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Recent Publications (2023-24)

Huiwang Ai, PhD

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Zhang, J., Li, Z., Pang, Y., Fan, Y., & Ai, H. -W. (2023). Genetically Encoded Boronolectin as a Specific Red Fluorescent UDP-GlcNAc Biosensor.. bioRxiv. doi:10.1101/2023.03.01.530644

Wu, T., Kumar, M., Zhang, J., Zhao, S., Drobizhev, M., McCollum, M., . . . Ai, H. -W. (2023). A genetically encoded far-red fluorescent indicator for imaging synaptically released Zn<sup>2</sup>.. Science advances9(9), eadd2058. doi:10.1126/sciadv.add2058

Zhang, J., Li, Z., Pang, Y., Fan, Y., & Ai, H. -W. (2023). Genetically Encoded Boronolectin as a Specific Red Fluorescent UDP-GlcNAc Biosensor. ACS SENSORS. doi:10.1021/acssensors.3c00409

Chen, C., Zhang, H., Zhang, J., Ai, H. -W., & Fang, C. (2023). Structural origin and rational development of bright red noncanonical variants of green fluorescent protein. PHYSICAL CHEMISTRY CHEMICAL PHYSICS25(23), 15624-15634. doi:10.1039/d3cp01315d

Pang, Y., Huang, M., Fan, Y., Yeh, H. -W., Xiong, Y., Ng, H. L., & Ai, H. -W. (2023). Development, Characterization, and Structural Analysis of a Genetically Encoded Red Fluorescent Peroxynitrite Biosensor. ACS CHEMICAL BIOLOGY18(6), 1388-1397. doi:10.1021/acschembio.3c00139

Zygmunt Derewenda, PhD

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Derewenda, Z. S. (2023). C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES24(17). doi:10.3390/ijms241713165

Janczyk, P. L., Zylkiewicz, E., De Hoyos, H., West, T., Matson, D. R., Choi, W. -C., . . . Stukenberg, P. T. (2023). Aurora A phosphorylates Ndel1 to reduce the levels of Mad1 and NuMA at spindle poles. MOLECULAR BIOLOGY OF THE CELL34(1). doi:10.1091/mbc.E21-09-0438

Brant Isakson, PhD

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Luse, M. A., Jackson, M. G., Juskiewicz, Z. J., & Isakson, B. E. (2023). Physiological functions of caveolae in endothelium. CURRENT OPINION IN PHYSIOLOGY35. doi:10.1016/j.cophys.2023.100701

Sveeggen, T. M., Isakson, B. E., Straub, A. C., & Bagher, P. (2023). Bedding as a variable affecting fasting blood glucose and vascular physiology in mice. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY325(2), H338-H345. doi:10.1152/ajpheart.00168.2023

Shah, S. A., Reagan, C. E., Bresticker, J. E., Wolpe, A. G., Good, M. E., Macal, E. H., . . . Epstein, F. H. (2023). Obesity-Induced Coronary Microvascular Disease Is Prevented by iNOS Deletion and Reversed by iNOS Inhibition. JACC-BASIC TO TRANSLATIONAL SCIENCE8(5), 501-514. doi:10.1016/j.jacbts.2022.11.005

Ruddiman, C. A., Peckham, R., Luse, M. A., Chen, Y. -L., Kuppusamy, M., Corliss, B. A., . . . Isakson, B. E. (2023). Polarized localization of phosphatidylserine in the endothelium regulates Kir2.1. JCI INSIGHT8(9). doi:10.1172/jci.insight.165715

Koval, M., Schug, W. J., & Isakson, B. E. (2023). Pharmacology of pannexin channels. CURRENT OPINION IN PHARMACOLOGY69. doi:10.1016/j.coph.2023.102359

Ragland, T. J., Heiston, E. M., Ballantyne, A., Stewart, N. R., La Salvia, S., Musante, L., . . . Malin, S. K. (2023). Extracellular vesicles and insulin-mediated vascular function in metabolic syndrome. PHYSIOLOGICAL REPORTS11(1). doi:10.14814/phy2.15530

