Biochemistry & Molecular Biology

Research Output 1975 2019

2019

A developmentally regulated spliced variant of PTBP1 is upregulated in type 1 diabetic hearts

Belanger, K. A., Nutter, C. A., Li, J., Yu, P. & Martinez, N., Feb 5 2019, In : Biochemical and Biophysical Research Communications. 509, 2, p. 384-389 6 p.

Research output: Contribution to journalArticle

Alternative Splicing
Medical problems
Genes
RNA
RNA-Binding Proteins

Aedes mosquitoes acquire and transmit Zika virus by breeding in contaminated aquatic environments

Du, S., Liu, Y., Liu, J., Zhao, J., Champagne, C., Tong, L., Zhang, R., Zhang, F., Qin, C. F., Ma, P., Chen, C. H., Liang, G., Liu, Q., Shi, P-Y., Cazelles, B., Wang, P., Tian, H. & Cheng, G., Dec 1 2019, In : Nature communications. 10, 1, 1324.

Research output: Contribution to journalArticle

Open Access
Aedes
viruses
Culicidae
Viruses
Breeding

Antibody-mediated protective mechanisms induced by a trivalent parainfluenza virus-vectored ebolavirus vaccine

Brian Kimble, J., Malherbe, D. C., Meyer, M., Gunn, B. M., Karim, M. M., Ilinykh, P. A., Iampietro, M., Mohamed, K. S., Negi, S., Gilchuk, P., Huang, K., Wolf, Y. I., Braun, W., Crowe, J. E., Alter, G. & Bukreyev, A., Feb 1 2019, In : Journal of Virology. 93, 4, e0184518.

Research output: Contribution to journalArticle

Ebolavirus
Paramyxoviridae Infections
Vaccines
Zaire Ebola virus
vaccines

Anti-Zika virus RNAi in neural progenitor cells

Xie, X. & Shi, P-Y., Apr 1 2019, In : Cell Research. 29, 4, p. 261-262 2 p.

Research output: Contribution to journalArticle

Open Access
RNA Interference
Stem Cells
Zika Virus

Biochemical and Next Generation Sequencing Approaches to Study RNA Regulation

Wagner, E. & Goldstrohm, A. C., Feb 15 2019, In : Methods. 155, p. 1-2 2 p.

Research output: Contribution to journalEditorial

RNA

Characterization of Triniti virus supports its reclassification in the family Peribunyaviridae

Lima, J. A., Nunes Neto, J. P., Castro, K. S., Travassos da Rosa, A. P. D. A., Tesh, R., Nunes, M. R. T., Popov, V., Vasilakis, N., Guzman, H., Widen, S., Silva, S. P. D., Medeiros, D. B. D. A., Cardoso, J. F., Martins, L. C., Azevedo, R. D. S. D. S., Vasconcelos, P. F. D. C. & Chiang, J. O., Feb 1 2019, In : The Journal of general virology. 100, 2, p. 137-144 8 p.

Research output: Contribution to journalArticle

Viruses
Orthobunyavirus
Togaviridae
Genome
Trinidad and Tobago

Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation

Weng, T., Ko, J., Masamha, C. P., Xia, Z., Xiang, Y., Chen, N. Y., Molina, J. G., Collum, S., Mertens, T. C., Luo, F., Philip, K., Davies, J., Huang, J., Wilson, C., Thandavarayan, R. A., Bruckner, B. A., Jyothula, S. S. K., Volcik, K. A., Li, L., Han, L. & 5 othersLi, W., Assassi, S., Karmouty-Quintana, H., Wagner, E. & Blackburn, M. R., May 1 2019, In : Journal of Clinical Investigation. 129, 5, p. 1984-1999 16 p.

