Biochemistry & Molecular Biology

Research Output

2020

2′-Hydroxyflavanone prevents LPS-induced inflammatory response and cytotoxicity in murine macrophages

Sonowal, H. & Ramana, K. V., Dec 2020, In : Toxicology in Vitro. 69, 104966.

Research output: Contribution to journalArticle

A cocrystal structure of dengue capsid protein in complex of inhibitor

Xia, H., Xie, X., Zou, J., Noble, C. G., Russell, W. K., Holthauzen, L. M. F., Choi, K. H., White, M. A. & Shi, P. Y., Jul 28 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 30, p. 17992-18001 10 p.

Research output: Contribution to journalArticle

Action of a minimal contractile bactericidal nanomachine

Ge, P., Scholl, D., Prokhorov, N. S., Avaylon, J., Shneider, M. M., Browning, C., Buth, S. A., Plattner, M., Chakraborty, U., Ding, K., Leiman, P. G., Miller, J. F. & Zhou, Z. H., Apr 30 2020, In : Nature. 580, 7805, p. 658-662 5 p.

Research output: Contribution to journalArticle

1 Scopus citations

Acupuncture Reduces Hypertrophy and Cardiac Fibrosis, and Improves Heart Function in Mice with Diabetic Cardiomyopathy

Ye, Y., Birnbaum, Y., Widen, S., Zhang, Z., Zhu, S., Bajaj, M. & Chen, H., 2020, (Accepted/In press) In : Cardiovascular Drugs and Therapy.

Research output: Contribution to journalArticle

A high-throughput neutralizing antibody assay for COVID-19 diagnosis and vaccine evaluation

Muruato, A. E., Fontes-Garfias, C. R., Ren, P., Garcia-Blanco, M. A., Menachery, V. D., Xie, X. & Shi, P. Y., Dec 1 2020, In : Nature communications. 11, 1, 4059.

Research output: Contribution to journalArticle

Open Access

A low fidelity virus shows increased recombination during the removal of an alphavirus reporter gene

Kautz, T. F., Jaworski, E., Routh, A. & Forrester, N. L., Jun 2020, In : Viruses. 12, 6, 660.

Research output: Contribution to journalArticle

Open Access

An antibody panel for highly specific detection and differentiation of Zika virus

Kabir, M. A., Soto-Acosta, R., Sharma, S., Bradrick, S. S., Garcia-Blanco, M. A., Caputi, M. & Asghar, W., Dec 1 2020, In : Scientific reports. 10, 1, 11906.

Research output: Contribution to journalArticle

Open Access

An Infectious cDNA Clone of SARS-CoV-2

Xie, X., Muruato, A., Lokugamage, K. G., Narayanan, K., Zhang, X., Zou, J., Liu, J., Schindewolf, C., Bopp, N. E., Aguilar, P. V., Plante, K. S., Weaver, S. C., Makino, S., LeDuc, J. W., Menachery, V. D. & Shi, P. Y., May 13 2020, In : Cell Host and Microbe. 27, 5, p. 841-848.e3

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

A rapid and simple quantitative method for specific detection of smaller coterminal RNA by PCR (DeSCo-PCR): Application to the detection of viral subgenomic RNAs

Kanodia, P., Reddisiva Prasanth, K., Roa-Linares, V. C., Bradrick, S. S., Garcia-Blanco, M. A. & Allen Miller, W., Jul 2020, In : RNA. 26, 7, p. 888-901 14 p.

Research output: Contribution to journalArticle

Open Access

A replication-defective Japanese encephalitis virus (JEV) vaccine candidate with NS1 deletion confers dual protection against JEV and West Nile virus in mice

Li, N., Zhang, Z. R., Zhang, Y. N., Liu, J., Deng, C. L., Shi, P. Y., Yuan, Z. M., Ye, H. Q. & Zhang, B., Dec 1 2020, In : npj Vaccines. 5, 1, 73.

Research output: Contribution to journalArticle

Open Access

Capsid protein structure in Zika virus reveals the flavivirus assembly process

Tan, T. Y., Fibriansah, G., Kostyuchenko, V. A., Ng, T. S., Lim, X. X., Zhang, S., Lim, X. N., Wang, J., Shi, J., Morais, M. C., Corti, D. & Lok, S. M., Dec 1 2020, In : Nature communications. 11, 1, 895.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Cell response to substrate rigidity is regulated by active and passive cytoskeletal stress

Doss, B. L., Pan, M., Gupta, M., Grenci, G., Mège, R. M., Lim, C. T., Sheetz, M. P., Voituriez, R. & Ladoux, B., Jun 9 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 23, p. 12817-12825 9 p.

