Shukti Chakravarti Lab

Publications

1. Friedrich CA, Chakravarti S, Ferrell RE. A general method for visualizing enzymes releasing adenosine or adenosine-5'-monophosphate.  Biochemical Genetics. 1984; 22:389-394.


2. Chakravarti S, Hamilton B, Sussman R. Relationship between cellular RecA protein concentration and untargeted mutagenesis in Escherichia coli.  Mutation Research. 1986; 160:179-193.


3. Durkin ME, Chakravarti S, Bartos B, Liu S-H, Friedman RL, Chung AE. Amino acid sequence and domain structure of entactin.  Homology with epidermal growth factor precursor and low density lipoprotein receptor.  J Cell Biol. 1988; 107:2749-2758.


4. Tsao T, Hsieh J-c,  Durkin M,  Wu C, Chakravarti S,  Dong L-J,  Lewis M, Chung AE, Characterization of the basement membrane glycoprotein entactin synthesized in the baculovirus expression system.  J. Biol. Chem. 1990; 265: 5188-5191.


5. Chakravarti S, Tam MF, Chung AE. The basement membrane glycoprotein entactin promotes cell attachment and binds calcium ions. J Biol Chem. 1990; 265:10597-10603.


6. Chakravarti S, Phillips S, Hassell JR. Assignment of the perlecan (heparan sulfate proteoglycan) gene to mouse chromosome 4. Mammalian Genome. 1991; 1: 270-272.


7. Chakravarti S, Hassell JR, Phillips SL. Perlecan gene expression precedes laminin gene expression during differentiation of F9 embryonal carcinoma cells. Develop Dynamics. 1993; 197:107-114.


8. Chakravarti S, Horchar T, Jefferson B, Laurie G, Hassell JR. Recombinant Domain III of Perlecan Promotes Cell Attachment through Its RGDS Sequence. J Biol Chem. 1995; 270: 404-409.


9. SunderRaj N, Fite D, Ledbetter S, Chakravarti S, and Hassell JR. Perlecan is a component of cartilage matrix and promotes chondrocyte attachment. J Cell Science. 1995;108: 2663-2672.


10. Chakravarti S, Stalling R, SunderRaj N, Cornuet PK, Hassell JR. Primary Structure of Human Lumican (Keratan Sulfate Proteoglycan) and Localization of the Gene (LUM) to Chromosome 12q21.3-q22. Genomics. 1995; 27:481-488.


11. Chakravarti S, Magnuson T. Localization of mouse lumican (keratan sulfate proteoglycan) to distal chromosome 10. Mammalian Genome. 1995; 6:367-368.


12. Dunlevy JR, Chakravarti S, Gyalzen P, Vergnes J-P, Hassell JR. Cloning of mouse keratocan cDNA and localization of the gene to distal chromosome 10. Mammalian Genome. 1998; 4: 316-319.


13. Chakravarti S, Magnuson T, Lass JH, LaMantia C, Jepsen KJ, Carroll H. Collagen fibril defects affecting skin and cornea in lumican-deficient mice. J Cell Biol. 1998; 141: 1277-1286.


14. Chakravarti S, Petroll WM, Hassell JH, Jester J, Lass JH, Paul J, Birk DE. Corneal opacity in lumican-null mice: defects in collagen fibril structure and packing in the posterior stroma. Invest Ophthalmol. Vis. Sci. 2000; 41(11):3365-3373.


15. Ezura Y, Chakravarti S, Oldberg A, Chervoneva I, Birk DE. Differential expression of lumican and fibromodulin regulate collagen fibrillogenesis in developing mouse tendons. J Cell Biol. 2000 ; 151: 779-787.


16. Lawrance IC, Fiocchi C, Chakravarti S.  Gene expression profiling identifies distinctive disease signatures for ulcerative colitis and Crohn's disease. Hum Molec Genet. 2001; 10:445-456.


17. Jester JV, Ghee Lee Y, Li J, Chakravarti S, Paul J, Petroll WM, Dwight Cavanagh H. Measurement of corneal sub layer thickness and transparency in transgenic mice with altered corneal clarity using in vivo confocal microscopy. Vision Res. 2001; 41: 1283-90.


18. Quantock AJ, Meek KM, Chakravarti S. An X-ray diffraction investigation of corneal structure in lumican-deficient mice. Invest Ophthalmol Vis Sci. 2001;  42: 1750-1756.


19. Jepsen K, Wu F, Peragallo JH, Paul J, Roberts L, Ezura Y, Oldberg A, Birk DE, Chakravarti S.  A syndrome of joint laxity and impaired tendon integrity in lumican- and fibromodulin-deficient mice. J Biol Chem. 2002; 277:35532-35540.


20. Chakravarti S, Paul J, Roberts L, Oldberg A, Birk DE. Ocular and scleral alterations in gene-targeted lumican-fibromodulin double-null mice. Invest Ophthalmol Vis Sci. 2003; 44(6):2422-32.


21. Song J, Lee Y-G, Houston J, Petroll WM, Chakravarti S, Cavanagh HD, Jester JV. Neonatal Corneal Stromal Development in the Normal and Lumican Knockout Mouse. Invest Ophthalmol Vis Sci. 2003; 44:548-557.


22. Troup S, Njue C, Kliewer EV, Parisien M, Roskelley C, Chakravarti S, Roughley PJ, Murphy LC, Watson PH. Reduced expression of small leucine-rich proteoglycans, lumican and decorin, is associated with poor outcome in node negative invasive breast cancer. Clinical Cancer Research. 2003; 9:207-214.