Research output: Contribution to journalArticle

Open Access
Idiopathic Pulmonary Fibrosis
Polyadenylation
Pulmonary Fibrosis
Fibroblasts
Down-Regulation

Comparative Loss-of-Function Screens Reveal ABCE1 as an Essential Cellular Host Factor for Efficient Translation of Paramyxoviridae and Pneumoviridae

Anderson, D. E., Pfeffermann, K., Kim, S. Y., Sawatsky, B., Pearson, J., Kovtun, M., Corcoran, D. L., Krebs, Y., Sigmundsson, K., Jamison, S. F., Yeo, Z. Z. J., Rennick, L. J., Wang, L. F., Talbot, P. J., Duprex, W. P., Garcia-Blanco, M. & von Messling, V., May 14 2019, In : mBio. 10, 3

Research output: Contribution to journalArticle

Open Access
Paramyxoviridae
Pneumovirus
Viruses
Mumps
Respiratory Syncytial Viruses
3 Citations (Scopus)

Design, Synthesis, and Characterization of 4-Undecylpiperidine-2-carboxamides as Positive Allosteric Modulators of the Serotonin (5-HT) 5-HT2C Receptor

Wild, C. T., Miszkiel, J. M., Wold, E. A., Soto, C. A., Ding, C., Hartley, R. M., White, M., Anastasio, N., Cunningham, K. & Zhou, J., Oct 1 2019, In : Journal of Medicinal Chemistry. 62, 1, p. 288-305 18 p.

Research output: Contribution to journalArticle

Receptor, Serotonin, 5-HT2C
Serotonin
Cocaine
Serotonin 5-HT2 Receptor Agonists
Allosteric Site

Development of Poly(A)-ClickSeq as a tool enabling simultaneous genome-wide poly(A)-site identification and differential expression analysis

Elrod, N. D., Jaworski, E. A., Ji, P., Wagner, E. & Routh, A., Jan 1 2019, (Accepted/In press) In : Methods.

Research output: Contribution to journalArticle

Poly A
Genes
Genome
RNA
Gene Expression
1 Citation (Scopus)

Didymin by suppressing NF-κB activation prevents VEGF-induced angiogenesis in vitro and in vivo

Shukla, K., Sonowal, H., Saxena, A. & Ramana, K., Jan 1 2019, (Accepted/In press) In : Vascular Pharmacology.

Research output: Contribution to journalArticle

Vascular Endothelial Growth Factor A
Human Umbilical Vein Endothelial Cells
Neoplasms
E-Selectin
Vascular Cell Adhesion Molecule-1

DNA polymerase θ accomplishes translesion synthesis opposite 1, N 6 -ethenodeoxyadenosine with a remarkably high fidelity in human cells

Yoon, J. H., Johnson, R. E., Prakash, L. & Prakash, S., Mar 1 2019, In : Genes and Development. 33, 5-6, p. 282-287 6 p.

Research output: Contribution to journalArticle

Open Access
DNA-Directed DNA Polymerase
Base Pairing
Catalytic Domain
Nucleotides
1,N(6)-ethenodeoxyadenosine

Editorial overview: Host-pathogen interactions: bacteria

Ottemann, K. M. & Kenney, L., Feb 1 2019, In : Current Opinion in Microbiology. 47, p. iii-v

Research output: Contribution to journalEditorial

Host-Pathogen Interactions
Bacteria

Endotoxin-induced uveitis in rodents

Yadav, U. C. S. & Ramana, K., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 161-168 8 p. (Methods in Molecular Biology; vol. 1960).

Research output: Chapter in Book/Report/Conference proceedingChapter

Uveitis
Endotoxins
Rodentia
Inflammation
Exudates and Transudates

Erratum for Chen et al., "Treatment of Human Glioblastoma with a Live Attenuated Zika Virus Vaccine Candidate"

Chen, Q., Wu, J., Ye, Q., Ma, F., Zhu, Q., Wu, Y., Shan, C., Xie, X., Li, D., Zhan, X., Li, C., Li, X. F., Qin, X., Zhao, T., Wu, H., Shi, P-Y., Man, J. & Qin, C. F., Apr 2 2019, In : mBio. 10, 2

Research output: Contribution to journalComment/debate

Open Access
Glioblastoma
Vaccines
Zika Virus
2 Citations (Scopus)

Error-Prone Replication through UV Lesions by DNA Polymerase θ Protects against Skin Cancers

Yoon, J. H., McArthur, M. J., Park, J., Basu, D., Wakamiya, M., Prakash, L. & Prakash, S., Mar 7 2019, In : Cell. 176, 6, p. 1295-1309.e15

Research output: Contribution to journalArticle

Skin Neoplasms
DNA-Directed DNA Polymerase
Skin
Mutation
Carcinogenesis

Exosomes mediate Zika virus transmission through SMPD3 neutral Sphingomyelinase in cortical neurons

Zhou, W., Woodson, M., Sherman, M., Neelakanta, G. & Sultana, H., Jan 1 2019, In : Emerging microbes & infections. 8, 1, p. 307-326 20 p.