Research output: Contribution to journalArticle

Characterization of port bolivar virus, a novel entomobirnavirus (birnaviridae) isolated from mosquitoes collected in east Texas, USA

Tesh, R. B., Bolling, B. G., Guzman, H., Popov, V. L., Wilson, A., Widen, S. G., Wood, T. G., Walker, P. J. & Vasilakis, N., 2020, In : Viruses. 12, 4, 390.

Research output: Contribution to journalArticle

Open Access
Open Access

Corrigendum: DNA polymerase θ accomplishes translesion synthesis opposite 1,N6-ethenodeoxyadenosine with a remarkably high fidelity in human cells

Yoon, J. H., Johnson, R. E., Prakash, L. & Prakash, S., Jan 1 2020, In : Genes & development. 34, 1-2, p. 146 1 p.

Research output: Contribution to journalComment/debate

Open Access

Dapagliflozin and Ticagrelor Have Additive Effects on the Attenuation of the Activation of the NLRP3 Inflammasome and the Progression of Diabetic Cardiomyopathy: an AMPK–mTOR Interplay

Chen, H., Tran, D., Yang, H. C., Nylander, S., Birnbaum, Y. & Ye, Y., Aug 1 2020, In : Cardiovascular Drugs and Therapy. 34, 4, p. 443-461 19 p.

Research output: Contribution to journalArticle

1 Scopus citations

Detecting Counterion Dynamics in DNA–Protein Association

Pletka, C. C., Nepravishta, R. & Iwahara, J., Jan 20 2020, In : Angewandte Chemie - International Edition. 59, 4, p. 1465-1468 4 p.

Research output: Contribution to journalArticle

1 Scopus citations

Dianke virus: A new mesonivirus species isolated from mosquitoes in Eastern Senegal

Diagne, M. M., Gaye, A., Ndione, M. H. D., Faye, M., Fall, G., Dieng, I., Widen, S. G., Wood, T. G., Popov, V., Guzman, H., Bâ, Y., Weaver, S. C., Diallo, M., Tesh, R., Faye, O., Vasilakis, N. & Sall, A. A., Jan 2 2020, In : Virus Research. 275, 197802.

Research output: Contribution to journalArticle

1 Scopus citations

Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP

Kim, B., Arcos, S., Rothamel, K., Jian, J., Rose, K. L., McDonald, W. H., Bian, Y., Reasoner, S., Barrows, N. J., Bradrick, S., Garcia-Blanco, M. A. & Ascano, M., May 21 2020, In : Molecular cell. 78, 4, p. 624-640.e7

Research output: Contribution to journalArticle

2 Scopus citations

Does Inhibition of Nuclear Factor Kappa B Explain the Protective Effect of Ticagrelor on Myocardial Ischemia-Reperfusion Injury?

Birnbaum, Y., Ye, Y. & Perez-Polo, J. R., Feb 1 2020, In : Journal of cardiovascular pharmacology. 75, 2, p. 108-111 4 p.

Research output: Contribution to journalArticle

Downregulation of CFIm25 amplifies dermal fibrosis through alternative polyadenylation

Weng, T., Huang, J., Wagner, E. J., Ko, J., Wu, M., Wareing, N. E., Xiang, Y., Chen, N. Y., Ji, P., Molina, J. G., Volcik, K. A., Han, L., Mayes, M. D., Blackburn, M. R. & Assassi, S., Feb 3 2020, In : The Journal of experimental medicine. 217, 2

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2 Scopus citations

Efficient identification of multiple pathways: RA-Seq analysis of livers from 56Fe ion irradiated mice

ia, A. M., Chen, T., Barnette, B. L., Khanipov, K., Ullrich, R. L., Bhavnani, S. K. & Emmett, M. R., Mar 20 2020, In : BMC bioinformatics. 21, 1, 118.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Envelope protein ubiquitination drives entry and pathogenesis of Zika virus

Giraldo, M. I., Xia, H., Aguilera-Aguirre, L., Hage, A., van Tol, S., Shan, C., Xie, X., Sturdevant, G. L., Robertson, S. J., McNally, K. L., Meade-White, K., Azar, S. R., Rossi, S. L., Maury, W., Woodson, M., Ramage, H., Johnson, J. R., Krogan, N. J., Morais, M. C., Best, S. M. & 2 others, Shi, P. Y. & Rajsbaum, R., 2020, (Accepted/In press) In : Nature.

