H. T., Philippou, Y., Magnussen, A. L., Tullis, I. D. C., Bridges, E., Chatrian, A., Lefebvre, J., Tam, K. H., Murphy, E. A., Rittscher, J., Preise, D., Agemy, L., Yechezkel, T., Smart, S. C., Kinchesh, P., Gilchrist, S., Allen, D. P., Scheiblin, D. A., Lockett, S. J., Wink, D.A., Lamb, A.D., Mills, I.G., Harris, A., Muschel, R.J., Vojnovic, B., Scherz, A., Hamdy, F.C. Bryant, R. J. (2021). Tumour irradiation combined with vascular-targeted photodynamic therapy enhances antitumour effects in pre-clinical prostate cancer. British Journal of Cancer, 125(4), 534–546. https://doi.org/10.1038/s41416-021-01450-6

Gilmore, A. C., Flaherty, S. J., Somasundaram, V., Scheiblin, D. A., Lockett, S. J., Wink, D. A., & Heinz, W. F. (2021). An in vitro tumorigenesis model based on live-cell- generated oxygen and nutrient gradients. Communications Biology, 4(477), 1–13. https://doi.org/10.1038/s42003-021-01954-0

Ramakrishnan, S., Stagno, J. R., Conrad, C. E., Ding, J., Yu, P., Bhandari, Y. R., Lee, Y., Pauly, G., Yefanov, O., Wiedorn, M. O., Knoska, J., Oberthür, D., White, T. A., Barty, A., Mariani, V., Li, C., Brehm, W., Heinz, W. F., Magidson, V., Wang, Y.-X. (2021). Synchronous RNA conformational changes trigger ordered phase transitions in crystals. Nature Communications. https://doi.org/10.1038/s41467-021-21838-5

Rausch, J. W., Heinz, W. F., Payea, M. J., Sherpa, C., Gorospe, M., & Le Grice, S. F. J. (2021). Characterizing and circumventing sequence restrictions for synthesis of circular RNA in vitro. Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa1256

2020

Renda, F., Magidson, V., Tikhonenko, I., Fisher, R., Miles, C., Mogilner, A., & Khodjakov, A. Effects of malleable kinetochore morphology on measurements of intrakinetochore tension. Open Biology, 10(7), 200101. (2020). https://doi.org/10.1098/rsob.200101

Biswas, K., Lipton, G. B., Stauffer, S., Sullivan, T., Cleveland, L., Southon, E., Reid, S., Magidson, V., Iversen, E. S. J., & Sharan, S. K. A computational model for classification of BRCA2 variants using mouse embryonic stem cell-based functional assays. NPJ Genomic Medicine, 5(1), 52. (2020). https://doi.org/10.1038/s41525-020-00158-5

Anderson, M. J., Magidson, V., Kageyama, R., & Lewandoski, M. Fgf4 maintains Hes7 levels critical for normal somite segmentation clock function. ELife, 9. (2020). https://doi.org/10.7554/eLife.55608

Chrisafis, G., Wang, T., Moissoglu, K., Gasparski, A. N., Ng, Y., Weigert, R., Lockett, S. J., & Mili, S. Collective cancer cell invasion requires RNA accumulation at the invasive front. Proceedings of the National Academy of Sciences of the United States of America, 117(44), 27423–27434. (2020). https://doi.org/10.1073/pnas.2010872117

Philippou, Y., Sjoberg, H. T., Murphy, E., Alyacoubi, S., Jones, K. I., Gordon-Weeks, A. N., Phyu, S., Parkes, E. E., Gillies McKenna, W., Lamb, A. D., Gileadi, U., Cerundolo, V., Scheiblin, D. A., Lockett, S. J., Wink, D. A., Mills, I. G., Hamdy, F. C., Muschel, R. J., & Bryant, R. J. Impacts of combining anti-PD-L1 immunotherapy and radiotherapy on the tumour immune microenvironment in a murine prostate cancer model. British Journal of Cancer, 123(7), 1089–1100. (2020). https://doi.org/10.1038/s41416-020-0956-x

Leng, Y., Sim, S., Magidson, V., & Wolin, S. L. Noncoding Y RNAs regulate the levels, subcellular distribution and protein interactions of their Ro60 autoantigen partner. Nucleic Acids Research, 48(12), 6919–6930. (2020). https://doi.org/10.1093/nar/gkaa414