Research output: Contribution to journalArticle

Open Access
Exosomes
Sphingomyelin Phosphodiesterase
Neurons
Viruses
Microcephaly
thermodynamic cycles
Free energy
Distribution functions
distribution functions
free energy

Genetic and biochemical characterizations of Zika virus NS2A protein

Zhang, X., Xie, X., Zou, J., Xia, H., Shan, C., Chen, X. & Shi, P-Y., Jan 1 2019, In : Emerging Microbes and Infections. 8, 1, p. 585-602 18 p.

Research output: Contribution to journalArticle

Open Access
Virion
Molecular Biology
Proteins
Viral Nonstructural Proteins
RNA

Genomic characterisation of Cuiaba and Charleville viruses: arboviruses (family Rhabdoviridae, genus Sripuvirus) infecting reptiles and amphibians

Vasilakis, N., Tesh, R. B., Widen, S., Mirchandani, D. & Walker, P. J., Feb 15 2019, In : Virus Genes. 55, 1, p. 87-94 8 p.

Research output: Contribution to journalArticle

Rhabdoviridae
Arboviruses
Reptiles
Amphibians
Viruses

High-throughput LPS profiling as a tool for revealing of bacteriophage infection strategies

Kulikov, E. E., Golomidova, A. K., Prokhorov, N., Ivanov, P. A. & Letarov, A. V., Dec 1 2019, In : Scientific reports. 9, 1, 2958.

Research output: Contribution to journalArticle

Open Access
Bacteriophages
O Antigens
Infection
Virus Receptors
Mass Screening
2 Citations (Scopus)

How do chemokines navigate neutrophils to the target site: Dissecting the structural mechanisms and signaling pathways

Rajarathnam, K., Schnoor, M., Richardson, R. M. & Rajagopal, S., Feb 1 2019, In : Cellular Signalling. 54, p. 69-80 12 p.

Research output: Contribution to journalReview article

Arrestin
Chemokines
GTP-Binding Proteins
Neutrophils
Interleukin-8B Receptors

Mobility of Histidine Side Chains Analyzed with 15 N NMR Relaxation and Cross-Correlation Data: Insight into Zinc-Finger-DNA Interactions

Kemme, C. A., Luu, R. H., Chen, C., Pletka, C. C., Pettitt, B. & Iwahara, J., May 2 2019, In : Journal of Physical Chemistry B. 123, 17, p. 3706-3710 5 p.

Research output: Contribution to journalArticle

histidine
Zinc Fingers
Histidine
cross correlation
Zinc
1 Citation (Scopus)

Mosquito cells persistently infected with dengue virus produce viral particles with host-dependent replication

Reyes-Ruiz, J. M., Osuna-Ramos, J. F., Bautista-Carbajal, P., Jaworski, E., Soto-Acosta, R., Cervantes-Salazar, M., Angel-Ambrocio, A. H., Castillo-Munguía, J. P., Chávez-Munguía, B., De Nova-Ocampo, M., Routh, A., del Ángel, R. M. & Salas-Benito, J. S., May 1 2019, In : Virology. 531, p. 1-18 18 p.

Research output: Contribution to journalArticle

Dengue Virus
Culicidae
Virion
Vertebrates
Arboviruses

Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients

Chu, Y., Elrod, N., Wang, C., Li, L., Chen, T., Routh, A., Xia, Z., Li, W., Wagner, E. & Ji, P., Jan 1 2019, In : Oncogene.