Research output: Contribution to journalArticle

1 Scopus citations

EnvZ/OmpR two-component signaling: An archetype system that can function noncanonically

Kenney, L. J. & Anand, G. S., 2020, In : EcoSal Plus. 9, 1, p. 1-30 30 p.

Research output: Contribution to journalArticle

Open Access

Evolution, purification, and characterization of rc0497: A peptidoglycan amidase from the prototypical spotted fever species rickettsia conorii

Patel, J. G., Narra, H. P., Sepuru, K. M., Sahni, A., Golla, S. R., Sahni, A., Singh, A., Schroeder, C. L. C., Chowdhury, I. H., Popov, V. L. & Sahni, S. K., Feb 1 2020, In : Biological Chemistry. 401, 2, p. 249-262 14 p.

Research output: Contribution to journalArticle

1 Scopus citations

Fetal membrane extracellular vesicle profiling reveals distinct pathways induced by infection and inflammation in vitro

Monsivais, L. A., Sheller-Miller, S., Russell, W., Saade, G. R., Dixon, C. L., Urrabaz-Garza, R. & Menon, R., Sep 1 2020, In : American Journal of Reproductive Immunology. 84, 3, e13282.

Research output: Contribution to journalArticle

Genes of the cGMP-PKG-Ca2+ signaling pathway are alternatively spliced in cardiomyopathy: Role of RBFOX2

Wan, X., Belanger, K. A., Widen, S. G., Kuyumcu-Martinez, M. N. & Garg, N. J., Mar 1 2020, In : Biochimica et Biophysica Acta - Molecular Basis of Disease. 1866, 3, 165620.

Research output: Contribution to journalArticle

Genetic evidence for reconfiguration of DNA polymerase θ active site for error-free translesion synthesis in human cells

Yoon, J. H., Johnson, R. E., Prakash, L. & Prakash, S., May 1 2020, In : Journal of Biological Chemistry. 295, 18, p. 5918-5927 10 p.

Research output: Contribution to journalArticle

Open Access

High flavivirus structural plasticity demonstrated by a non-spherical morphological variant

Morrone, S. R., Chew, V. S. Y., Lim, X. N., Ng, T. S., Kostyuchenko, V. A., Zhang, S., Wirawan, M., Chew, P. L., Lee, J., Tan, J. L., Wang, J., Tan, T. Y., Shi, J., Screaton, G., Morais, M. C. & Lok, S. M., Dec 1 2020, In : Nature communications. 11, 1, 3112.

Research output: Contribution to journalArticle

Open Access

Hydrogen-exchange kinetics studied through analysis of self-decoupling of nuclear magnetic resonance

Nepravishta, R., Yu, B. & Iwahara, J., Mar 2020, In : Journal of Magnetic Resonance. 312, 106687.

Research output: Contribution to journalArticle

Open Access

Interactions between identical DNA double helices

Lai, C. L., Chen, C., Ou, S. C., Prentiss, M. & Pettitt, B. M., Mar 2020, In : Physical Review E. 101, 3, 032414.

Research output: Contribution to journalArticle

1 Scopus citations

JAK2 regulates Nav1.6 channel function via FGF14Y158 phosphorylation

Wadsworth, P. A., Singh, A. K., Nguyen, N., Dvorak, N. M., Tapia, C. M., Russell, W. K., Stephan, C. & Laezza, F., Oct 2020, In : Biochimica et Biophysica Acta - Molecular Cell Research. 1867, 10, 118786.

Research output: Contribution to journalArticle

Open Access
Open Access

MicroRNA sequencing of rat hippocampus and human biofluids identifies acute, chronic, focal and diffuse traumatic brain injuries

Weisz, H. A., Kennedy, D., Widen, S., Spratt, H., Sell, S. L., Bailey, C., Sheffield-Moore, M., DeWitt, D. S., Prough, D. S., Levin, H., Robertson, C. & Hellmich, H. L., Dec 1 2020, In : Scientific reports. 10, 1, 3341.

