Center for Gene Regulation in Health and Disease (GRHD)

Sailen Barik

Suppression of innate immunity by RNA viruses; Interactions between host and Toxoplasma gondii; RNA interference in lower eukaryotes.

  • Jayeeta Dhar
    PhD Student
  • Dr. Evgeny Ozhegov
    Post Doctoral Fellow

Selected publications out of 124; updated Jan 15, 2013; Approximately 70 conference abstracts are NOT shown:

3. Das A, Ghosh B, Barik S, Wolska K (1985) Evidence that ribosomal protein S10 itself is a cellular component necessary for transcription antitermination by phage lambda N protein. Proc Natl Acad Sci USA. 82:4070-74
4. Barik S, Bhattacharya P, Das A (1985) Autogenous regulation of transcription termination factor Rho. J Mol Biol 182: 405-508
5. Barik S, Ghosh B, Whalen W, Lazinski D, Das A (1987) An antitermination protein engages the elongating transcription apparatus at a promoter-proximal recognition site. Cell 50: 885-99
6. Barik S, Das A (1990) An analysis of the role of host factors in transcription antitermination in vitro by Q protein of coliphage lambda. Mol Gen Genet 222:152-6
7. Barik S, Rud EW, Luk D, Banerjee AK, Yong Kang C (1990) Nucleotide sequence analysis of the L gene of vesicular stomatitis virus (New Jersey serotype): Identification of conserved domains in L proteins of nonsegmented negative-strand RNA viruses.  Virology 175: 332-7
9. Barik S, Banerjee AK (1991) Cloning and Expression of vesicular stomatitis virus phosphoprotein gene in Escherichia coli: Analysis of phosphorylation status versus transcriptional activity. J Virol 65: 1719-26
10. Banerjee AK, Barik S, De BP (1991) Gene expression of nonsegmented negative-strand RNA viruses. Pharmacol Ther 51: 47-70
11. Barik S, Galinski MS (1991) "Megaprimer" method of PCR: increased template
concentration improves yield. Biotechniques 10:489-90
12. Takacs A, Barik S, Das T, Banerjee AK (1992) Phosphorylation of specific serine residues within the acidic domain of the phosphoprotein of vesicular stomatitis virus regulates transcription in vitro. J. Virol. 66: 5842-8
13. Barik S, Banerjee AK (1992) Phosphorylation by cellular casein kinase II is essential for transcriptional activity of the vesicular stomatitis virus phosphoprotein P. Proc Natl Acad Sci USA 89: 6570-4
14. Banerjee AK, Barik S (1992) Minireview: Gene expression of vesicular stomatitis virus genome RNA. Virology 188: 417-28
15. Barik S, Banerjee AK (1992) Sequential phosphorylation of the phosphoprotein of vesicular stomatitis virus by cellular and viral protein kinases is essential for transcription activation. J. Virol. 66: 1109-18
17. Barik S (1992) Transcription of human respiratory syncytial virus genome RNA in vitro: Requirement of cellular factor(s).  J. Virol. 66, 6813-8
18. Barik S, Banerjee AK (1993) Ungrouped rhabdoviruses of birds, mammals, and fish: In Encyclopedia of Virology, eds. R. Webster and R. Granoff (W. B. Saunders)
19. Barik S, Banerjee AK (1993) Vesiculoviruses: Chandipura, Piry, and Isfahan: In Encyclopedia of Virology, eds. R. Webster and R. Granoff (W. B. Saunders)
22. Barik S (1993) The structure of the 5' terminal cap of the respiratory syncytial virus mRNA. J Gen Virol 74: 485-90
23. Barik S (1993) Expression and biochemical properties of a novel protein serine-threonine phosphatase encoded by bacteriophage ¿. Proc Natl Acad Sci USA 90:10633-7
24. Mazumder B, Adhikary G, Barik S (1994)  Bacterial expression of human respiratory syncytial virus phosphoprotein P and identification of Ser237 as the site of phosphorylation by cellular casein kinase II. Virology 205: 93-103
25. Mazumder B, Barik S (1994) Requirement of casein kinase II-mediated phosphorylation for the transcriptional activity of human respiratory syncytial virus phosphoprotein P: transdominant negative phenotype of phosphorylation-defective P mutants. Virology 205:104-11
26. Barik S (1995) Site-directed mutagenesis by PCR: substitution, insertion, deletion, and gene fusion. Methods in Neurosciences 26: 309-23
27. Barik S, McLean T, Dupuy L (1995) Phosphorylation of Ser232 directly regulates the transcriptional activity of the P protein of human respiratory syncytial virus: Phosphorylation of Ser237 may play an accessory role. Virology 213: 405-12
30. Das A, Barik S, Ghosh B, Whalen W (1996) Immunoprinting: a technique used to study dynamic protein-nucleic acid interactions within transcription elongation complex. Methods Enzymol 274: 363-74
31. Barik S (1996) Protein phosphorylation and signal transduction. Subcell Biochem 26:115-64
32. Ansai T, Dupuy LC, Barik S (1996) Interactions between a minimal protein serine/threonine phosphatase and its phosphopeptide substrate sequence. J Biol Chem 271:24401-7.