Research output: Contribution to journalArticle

Polyadenylation
Glioblastoma
3' Untranslated Regions
Glioma
Genes

Price of disorder in the lac repressor hinge helix

Seckfort, D. & Pettitt, B., Jan 1 2019, In : Biopolymers. 110, 1, e23239.

Research output: Contribution to journalArticle

Lac Repressors
Hinges
Repressor Proteins
Proteins
Lac Operon

Small molecule nicotinamide N-methyltransferase inhibitor activates senescent muscle stem cells and improves regenerative capacity of aged skeletal muscle

Neelakantan, H., Brightwell, C. R., Graber, T., Maroto, R., Wang, H. Y. L., McHardy, S. F., Papaconstantinou, J., Fry, C. & Watowich, S., Jan 1 2019, In : Biochemical Pharmacology.

Research output: Contribution to journalArticle

Nicotinamide N-Methyltransferase
Stem cells
Muscle Cells
Muscle
Skeletal Muscle
2 Citations (Scopus)

Strategies for Zika drug discovery

Zou, J. & Shi, P-Y., Apr 1 2019, In : Current Opinion in Virology. 35, p. 19-26 8 p.

Research output: Contribution to journalReview article

Drug Discovery
Vaccines
Antiviral Agents
Viral Proteins
Pharmaceutical Preparations
1 Citation (Scopus)

Structure and transformation of bacteriophage A511 baseplate and tail upon infection of Listeria cells

Guerrero-Ferreira, R. C., Hupfeld, M., Nazarov, S., Taylor, N. M. I., Shneider, M. M., Obbineni, J. M., Loessner, M. J., Ishikawa, T., Klumpp, J. & Leiman, P., Jan 1 2019, (Accepted/In press) In : EMBO Journal. e99455.

Research output: Contribution to journalArticle

Bacteriophages
Infection
Pyocins
Electron Microscope Tomography
Cryoelectron Microscopy
1 Citation (Scopus)

Targeting the Achilles Heel of Mosquito-Borne Viruses for Antiviral Therapy

Jackman, J. A., Shi, P-Y. & Cho, N. J., Nov 1 2019, In : ACS Infectious Diseases. 5, 1, p. 4-8 5 p.

Research output: Contribution to journalArticle

Culicidae
Antiviral Agents
Viruses
Virus Diseases
Lipids
1 Citation (Scopus)

The Dynamic Capsid Structures of the Noroviruses

Smith, H. Q. & Smith, T., Mar 8 2019, In : Viruses. 11, 3

Research output: Contribution to journalReview article

Open Access
Norovirus
Capsid
Herd Immunity
Antibodies
Viral Genome

Transmembrane scf nanodiscs enhance revascularization in ischemia and induce cd34-/cd133+ endothelial progenitor cells

Takematsu, E., Auster, J., Singh, A., Chen, P. C., Canga, S., Degroot, A., Sherman, M., Stachowiak, J., Dunn, A. K. & Baker, A. B., Jan 1 2019, Society for Biomaterials Annual Meeting and Exposition 2019: The Pinnacle of Biomaterials Innovation and Excellence - Transactions of the 42nd Annual Meeting. Society for Biomaterials, 1 p. (Transactions of the Annual Meeting of the Society for Biomaterials and the Annual International Biomaterials Symposium; vol. 40).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Endothelial cells
Stem Cell Factor
Blood
Ischemia
Peripheral Vascular Diseases

Use of the immunoglobulin G avidity assay to differentiate between recent Zika and past dengue virus infections

Furuya, A. K. M., Hunt, D., St. George, K., Dupuis, A. P., Kramer, L. D., Shi, P-Y. & Wong, S., Apr 15 2019, In : Clinical Science. 133, 7, p. 859-867 9 p.

Research output: Contribution to journalArticle

Dengue Virus
Virus Diseases
Flavivirus
Microspheres
Immunoassay
2018
17 Citations (Scopus)

3′ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk

Park, H. J., Ji, P., Kim, S., Xia, Z., Rodriguez, B., Li, L., Su, J., Chen, K., Masamha, C. P., Baillat, D., Fontes-Garfias, C. R., Shyu, A. B., Neilson, J. R., Wagner, E. & Li, W., May 21 2018, (Accepted/In press) In : Nature Genetics. p. 1-7 7 p.