Dunaway, L. S., Billaud, M., Macal, E., Good, M. E., Medina, C. B., Lorenz, U., . . . Isakson, B. E. (2023). Amount of Pannexin 1 in Smooth Muscle Cells Regulates Sympathetic Nerve-Induced Vasoconstriction. HYPERTENSION80(2), 416-425. doi:10.1161/HYPERTENSIONAHA.122.20280

Chu, P. -L., Gigliotti, J. C., Cechova, S., Bodonyi-Kovacs, G., Wang, Y. T., Chen, L., . . . Le, T. H. (2023). Collectrin<i> (Tmem27)</i> deficiency in proximal tubules causes hypertension in mice and a<i> TMEM27</i> variant associates with blood pressure in males in a Latino cohort. AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY324(1), F30-F42. doi:10.1152/ajprenal.00176.2022

Baldwin, S. N., Forrester, E. A., Homer, N. Z. M., Andrew, R., Barrese, V., Stott, J. B., . . . Greenwood, I. A. (2023). Marked oestrous cycle-dependent regulation of rat arterial K<sub>V</sub>7.4 channels driven by GPER1. BRITISH JOURNAL OF PHARMACOLOGY180(2), 174-193. doi:10.1111/bph.15947

Ahmad Jomaa, PhD

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Gamerdinger, M., Jia, M., Schloemer, R., Rabl, L., Jaskolowski, M., Khakzar, K. M., . . . Deuerling, E. (2023). NAC controls cotranslational N-terminal methionine excision in eukaryotes.. Science (New York, N.Y.)380(6651), 1238-1243. doi:10.1126/science.adg3297

Jaskolowski, M., Jomaa, A., Gamerdinger, M., Shrestha, S., Leibundgut, M., Deuerling, E., & Ban, N. (2023). Molecular basis of the TRAP complex function in ER protein biogenesis. NATURE STRUCTURAL & MOLECULAR BIOLOGY30(6), 770-+. doi:10.1038/s41594-023-00990-0

Fromm, S. A. A., O’Connor, K. M. M., Purdy, M., Bhatt, P. R. R., Loughran, G., Atkins, J. F. F., . . . Mattei, S. (2023). The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services. NATURE COMMUNICATIONS14(1). doi:10.1038/s41467-023-36742-3

Anne Kenworthy, PhD

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Balakrishnan, M., & Kenworthy, A. K. (2024). Lipid Peroxidation Drives Liquid-Liquid Phase Separation and Disrupts Raft Protein Partitioning in Biological Membranes.. Journal of the American Chemical Society. doi:10.1021/jacs.3c10132

Balakrishnan, M., & Kenworthy, A. K. (2023). Lipid peroxidation drives liquid-liquid phase separation and disrupts raft protein partitioning in biological membranes.. bioRxiv. doi:10.1101/2023.09.12.557355

Kenworthy, A. K., Han, B., Ariotti, N., & Parton, R. G. (2023). The Role of Membrane Lipids in the Formation and Function of Caveolae. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY15(9). doi:10.1101/cshperspect.a041413

Kenworthy, A. K. (2023). What’s past is prologue: FRAP keeps delivering 50 years later. BIOPHYSICAL JOURNAL122(18), 3577-3586. doi:10.1016/j.bpj.2023.05.016

Kenworthy, A. K. (2023). The building blocks of caveolae revealed: caveolins finally take center stage. BIOCHEMICAL SOCIETY TRANSACTIONS51(2), 855-869. doi:10.1042/BST20221298

Han, B., Gulsevin, A., Connolly, S., Wang, T., Meyer, B., Porta, J., . . . Kenworthy, A. K. (2023). Structural analysis of the P132L disease mutation in caveolin-1 reveals its role in the assembly of oligomeric complexes. JOURNAL OF BIOLOGICAL CHEMISTRY299(4). doi:10.1016/j.jbc.2023.104574

Gulsevin, A., Han, B., Porta, J. C., Mchaourab, H. S., Meiler, J., & Kenworthy, A. K. (2023). Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2. BIOPHYSICAL JOURNAL122(11), 2041-2052. doi:10.1016/j.bpj.2022.11.011

Muge Kuyumcu-Martinez, PhD

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Deberneh, H. M., Abdelrahman, D. R., Verma, S. K., Linares, J. J., Murton, A. J., Russell, W. K., . . . Sadygov, R. G. (2023). A large-scale LC-MS dataset of murine liver proteome from time course of heavy water metabolic labeling. SCIENTIFIC DATA10(1). doi:10.1038/s41597-023-02537-w