34. Bitko V, Velazquez A, Yang L, Yang YC, Barik S (1997) Transcriptional activation of multiple cytokines by respiratory syncytial virus requires activation of NF-¿B and is inhibited by sodium salicylate and aspirin. Virology 232:369-78
35. Bichko V, Barik S, Taylor J (1997) Phosphorylation of the hepatitis delta virus antigens. J Virol 71: 512-8
36. Barik S, Taylor RE, Chakrabarti D (1997) Identification, cloning, and mutational analysis of the casein kinase 1 cDNA of the malaria parasite, Plasmodium falciparum. J Biol Chem 272:26132-8
39. Barik S (1997) Relationship between opacity of transformed E. coli colonies and over-expression of the recombinant transcript. Biotechniques 22:112-8.
41. Bitko V, Barik S (1998) Persistent activation of RelA by respiratory syncytial virus involves protein kinase C, underphosphorylated I¿B¿, and sequestration of protein phosphatase 2A by the viral phosphoprotein. J Virol 72: 5610-8
44. Barik S (1998) Mutagenesis by megaprimer PCR. In "Genetic engineering with PCR" (eds. RM Horton and RC Tait), pp. 25-37, Horizon Scientific Press, Wymondham, UK.
45. Burke E, Barik S (1998) Specific detection of native multi-subunit proteins by slot-blot assay. BioTechniques 25:574-82
46. Connor JH, Quan HN, Ramaswamy NT, Zhang L, Barik S, Zheng J, Cannon JF, Lee EYC, Shenolikar S (1998) Inhibitor-1 interaction domain that mediates the inhibition of protein phosphatase-1.  J Biol Chem 273:27716-24
47. Burke E, Dupuy L, Wall C, Barik S (1998) Role of cellular actin in the gene expression and morphogenesis of human respiratory syncytial virus. Virology 252:137-48
48. Dupuy LC, Dobson S, Bitko V, Barik S (1999) Casein kinase 2-mediated phosphorylation of respiratory syncytial virus phosphoprotein P is essential for the transcription elongation activity of the viral polymerase; phosphorylation by casein kinase 1 occurs mainly at Ser215 and is without effect. J Virol 73:8384-92
50. Chen X, Ansai T, Awano S, Iida T, Barik S, Takehara T (1999) Isolation, cloning, and expression of an acid phosphatase containing phosphotyrosyl phosphatase activity from Prevotella intermedia. J. Bacteriol 181:7107-14
51. Connor JH, Kleeman T, Barik S, Honkanen RE, Shenolikar S (1999) Importance of the beta12-beta13 loop in protein phosphatase-1 catalytic subunit for inhibition by toxins and mammalian protein inhibitors. J Biol Chem 274:22366-72
52. Dobson S, May T, Berriman M, DelVecchio C, Fairlamb A, Chakrabarti D, Barik S (1999)Characterization of protein Ser/Thr phosphatases of the malarial parasite: Plasmodioum falciparum: Inhibition of the parasitic calcineurin by cyclophilin-cyclosporin complex. Mol Biochem Parasitol 99:167-81
53. Garcia A, Cayla X, Barik S, Langsley G (1999) A family of PP2 phosphatases in
Plasmodium falciparum and parasitic protozoa. Parasitol Today 15:90-2.