Research output: Contribution to journalArticle

3' Untranslated Regions
Tumor Suppressor Genes
Proto-Oncogenes
MicroRNAs
Neoplasms
1 Citation (Scopus)

Aldose reductase inhibitor, fidarestat prevents doxorubicin-induced endothelial cell death and dysfunction

Sonowal, H., Pal, P., Shukla, K., Saxena, A., Srivastava, S. K. & Ramana, K., Apr 1 2018, In : Biochemical Pharmacology. 150, p. 181-190 10 p.

Research output: Contribution to journalArticle

Aldehyde Reductase
Endothelial cells
Cell death
Doxorubicin
Cell Death

Aldose reductase inhibitor, fidarestat prevents high-fat diet-induced intestinal polyps in APCmin/+ mice

Saxena, A., Tammali, R., Ramana, K. & Srivastava, S., Jan 1 2018, In : Current Cancer Drug Targets. 18, 9, p. 905-911 7 p.

Research output: Contribution to journalArticle

Intestinal Polyps
Aldehyde Reductase
High Fat Diet
Large Intestine
Polyps
1 Citation (Scopus)

Analysis By Deep Sequencing of Discontinued Neurotropic Yellow Fever Vaccine Strains

Beck, A. S., Wood, T., Widen, S., Thompson, J. K. & Barrett, A., Dec 1 2018, In : Scientific Reports. 8, 1, 13408.

Research output: Contribution to journalArticle

Yellow Fever Vaccine
High-Throughput Nucleotide Sequencing
Vaccines
Viruses
Yellow fever virus

An attenuated replication-competent chikungunya virus with a fluorescently tagged envelope

Jin, J., Sherman, M., Chafets, D., Dinglasan, N., Lu, K., Lee, T. H., Carlson, L. A., Muench, M. O. & Simmons, G., Jul 31 2018, In : PLoS Neglected Tropical Diseases. 12, 7, e0006693.

Research output: Contribution to journalArticle

Chikungunya virus
Alphavirus
Viruses
Arthralgia
Knockout Mice
29 Citations (Scopus)

An evolutionary NS1 mutation enhances Zika virus evasion of host interferon induction

Xia, H., Luo, H., Shan, C., Muruato, A. E., Nunes, B. T. D., Medeiros, D. B. A., Zou, J., Xie, X., Giraldo Giraldo, M., Vasconcelos, P. F. C., Weaver, S., Wang, T., Rajsbaum Gorodezky, R. & Shi, P-Y., Dec 1 2018, In : Nature Communications. 9, 1, 414.

Research output: Contribution to journalArticle

interferon
viruses
mutations
Viruses
Interferons
6 Citations (Scopus)

Arthropod EVs mediate dengue virus transmission through interaction with a tetraspanin domain containing glycoprotein Tsp29Fb

Vora, A., Zhou, W., Londono-Renteria, B., Woodson, M., Sherman, M., Colpitts, T. M., Neelakanta, G. & Sultana, H., Jul 10 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 28, p. E6604-E6613

Research output: Contribution to journalArticle

Dengue Virus
Arthropods
Glycoproteins
Culicidae
Viral RNA
3 Citations (Scopus)

A Single-Dose Live-Attenuated Zika Virus Vaccine with Controlled Infection Rounds that Protects against Vertical Transmission

Xie, X., Kum, D. B., Xia, H., Luo, H., Shan, C., Zou, J., Muruato, A. E., Medeiros, D. B. A., Nunes, B. T. D., Dallmeier, K., Rossi, S., Weaver, S., Neyts, J., Wang, T., Vasconcelos, P. F. C. & Shi, P-Y., Oct 10 2018, In : Cell Host and Microbe. 24, 4, p. 487-499.e5

Research output: Contribution to journalArticle

Vaccines
Infection
Attenuated Vaccines
Viremia
Capsid Proteins
2 Citations (Scopus)

A single-dose plasmid-launched live-attenuated Zika vaccine induces protective immunity

Zou, J., Xie, X., Luo, H., Shan, C., Muruato, A. E., Weaver, S., Wang, T. & Shi, P-Y., Jan 1 2018, (Accepted/In press) In : EBioMedicine.