Mehlferber, M. M., Kuyumcu-Martinez, M., Miller, C. L., & Sheynkman, G. M. (2023). Transcription Factors and Splice Factors-Interconnected Regulators of Stem Cell Differentiation. CURRENT STEM CELL REPORTS9(2), 31-41. doi:10.1007/s40778-023-00227-2

Deberneh, H. M., Abdelrahman, D. R., Verma, S. K., Linares, J. J., Murton, A. J., Russell, W. K., . . . Sadygov, R. G. (2023). Quantifying label enrichment from two mass isotopomers increases proteome coverage for in vivo protein turnover using heavy water metabolic labeling. COMMUNICATIONS CHEMISTRY6(1). doi:10.1038/s42004-023-00873-x

Cao, J., & Kuyumcu-Martinez, M. N. (2023). Alternative polyadenylation regulation in cardiac development and cardiovascular disease. CARDIOVASCULAR RESEARCH119(6), 1324-1335. doi:10.1093/cvr/cvad014

Gary Owens, PhD

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Karnewar, S., Karnewar, V., Deaton, R., Shankman, L. S., Benavente, E. D., Williams, C. M., . . . Owens, G. K. (2023). IL-1β inhibition partially negates the beneficial effects of diet-induced lipid lowering.. bioRxiv. doi:10.1101/2023.10.13.562255

Karnewar, S., Karnewar, V., Shankman, L. S., & Owens, G. K. (2023). Treatment of advanced atherosclerotic mice with the senolytic agent ABT-263 is associated with reduced indices of plaque stability and increased mortality.. bioRxiv. doi:10.1101/2023.07.12.548696

Benavente, E. D., Karnewar, S., Buono, M., Mili, E., Hartman, R. J. G., Kapteijn, D., . . . den Ruijter, H. M. (2023). Female gene networks are expressed in myofibroblast-like smooth muscle cells in vulnerable atherosclerotic plaques.. bioRxiv. doi:10.1101/2023.02.08.527690

Benavente, E. D., Karnewar, S., Buono, M., Mili, E., Hartman, R. J. G., Kapteijn, D., . . . den Ruijter, H. M. (2023). Female Gene Networks Are Expressed in Myofibroblast-Like Smooth Muscle Cells in Vulnerable Atherosclerotic Plaques. ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY43(10), 1836-1850. doi:10.1161/ATVBAHA.123.319325

Serbulea, V., Deaton, R. A. A., & Owens, G. K. K. (2023). Old bones control smooth muscle clones. NATURE AGING3(1), 9-10. doi:10.1038/s43587-022-00346-1

Deaton, R. A., Bulut, G., Serbulea, V., Salamon, A., Shankman, L. S., Nguyen, A. T., & Owens, G. K. (2023). A New Autosomal <i>Myh11-CreER<SUP>T2</SUP></i> Smooth Muscle Cell Lineage Tracing and Gene Knockout Mouse Model-Brief Report. ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY43(2), 203-211. doi:10.1161/ATVBAHA.122.318160

Owens, G. K., & Deaton, R. A. (2023). Response by Owens and Deaton to Letter Regarding Article, “Dichotomous Roles of Smooth Muscle Cell-Derived MCP1 (Monocyte Chemoattractant Protein 1) in Development of Atherosclerosis”. ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY43(1), E64. doi:10.1161/ATVBAHA.122.318638

Ling Qi, PhD (Department Chair)

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Steafanie Redemann, PhD

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Chen, Y. -Z., Zimyanin, V., & Redemann, S. (2023). Loss of the mitochondrial protein SPD-3 elevates PLK-1 levels and dysregulates mitotic events.. Life science alliance6(11), e202302011. doi:10.26508/lsa.202302011

Zimyanin, V., Magaj, M., Yu, C. -H., Gibney, T., Mustafa, B., Horton, X., . . . Redemann, S. (2023). Lack of chromokinesin Klp-19 creates a more rigid midzone and affects force transmission during anaphase in C. elegans.. bioRxiv. doi:10.1101/2023.10.26.564275