55. Bracchi-Ricard V, Barik S, DelVecchio C, Doerig C, Chakrabarti R, Chakrabarti D (2000)PfPK6, a novel cyclin-dependent kinase / mitogen-activated protein kinase-related protein kinase from Plasmodium falciparum. Biochem J 347:255-63
56. Burke E, Mahoney NM, Almo SC, Barik S (2000) Profilin is required for optimal actin-dependent transcription of respiratory syncytial virus genome RNA. J Virol 74:669-75
57. Bitko V, Barik S (2001) An endoplasmic reticulum-specific stress-activated caspase(caspase-12) is implicated in the apoptosis of A549 epithelial cells by respiratory syncytial virus. J Cell Biochem 80:441-54
59. Dobson S, Kar B, Kumar R, Adams B, Barik S (2001) A novel tetratricopeptide repeat(TPR)-containing PP5 serine/threonine protein phosphatase in the malaria parasite, Plasmodium falciparum. BMC Microbiol 1:31
60. Dobson S, Bracchi V, Chakrabarti D, Barik S (2001) Characterization of a novel serine/threonine protein phosphatase (PfPPJ) from the malaria parasite, Plasmodium falciparum. Mol Biochem Parasitol 115:29-39
61. Bitko V, Barik S (2001) Phenotypic silencing of cytoplasmic genes using sequence-specific double-stranded short interfering RNA and its application in the reverse genetics of wild type negative-strand RNA viruses. BMC Microbiol 1:34 (Editor¿s Choice List; Press Release; "All time most-viewed paper" in this Journal for 7 years, currently in 3rd position)
62. Kumar R, Adams B, Oldenburg A, Musiyenko A, Barik S (2002) Characterization and expression of a PP1 serine/threonine protein phosphatase from the malaria parasite, Plasmodium falciparum: demonstration of its essential role using RNAi. Malar J 1:5
63. Ansai T, Chen X, Barik S, Takehara T (2002) Conserved proline residues near the N-terminus are important for enzymatic activity of class A bacterial acid phosphatases. Arch Biochem Biophys 408:144-6
66. Kumar R, Musiyenko A, Barik S (2003) The heat shock protein 90 of Plasmodium falciparum and antimalarial activity of its inhibitor, geldanamycin. Malar J 2:30
67. Bitko V, Oldenburg A, Garmon NE, Barik S (2003) Profilin is required for viral morphogenesis, syncytium formation, and cell-specific stress fiber induction by respiratory syncytial virus. BMC Microbiol 3:9
69. Dobson S, Kumar R, Bracchi-Ricard V, Freeman S, Al-Murrani SW, Johnson C, Damuni Z, Chakrabarti D, Barik S (2003) Characterization of a unique aspartate-rich protein of the SET/TAF-family in the human malaria parasite, Plasmodium falciparum, which inhibits protein phosphatase 2A. Mol Biochem Parasitol 126:239-50
71. Kumar R, Musiyenko R, Cioffi E, Oldenburg A, Adams B, Bitko V, Krishna SS, Barik S (2004) A zinc-binding dual-specificity YVH1 phosphatase in the malaria parasite, Plasmodium falciparum, and its interaction with the nuclear protein, pescadillo. Mol Biochem Parasitol 133:297-310
72. Barik S (2004) When proteome meets genome: the alpha helix and the beta strand of proteins are eschewed by mRNA splice junctions and may define the minimal indivisible modules of protein architecture. J Biosci 29:261-73
74. Bitko V, Garmon NE, Cao T, Estrada B, Oakes JE, Lausch RN, Barik S (2004) Activation of cytokines and NF-kappa B in corneal epithelial cells infected by respiratory syncytial virus: potential relevance in ocular inflammation and respiratory infection. BMC Microbiol 4:28
75. Kumar R, Musiyenko A, Oldenburg A, Adams B, Barik S (2004) Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics. BMC Mol Biol 5:6
76. Barik S (2004) Development of gene-specific double-stranded RNA drugs. Ann Med 36:540-51
77. Maggon K, Barik S (2004) New drugs and treatment for respiratory syncytial virus. Rev Med Virol 14:149-68
78. Barik S (2004) Control of nonsegmented negative-strand RNA virus replication by siRNA. Virus Res 102:27-35
79. Barik S (2005) Silence of the transcripts: RNA interference in medicine. J Mol Med. 83:764-73
80. Barik S (2005) Inhaled short interfering RNA as a promising approach to the therapy of viral respiratory infections. Drugs Fut 30:567-72
81. Adams B, Musiyenko A, Kumar R, Barik S (2005) A novel class of dual-family immunophilins. J Biol Chem 280:24308-14
82. Kumar R, Adams B, Musiyenko A, Shulyayeva O, Barik S (2005) The FK506-binding protein of the malaria parasite, Plasmodium falciparum, is a FK506-sensitive chaperone with FK506-independent calcineurin-inhibitory activity. Mol Biochem Parasitol 141:163-73
83. Kumar R, Musiyenko A, Barik S (2005) Plasmodium falciparum calcineurin and its association with heat shock protein 90: mechanisms for the antimalarial activity of cyclosporin A and synergism with geldanamycin. Mol Biochem Parasitol 141:29-37
84. Barik S, Bitko V (2005) Pharmacology and emerging clinical applications of RNA. Encyclopedia of Mol Cell Biol and Mol Med, 10:241-75 (Ed. R. A. Meyers)
85. Bitko V, Musiyenko A, Shulyayeva O, Barik S (2005) Inhibition of respiratory viruses by nasally administered siRNA. Nat Med 11:50-5 (563 citations as of Dec 2, 2012).