Research output: Contribution to journalArticle

Attenuated Vaccines
Immunity
Plasmids
DNA
Vaccines
2 Citations (Scopus)

A single residue in the αb helix of the e protein is critical for Zika virus thermostability correspondence

Xie, D. Y., Liu, Z. Y., Nian, Q. G., Zhu, L., Wang, N., Deng, Y. Q., Zhao, H., Ji, X., Li, X. F., Wang, X., Shi, P-Y. & Qin, C. F., Dec 1 2018, In : Emerging Microbes and Infections. 7, 1, 0006.

Research output: Contribution to journalLetter

Proteins
Zika Virus

Attenuation of murine allergic airway inflammation with a CXCR1/CXCR2 chemokine receptor inhibitor

Hosoki, K., Rajarathnam, K. & Sur, S., Jan 1 2018, (Accepted/In press) In : Clinical and Experimental Allergy.

Research output: Contribution to journalArticle

Interleukin-8B Receptors
Chemokine Receptors
Inflammation
5 Citations (Scopus)

A Zika virus vaccine expressing premembrane-envelope-NS1 polyprotein

Li, A., Yu, J., Lu, M., Ma, Y., Attia, Z., Shan, C., Xue, M., Liang, X., Craig, K., Makadiya, N., He, J. J., Jennings, R., Shi, P-Y., Peeples, M. E., Liu, S. L., Boyaka, P. N. & Li, J., Dec 1 2018, In : Nature Communications. 9, 1, 3067.

Research output: Contribution to journalArticle

vaccines
Polyproteins
viruses
Viruses
envelopes

Better Safe than Sorry: A Dual-Function Viral Protein Inhibiting Host Defense

Lechtenberg, B. C. & Routh, A., Oct 10 2018, In : Cell Host and Microbe. 24, 4, p. 467-469 3 p.

Research output: Contribution to journalShort survey

Viral Proteins
Gryllidae
Viruses
Paralysis
Immune System
8 Citations (Scopus)

Biochemistry and Molecular Biology of Flaviviruses

Barrows, N. J., Campos, R. K., Liao, K. C., Prasanth, K. R., Soto-Acosta, R., Yeh, S. C., Schott-Lerner, G., Pompon, J., Sessions, O. M., Bradrick, S. & Garcia-Blanco, M., Apr 25 2018, In : Chemical Reviews. 118, 8, p. 4448-4482 35 p.

Research output: Contribution to journalArticle

Biochemistry
Molecular biology
Pathogens
Viruses
Antiviral Agents
1 Citation (Scopus)

CELF1 contributes to aberrant alternative splicing patterns in the type 1 diabetic heart

Belanger, K. A., Nutter, C. A., Li, J., Tasnim, S., Liu, P., Yu, P. & Martinez, N., Sep 18 2018, In : Biochemical and Biophysical Research Communications. 503, 4, p. 3205-3211 7 p.

Research output: Contribution to journalArticle

Alternative Splicing
Medical problems
RNA-Binding Proteins
Genes
Binding Sites
1 Citation (Scopus)

Cellular production of a counterfeit viral protein confers immunity to infection by a related virus

Warner, B. E., Ballinger, M. J., Yerramsetty, P., Reed, J., Taylor, D. J., Smith, T. & Bruenn, J. A., Jan 1 2018, In : PeerJ. 2018, 9, e5679.

Research output: Contribution to journalArticle

viral proteins
Viral Proteins
Viruses
Immunity
immunity
1 Citation (Scopus)

Characterization of a candidate tetravalent vaccine based on 2’-O-methyltransferase mutants

Züst, R., Li, S. H., Xie, X., Velumani, S., Chng, M., Toh, Y. X., Zou, J., Dong, H., Shan, C., Pang, J., Qin, C. F., Newell, E. W., Shi, P-Y. & Fink, K., Jan 1 2018, In : PLoS One. 13, 1, e0189262.

Research output: Contribution to journalArticle

Dengue virus
Dengue Virus
methyltransferases
Methyltransferases
Viruses