Lantzsch, I., Yu, C. -H., Chen, Y. -Z., Zimyanin, V., Yazdkhasti, H., Lindow, N., . . . Redemann, S. (2023). Correction: Microtubule reorganization during female meiosis in <i>C. elegans</i>.. eLife12, e86893. doi:10.7554/elife.86893

Zimyanin, V. L., Pielka, A. -M., Glass, H., Japtok, J., Grossmann, D., Martin, M., . . . Hermann, A. (2023). Live Cell Imaging of ATP Levels Reveals Metabolic Compartmentalization within Motoneurons and Early Metabolic Changes in <i>FUS</i> ALS Motoneurons. CELLS12(10). doi:10.3390/cells12101352

Chen, Y. -Z., Zimyanin, V., & Redemann, S. (2023). Mitotic events depend on regulation of PLK-1 levels by the mitochondrial protein SPD-3. doi:10.1101/2023.01.11.523633

Gloria Sheynkman, PhD

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Pardo-Palacios, F. J., Wang, D., Reese, F., Diekhans, M., Carbonell-Sala, S., Williams, B., . . . Brooks, A. N. (2023). Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. bioRxiv. doi:10.1101/2023.07.25.550582

Joglekar, A., Hu, W., Zhang, B., Narykov, O., Diekhans, M., Balacco, J., . . . Tilgner, H. U. (2023). Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development.. bioRxiv. doi:10.1101/2023.04.02.535281

Mehlferber, M. M., Kuyumcu-Martinez, M., Miller, C. L., & Sheynkman, G. M. (2023). Transcription Factors and Splice Factors-Interconnected Regulators of Stem Cell Differentiation. CURRENT STEM CELL REPORTS9(2), 31-41. doi:10.1007/s40778-023-00227-2

Li, M. M., Awasthi, S., Ghosh, S., Bisht, D., Coban Akdemir, Z. H., Sheynkman, G. M., . . . Yi, S. S. (2023). Gain-of-Function Variomics and Multi-omics Network Biology for Precision Medicine.. Methods in molecular biology (Clifton, N.J.)2660, 357-372. doi:10.1007/978-1-0716-3163-8_24

Acharya, B. R., Fang, J. S., Jeffery, E., Chavkin, N. W., Genet, G., Vasavada, H., . . . Hirschi, K. K. (2023). Connexin 37 sequestering of activated-ERK in the cytoplasm promotes p27-mediated endothelial cell cycle arrest. LIFE SCIENCE ALLIANCE6(8). doi:10.26508/lsa.202201685

de Souza, V. B. C., Jordan, B. T. T., Tseng, E., Nelson, E. A. A., Hirschi, K. K. K., Sheynkman, G., & Robinson, M. D. D. (2023). Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data. GENOME BIOLOGY24(1). doi:10.1186/s13059-023-02923-y

Abood, A., Mesner, L., Jeffery, E., Murali, M., Lehe, M., Saquing, J., . . . Sheynkman, G. (2023). Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease. doi:10.1101/2023.03.17.531557

Pan, X., Akdemir, Z. H. C., Gao, R., Jiang, X., Sheynkman, G. M., Wu, E., . . . Yi, S. S. (2023). AD-Syn-Net: systematic identification of Alzheimer’s disease-associated mutation and co-mutation vulnerabilities via deep learning. BRIEFINGS IN BIOINFORMATICS24(2). doi:10.1093/bib/bbad030

Aherrahrou, R., Lue, D., Perry, R. N., Aberra, Y. T., Khan, M. D., Soh, J. Y., . . . Civelek, M. (2023). Genetic Regulation of SMC Gene Expression and Splicing Predict Causal CAD Genes. CIRCULATION RESEARCH132(3), 323-338. doi:10.1161/CIRCRESAHA.122.321586

Swapnil Sonkusare, PhD

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Kuppusamy, M., Ta, H. Q., Davenport, H. N., Bazaz, A., Kulshrestha, A., Daneva, Z., . . . Sonkusare, S. K. (2023). Purinergic P2Y2 receptor-induced activation of endothelial TRPV4 channels mediates lung ischemia-reperfusion injury.. Science signaling16(808), eadg1553. doi:10.1126/scisignal.adg1553