Published by Nature a 2nd time to celebrate the Nobel Prize award to Fire and Mello in a special issue in 2006 that included only one other full paper.
86. Barik S (2006) Immunophilins: for the love of proteins. Cell Mol Life Sci 63:2889-900
87. Barik S, Bitko V (2006) Prospects of RNA interference therapy in respiratory viral diseases: update 2006. Expert Opin Biol Ther. 6:1151-60
88. Barik S (2006) RNAi in moderation. Nat Biotechnol 24:796-7
89. Urnowey S, Ansai T, Bitko V, Nakayama K, Takehara T, Barik S (2006) Temporal activation of anti- and pro-apoptotic factors in human gingival fibroblasts infected with the periodontal pathogen, Porphyromonas gingivalis: potential role of bacterial proteases in host signalling. BMC Microbiol 6:26
90. Ramaswamy M, Shi L, Varga SM, Barik S, Behlke MA, Look DC (2006) Respiratory syncytial virus nonstructural protein 2 specifically inhibits type I interferon signal transduction. Virology 344:328-39
91. Bitko V, Musiyenko A, Barik S (2007) Viral infection of the lungs through the eye. J Virol 81:783-90
92. Chaudhuri S, Vyas K, Kapasi P, Komar AA, Dinman JD, Barik S, Mazumder B. (2007) Human ribosomal protein L13a is dispensable for canonical ribosome function but indispensable for efficient rRNA methylation. RNA 13:2224-37
93. Bitko V, Barik S (2007) Intranasal antisense therapy: preclinical models with a clinical future? Curr Opin Mol Ther 9:119-25
94. Estrada B, Carter M, Barik S, Vidal R, Herbert D, Ramsey KM (2007) Severe human metapneumovirus infection in hospitalized children. Clin Pediatr (Phila). 46:258-62.
95. Musiyenko A, Bitko V, Barik S (2007) RNAi-dependent and -independent antiviral phenotypes of chromosomally integrated shRNA clones: Role of VASP in respiratory syncytial virus growth. J Mol Med 85:745-52
96. Bitko V, Barik S (2007) Respiratory viral diseases: access to RNA interference therapy. Drug Discov Today Ther Strateg 4:273-6
97. Bitko V, Shulyayeva O, Mazumder B, Musiyenko A, Ramaswamy M, Look DC, Barik S
(2007) The nonstructural proteins of RSV suppress premature apoptosis by a NF-¿B-dependent, IFN-independent mechanism and facilitate virus growth. J Virol 81:1786-95
98. Barik S (2007) The thrill can kill: murder by methylation. Mol Pharmacol. 71:1203-5
99. Bitko V, Barik S (2008) Nasal delivery of siRNA. Methods Mol Biol 442:75-82
100. Musiyenko A, Bitko V, Barik S (2008) Ectopic expression of miR-126*, an intronic product of the vascular endothelial EGF-like 7 gene, regulates prostein translation and invasiveness of prostate cancer LNCaP cells. J Mol Med 86:313-22
101. Vyas K, Chaudhuri S, Leaman DW, Komar AA, Musiyenko A, Barik S, Mazumder B (2008) Genome-wide polysome profiling reveals an inflammation-responsive post-transcriptional operon in IFN-¿-activated monocytes. Mol Cell Biol 29:458-70
102. Bitko V, Musiyenko A, Bayfield MA, Maraia RJ, Barik S (2008) Cellular La protein shields nonsegmented negative-strand RNA viral leader RNA from RIG-I and enhances virus growth by diverse mechanisms. J Virol. 82:7977-87. Faculty of 1000.