Research output: Contribution to journalArticle

Open Access

Micro-stepping extended focus reduces photobleaching and preserves structured illumination super-resolution features

Hu, X., Jalal, S., Sheetz, M., Bakke, O. & Margadant, F., May 2020, In : Journal of Cell Science. 133, 10, 240796.

Research output: Contribution to journalArticle

Open Access

Near-atomic-resolution cryo-electron microscopy structures of cucumber leaf spot virus and red clover necrotic mosaic virus: Evolutionary divergence at the icosahedral three-fold axes

Sherman, M. B., Guenther, R., Reade, R., D’Ann, R., Sit, T. & Smitha, T. J., Jan 1 2020, In : Journal of virology. 94, 2, e01439-19.

Research output: Contribution to journalArticle

NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups

Yu, B., Pletka, C. C. & Iwahara, J., Feb 13 2020, In : Journal of Physical Chemistry B. 124, 6, p. 1065-1070 6 p.

Research output: Contribution to journalArticle

1 Scopus citations

NS5 from dengue virus serotype 2 can adopt a conformation analogous to that of its zika virus and Japanese encephalitis virus homologues

El Sahili, A., Soh, T. S., Schiltz, J., Gharbi-Ayachi, A., Seh, C. C., Shi, P. Y., Lim, S. P. & Lescar, J., Jan 1 2020, In : Journal of virology. 94, 1, e01294-19.

Research output: Contribution to journalArticle

2 Scopus citations

Oxidative damage diminishes mitochondrial DNA polymerase replication fidelity

Anderson, A. P., Luo, X., Russell, W. & Yin, Y. W., Jan 24 2020, In : Nucleic acids research. 48, 2, p. 817-829 13 p.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Partial loss of CFIM25 causes learning deficits and aberrant neuronal alternative polyadenylation

Alcott, C. E., Yalamanchili, H. K., Ji, P., van der Heijden, M. E., Saltzman, A., Elrod, N., Lin, A., Leng, M., Bhatt, B., Hao, S., Wang, Q., Saliba, A., Tang, J., Malovannaya, A., Wagner, E. J., Liu, Z. & Zoghbi, H. Y., Apr 2020, In : eLife. 9, e50895.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Peli1 signaling blockade attenuates congenital zika syndrome

Luo, H., Li, G., Wang, B., Tian, B., Gao, J., Zou, J., Shi, S., Zhu, S., Peng, B. H., Adam, A., Martinez, A., Hein, K., Winkelmann, E. R., Mahmoud, Y., Zhou, X., Shan, C., Rossi, S., Weaver, S., Barrett, A. D. T., Sun, S. C. & 4 others, Zhang, W., Shi, P. Y., Wu, P. & Wang, T., Jun 2020, In : PLoS pathogens. 16, 6, e1008538.

Research output: Contribution to journalArticle

Open Access

Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder

Drake, J. A., Drake, J. A. & Pettitt, B. M., Jun 4 2020, In : Journal of Physical Chemistry B. 124, 22, p. 4379-4390 12 p.

Research output: Contribution to journalArticle

PI4KIIIβ is a therapeutic target in chromosome 1q-amplified lung adenocarcinoma

Tan, X., Banerjee, P., Pham, E. A., Rutaganira, F. U. N., Basu, K., Bota-Rabassedas, N., Guo, H. F., Grzeskowiak, C. L., Liu, X., Yu, J., Shi, L., Peng, D. H., Leticia Rodriguez, B., Zhang, J., Zheng, V., Duose, D. Y., Solis, L. M., Mino, B., Raso, M. G., Behrens, C. & 15 others, Wistuba, I. I., Scott, K. L., Smith, M., Nguyen, K., Lam, G., Choong, I., Mazumdar, A., Hill, J. L., Gibbons, D. L., Brown, P. H., Russell, W. K., Shokat, K., Creighton, C. J., Glenn, J. S. & Kurie, J. M., Jan 22 2020, In : Science Translational Medicine. 12, 527, eaax3772.

Research output: Contribution to journalArticle

3 Scopus citations

PolyA-miner: accurate assessment of differential alternative poly-adenylation from 3'Seq data using vector projections and non-negative matrix factorization

Yalamanchili, H. K., Alcott, C. E., Ji, P., Wagner, E. J., Zoghbi, H. Y. & Liu, Z., Jul 9 2020, In : Nucleic acids research. 48, 12, p. e69

Research output: Contribution to journalArticle

Open Access