Villalba, N., Sackheim, A. M., Lawson, M. A., Haines, L., Chen, Y. -L., Sonkusare, S. K., . . . Freeman, K. (2023). The Polyanionic Drug Suramin Neutralizes Histones and Prevents Endotheliopathy.. Journal of immunology (Baltimore, Md. : 1950)211(4), 648-657. doi:10.4049/jimmunol.2200703

Ruddiman, C. A., Peckham, R., Luse, M. A., Chen, Y. -L., Kuppusamy, M., Corliss, B. A., . . . Isakson, B. E. (2023). Polarized localization of phosphatidylserine in the endothelium regulates Kir2.1. JCI INSIGHT8(9). doi:10.1172/jci.insight.165715

Wong, D., Auguste, G., Lino Cardenas, C. L., Turner, A. W., Chen, Y., Song, Y., . . . Miller, C. L. (2023). FHL5 Controls Vascular Disease-Associated Gene Programs in Smooth Muscle Cells. CIRCULATION RESEARCH132(9), 1144-1161. doi:10.1161/CIRCRESAHA.122.321692

Daneva, Z., Chen, Y. -L., Ta, H. Q., Manchikalapudi, V., Bazaz, A., Laubach, V. E., & Sonkusare, S. K. (2023). Endothelial IK and SK channel activation decreases pulmonary arterial pressure and vascular remodeling in pulmonary hypertension. PULMONARY CIRCULATION13(1). doi:10.1002/pul2.12186

Lukas Tamm, PhD

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Jahn, R., Cafiso, D. C., & Tamm, L. K. (2023). Mechanisms of SNARE proteins in membrane fusion. NATURE REVIEWS MOLECULAR CELL BIOLOGY. doi:10.1038/s41580-023-00668-x

Odongo, L., Habtegebrael, B. H., Kiessling, V., White, J. M., & Tamm, L. K. (2023). A novel <i>in vitro</i> system of supported planar endosomal membranes (SPEMs) reveals an enhancing role for cathepsin B in the final stage of Ebola virus fusion and entry. MICROBIOLOGY SPECTRUM11(5). doi:10.1128/spectrum.01908-23

Ward, A. E., Sokovikova, D., Waxham, M. N., Heberle, F. A., Levental, I., Levental, K. R., . . . Tamm, L. K. (2023). Serinc5 Restricts HIV Membrane Fusion by Altering Lipid Order and Heterogeneity in the Viral Membrane. ACS INFECTIOUS DISEASES9(4), 773-784. doi:10.1021/acsinfecdis.2c00478

Jinghang Xie, PhD

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Yin, Q., Luo, W., Mallajosyula, V., Bo, Y., Guo, J., Xie, J., . . . Davis, M. M. M. (2023). A TLR7-nanoparticle adjuvant promotes a broad immune response against heterologous strains of influenza and SARS-CoV-2. NATURE MATERIALS22(3), 380-+. doi:10.1038/s41563-022-01464-2

Dai, T., Xie, J., Buonomo, J. A., Moreno, A., Banaei, N., Bertozzi, C. R., & Rao, J. (2023). Bioluminogenic Probe for Rapid, Ultrasensitive Detection of ?-Lactam-Resistant Bacteria. ANALYTICAL CHEMISTRY95(18), 7329-7335. doi:10.1021/acs.analchem.3c00478

Jochen Zimmer, PhD

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DeAngelis, P. L., & Zimmer, J. (2023). Hyaluronan synthases; mechanisms, myths, & mysteries of three types of unique bifunctional glycosyltransferases.. Glycobiology, cwad075. doi:10.1093/glycob/cwad075

Verma, P., Kwansa, A. L., Ho, R., Yingling, Y. G., & Zimmer, J. (2023). Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8. STRUCTURE31(10), 1166-+. doi:10.1016/j.str.2023.07.010

Hrmova, M., Zimmer, J., Bulone, V., & Fincher, G. B. (2023). Enzymes in 3D: Synthesis, remodelling, and hydrolysis of cell wall (1,3;1,4)-β-glucans. PLANT PHYSIOLOGY. doi:10.1093/plphys/kiad415

Stephens, Z., Wilson, L. F. L., & Zimmer, J. (2023). Diverse mechanisms of polysaccharide biosynthesis, assembly and secretion across kingdoms. CURRENT OPINION IN STRUCTURAL BIOLOGY79. doi:10.1016/j.sbi.2023.102564