Somasundaram, V., Gilmore, A.C., Basudhar, D., Palmieri, E.M., Scheiblin, D.A., Heinz, W.F., Cheng, R.Y.S., Ridnour, L.A., Altan-Bonnet, G., Lockett, S.J., McVicar, D.W. & Wink, D.A. Inducible nitric oxide synthase-derived extracellular nitric oxide flux regulates proinflammatory responses at the single cell level. Redox Biology 28, 101354 (2020). https://doi.org/10.1016/j.redox.2019.101354

Zakrevsky P, Kasprzak WK, Heinz WF, Wu W, Khant H, Bindewald E, et al. Truncated Tetrahedral RNA Nanostructures Exhibit Enhanced Features for Delivery of RNAi Substrates. Nanoscale 12(4) 2555–2568 (2020). https://doi.org/10.1039/c9nr08197f

2019

Sun, Z., Cagliero, C., Izard, J., Chen, Y., Zhou, Y.N., Heinz, W. F., Schneider, T.D. & Jin, D.J. Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli Nucleic Acids Research 47, 3970-3985 (2019). https://doi.org/10.1093/nar/gkz159

Sahabandu, N., Kong, D., Magidson, V., Nanjundappa, R., Sullenberger, C., Mahjoub, M.R. & Loncarek, J. Expansion microscopy for the analysis of centrioles and cilia. J Microsc 276, 145-159 (2019). https://doi.org/10.1111/jmi.12841

Nunn, N., Prabhakar, N., Reineck, P., Magidson, V., Kamiya, E., Heinz, W.F., Torelli, M.D., Rosenholm, J., Zaitsev, A. & Shenderova, O. Brilliant blue, green, yellow, and red fluorescent diamond particles: synthesis, characterization, and multiplex imaging demonstrations. Nanoscale (2019). https://doi.org/10.1039/c9nr02593f

Matarlo, J.S., Krumpe, L.R.H., Heinz, W.F., Oh, D., Shenoy, S.R., Thomas, C.L., Goncharova, E.I., Lockett, S.J. & O’Keefe, B.R. The Natural Product Butylcycloheptyl Prodiginine Binds Pre-miR-21, Inhibits Dicer-Mediated Processing of Pre-miR-21, and Blocks Cellular Proliferation. Cell Chemical Biology, 1-10 (2019). https://doi.org/10.1016/j.chembiol.2019.04.011 

Kulkarni, R.A., Briney, C.A., Crooks, D.R., Bergholtz, S.E., Mushti, C., Lockett, S.J., Lane, A.N., Fan, T.W., Swenson, R.E., Marston Linehan, W. & Meier, J.L. Photoinducible Oncometabolite Detection. Chembiochem 20, 360-365 (2019. https://doi.org/10.1002/cbic.201800651

Insinna, C., Lu, Q., Teixeira, I., Harned, A., Semler, E.M., Stauffer, J., Magidson, V., Tiwari, A., Kenworthy, A.K., Narayan, K. & Westlake, C.J. Investigation of F-BAR domain PACSIN proteins uncovers membrane tubulation function in cilia assembly and transport. Nat Commun 10, 428 (2019). https://doi.org/10.1038/s41467-018-08192-9

Fernandez, M.V., Delviks-Frankenberry, K.A., Scheiblin, D.A., Happel, C., Pathak, V.K. & Freed, E.O. Authentication Analysis of MT-4 Cells Distributed by the National Institutes of Health AIDS Reagent Program. Journal of Virology 93 (2019). https://doi.org/10.1128/jvi.01390-19 

Basudhar, D., Bharadwaj, G., Somasundaram, V., Cheng, R.Y.S., Ridnour, L.A., Fujita, M., Lockett, S.J., Anderson, S.K., McVicar, D.W. & Wink, D.A. Understanding the tumour micro-environment communication network from an NOS2/COX2 perspective. Br J Pharmacol 176, 155-176 (2019). https://doi.org/10.1111/bph.14488

2018

Singh, S.K., Singh, S., Gadomski, S., Sun, L., Pfannenstein, A., Magidson, V., Chen, X., Kozlov, S., Tessarollo, L., Klarmann, K.D. & Keller, J.R. Id1 Ablation Protects Hematopoietic Stem Cells from Stress-Induced Exhaustion and Aging. Cell Stem Cell 23, 252-265.e258 (2018). https://doi.org/10.1016/j.stem.2018.06.001

Liu, J., Kline, B.A., Kenny, T.A., Smith, D.R., Soloveva, V., Beitzel, B., Pang, S., Lockett, S., Hess, H.F., Palacios, G., Kuhn, J.H., Sun, M.G. & Zeng, X.K. A novel sheet-like virus particle array is a hallmark of Zika virus infection. Emerging Microbes & Infections 7 (2018).  https://doi.org/10.1038/s41426-018-0071-8