103. Barik S (2008) An intronic microRNA silences genes that are functionally antagonistic to its host gene. Nucleic Acids Res 36:5232-41
104. Barik S (2008) RNA interference (RNAi): design and application. Preface. Methods Mol Biol. 442:vii-viii.
105. Barik S (2009) Treating respiratory viral diseases with chemically modified, second-generation intranasal siRNAs. Methods Mol Biol 487:331-41
106. Harpen M, Barik T, Musiyenko A, Barik S (2009) Mutational analysis reveals a non-contractile but interactive role of actin and profilin in viral RNA-dependent RNA synthesis. J Virol 83:10869-76
107. Swedan S, Musiyenko A, Barik S (2009) RSV nonstructural proteins decrease the levels of multiple members of the cellular interferon pathways. J Virol 83:9682-93
108. Musiyenko A, Correa L, Stock N, Hutchinson JH, Lorrain DS, Bain G, Evans JF, Barik S. (2009) A novel 5-Lipoxygenase-Activating Protein (FLAP) inhibitor AM679 reduces inflammation in the RSV-infected mouse eye. Clin Vaccine Immunol 16:1654-9
109. Barik S (2009) RNAi applications to defeat respiratory viral infections. In "RNA Interference and Viruses: Current Innovations and Future Trends", pp. 187-96; Ed. Manuel A. Martinez, Caister Academic Press, Norfolk, UK
110. Barik S, Barik T (2009) Intronic miRNA: Creation, evolution and regulation. In "MicroRNA Profiling in Cancer: A Bioinformatic Perspective", pp. 117-131; Ed. Yuriy Gusev; Pan Stanford Publishing Pvt. Ltd., Singapore
111. Mazumder B, Li X, Barik S (2010) Translation control: a multifaceted regulator of
inflammatory response. J Immunol 184:3311-9
112. Barik S (2010). siRNA for Influenza Therapy. Viruses 2:1448-57
113. Barik S (2011) Novel Apicomplexan phosphatases and immunophilins as domain-specific drug targets. In Apicomplexan Parasites: Molecular Approaches toward Targeted Drug Development, pp. 289-306. Ed. Katja Becker, Wiley-Blackwell, Weinheim, Germany
114. Prasad GS,, Cosford NDP, Barik S (2011) Plasmodium Hsp90 as an antimalarial target. In Apicomplexan Parasites: Molecular Approaches toward Targeted Drug Development, pp. 431-451. Ed. Katja Becker, Wiley-Blackwell, Weinheim, Germany
115. Swedan S, Andrews J, Majumdar T, Musiyenko A, Barik S (2011) Multiple functional domains and complexes of the two nonstructural proteins of human respiratory syncytial virus contribute to interferon suppression and cellular location. J Virol 85:10090-100
116. Barik S. (2011) Intranasal delivery of antiviral siRNA. Methods Mol Biol 721:333-8
117. Basu A, Das P, Chaudhuri S, Bevilacqua E, Andrews J, Barik S, Hatzoglou M, Komar AA, Mazumder B. (2011) Requirement of rRNA methylation for 80S ribosome assembly on a cohort of cellular internal ribosome entry sites. Mol Cell Biol 31:4482-99
118. Shukla GC, Singh J, Barik S (2011) MicroRNAs: processing, maturation, target recognition, and regulatory functions. Mol Cell Pharmacol 3:83-92
119. Sikand K, Barik S, Shukla GC (2011) Missing link in castration-resistant prostate cancer? Mol Cell Pharmacol 3:107-13
120. Stebbins KJ, Broadhead AR, Musiyenko A, Barik S, Scott JM, Truong YP, Stearns BA, Hutchinson JH, Prasit P, Evans JF, Lorrain DS. (2012) DP2 (CRTh2) Antagonism reduces ocular inflammation induced by allergen challenge and respiratory syncytial virus. Int Arch Allergy Immunol 157:259-268
121. Haque SJ, Majumdar T, Barik S (2012) Redox-assisted protein folding systems in eukaryotic parasites. Antioxid Redox Signal 17:674-83. Journal cover page.
122. Musiyenko A, Majumdar T, Andrews J, Adams B, Barik S (2012) PRMT1 methylates the
single Argonaute of Toxoplasma gondii and is important for the recruitment of Tudor nuclease for target RNA cleavage by antisense guide RNA. Cell Microbiol 14:882-901.
123. Barik S (2012) New treatments for influenza. BMC Medicine 10:104.
124. Barik S (2012) Anti-parasite drug targets in the post-genome era: What have we learnt and what's next? Mol Cell Pharmacol 4: 89-90; 91-5.