Kunduri, G., Turner-Evans, D., Konya, Y., Izumi, Y., Nagashima, K., Lockett, S., Holthuis, J., Bamba, T., Acharya, U. & Acharya, J.K. Defective cortex glia plasma membrane structure underlies light-induced epilepsy in cpes mutants. Proceedings of the National Academy of Sciences of the United States of America 115, E8919-E8928 (2018).  https://doi.org/10.1073/pnas.1808463115

Michie, M.S., Gotz, R., Franke, C., Bowler, M., Kumari, N., Magidson, V., Levitus, M., Loncarek, J., Sauer, M. & Schnermann, M.J. Cyanine Conformational Restraint in the Far-Red Range. Journal of the American Chemical Society 139, 12406-12409 (2017). https://doi.org/10.1021/jacs.7b07272

Yiran Li, Stephen J. Lockett, Robert J. Kinders, Wojciech Czaja: Detection of epithelial versus mesenchymal regions in 2D images of tumor biopsies using shearlets. https://doi.org/10.1109/ISBI.2018.8363720

2017

Insinna-Kettenhofen, C., Lu, Q., Teixeira, I., Harned, A.S., Semler, E., Stauffer, J., Magidson, V., Narayan, K. & Westlake, C. Exploring PACSIN membrane tubulation regulation during intracellular ciliogenesis using 3D electron microscopy. https://doi.org/10.1038/s41467-018-08192-9.

Chua, J., Senft, J.L., Lockett, S.J., Brett, P.J., Burtnick, M.N., DeShazer, D. & Friedlander, A.M. pH Alkalinization by Chloroquine Suppresses Pathogenic Burkholderia Type 6 Secretion System 1 and Multinucleated Giant Cells. Infection and Immunity 85 (2017). https://doi.org/10.1128/iai.00586-16  Basudhar, D., Glynn, S.A., Greer, M., Somasundaram, V., No, J.H., Scheiblin, D.A., Garrido, P., Heinz, W.F., Ryan, A.E., Weiss, J.M., Cheng, R.Y.S., Ridnour, L.A., Lockett, S.J., McVicar, D.W., Ambs, S. & Wink, D.A. Coexpression of NOS2 and COX2 accelerates tumor growth and reduces survival in estrogen receptor-negative breast cancer. Proceedings of the National Academy of Sciences 114, 13030-13035 (2017). https://doi.org/10.1073/pnas.1709119114

2016

Thirthagiri, E., Klarmann, K.D., Shukla, A.K., Southon, E., Biswas, K., Martin, B.K., North, S.L., Magidson, V., Burkett, S., Haines, D.C., Noer, K., Matthai, R., Tessarollo, L., Loncarek, J., Keller, J.R. & Sharan, S.K. BRCA2 minor transcript lacking exons 4-7 supports viability in mice and may account for survival of humans with a pathogenic biallelic mutation. Human Molecular Genetics 25, 1934-1945 (2016). https://doi.org/10.1093/hmg/ddw066 

Nandy, K., Chellappa, R., Kumar, A. & Lockett, S.J. Segmentation of Nuclei from 3D Microscopy Images of Tissue via Graphcut Optimization. IEEE Journal on Selected Topics in Signal Processing 10, 140-150 (2016). https://doi.org/10.1109/JSTSP.2015.2505148 Kuhns, D.B., Fink, D.L., Choi, U., Sweeney, C., Lau, K., Priel, D.L., Riva, D., Mendez, L., Uzel, G., Freeman, A.F., Olivier, K.N., Anderson, V.L., Currens, R., Mackley, V., Kang, A., Al-Adeli, M., Mace, E., Orange, J.S., Kang, E., Lockett, S.J., Chen, D., Steinbach, P.J., Hsu, A.P., Zarember, K.A., Malech, H.L., Gallin, J.I. & Holland, S.M. Cytoskeletal abnormalities and neutrophil dysfunction in WDR1 deficiency. Blood 128, 2135-2143 (2016). https://doi.org/10.1182/blood-2016-03-706028  Jiang, H., Promchan, K., Lin, B.R., Lockett, S., Chen, D., Marshall, H., Badralmaa, Y. & Natarajan, V. LZTFL1 Upregulated by All-Trans Retinoic Acid during CD4(+) T Cell Activation Enhances IL-5 Production. Journal of Immunology 196, 1081-1090 (2016). https://doi.org/10.4049/jimmunol.1500719