23. Lawrance IC, Wu F, Leite AZA, Willis J,West GA, Fiocchi C, Chakravarti S. A murine model of chronic inflammation-induced intestinal fibrosis down regulated by antisense NF-κB. Gastroenterology. 2003; 125: 1750-1761.


24. Vij N, Roberts L, Joyce S, Chakravarti S. Lumican suppresses cell proliferation and aids Fas-Fas ligand mediated apoptosis: implications in the cornea. Exp Eye Res. 2004; 78:957-71.


25. Chakravarti S, Wu F, Vij N, Roberts L, Joyce S. Microarray studies reveal macrophage-like function of stromal keratocytes in the cornea. Invest Ophthalmol Vis Sci. 2004; 45:3475-84.


26. Vij N, Roberts L, Joyce S, Chakravarti S. Lumican regulates corneal inflammatory responses by modulating Fas-Fas ligand signaling. Invest Ophthalmol Vis Sciences.  2005; 46: 88- 95.


27. Beecher N, Chakravarti S, Joyce S, Meek KM, Quantock AJ. Neonatal development of the corneal stroma in wild-type and lumican-null mice. Invest Ophthalmol Vis Sci. 2006; 47:146-50.


28. Jun AS, Chakravarti S, Edelhauser HF, Kimos M. Aging Changes of Mouse Corneal Endothelium and Descemet’s Membrane. Exp Eye Res. 2006:83:890-896.


29. Chakravarti S, Zhang G, Chervoneva I, Roberts L, Birk D.  Collagen fibril assembly during postnatal development and dysfunctional regulation in the lumican-deficient murine cornea. Dev Dyn. 2006; 235:2493-2506.


30. Suh LH, Zhang C, Chuck RS, Stark WJ, Naylor S, Binley K, Chakravarti S, Jun AS. Cryopreservation and lentiviral-mediated genetic modification of human primary cultured corneal endothelial cells. Invest Ophthalmol Vis Sci. 2007. 48: 3056-3061.


31.  Wu F, Dassopoulos T, Cope L, Brant SR, Harris M, Maitra M, Bayless TM, Parmigiani G,  Chakravarti S. Genome-wide gene expression differences between Crohn’s and ulcerative colitis from endoscopic pinch biopsies: insights into distinctive pathogenesis. Inflamm Bowel Diseases, 2007; 13:807-821. | PMID: 17262812


32. Wu F, Chakravarti S. Differential Expression of Inflammatory and Fibrogenic Genes and Their Regulation by NF-κB Inhibition in a Mouse Model of Chronic Colitis. J Immunol. 2007; 179: 6988-7000.


33. Wu F, Vij N, Roberts L, Lopez-Briones S, Joyce S, Chakravarti S. A novel role of the lumican core protein in bacterial lipopolysaccharide-induced innate immune response. J Biol Chem. 2007; 282: 26409-26417. | PMID: 17616530


34. Wu F, Lee S, Schumacher M, Jun A, Chakravarti S. Differential gene expression patterns of the developing and adult mouse cornea compared to the lens and tendon. Exp Eye Res. 2008 Sep; 87:214-25. | PMID: 18582462


35.  Garagorri N, Fermanian S, Thibault R, Ambrose WM, Schein OD, Chakravarti S, Elisseeff J. Keratocyte behavior in three-dimensional photopolymerizable poly(ethylene glycol) hydrogels. Acta Biomater. 2008 Sep; 4:1139-47. | PMID: 18567550


36. Mohamood AS, Bargatze D, Xiao Z, Jie C, Yagita H, Ruben D, Watson J, Chakravarti S, Schneck JP, Hamad AR. Fas-mediated apoptosis regulates the composition of peripheral alphabeta T cell repertoire by constitutively purging out double negative T cells. PLoS ONE. 2008; 3:e3465. | PMID: 18941614


37. Wu F, Zikusoka M, Trindade A, Dassopoulos T, Harris ML, Bayless TM, Brant SR,

Chakravarti S, Kwon JH. MicroRNAs are Differentially Expressed and Alter Expression of Macrophage Inflammatory Peptide-2alpha. Gastroenterology. 2008 Nov; 135:1624-1635. | PMID: 18835392


38. Ghosh A, Lee S, Chakravarti S. A novel antimicrobial peptidoglycan recognition protein in the cornea. Invest Ophthalmol Vis Sci. 2009. 50:4185-91 | PMID: 19387073


39. Lee S, Bowrin K, Hamad AR, Chakravarti S. Extracellular matrix lumican deposited on the surface of neutrophils promotes migration by binding to β2 integrin. J Biol Chem. 2009 284:23662-9. | PMID: 19531489


40. Chen S, Oldberg A, Chakravarti S, Birk DE. Fibromodulin Regulates Collagen Fibrillogenesis During Peripheral Corneal Development. Dev Dyn. 2010 Mar; 239:844-54. | PMID: 20108350


41. Engler, C, Chakravarti, S., Doyle  J, Eberhart CG, Meng H, Stark WJ, Kelliher C,  Jun, AS. TGF β Signaling Pathway Activation in Keratoconus. American J. Ophthal., 2011 Feb 8. [Epub ahead of print].


42. Jun AS, Cope L, Speck S, Feng, X, Lee, S, Meng H, Hamad, AR, and Chakravarti S. Subnormal Cytokine Profile in the Tear Fluid of Keratoconus Patients. PLoS ONE, 2011 Jan 27;6(1):e16437.


43. Lohr, K, Sardana, H, Lee, S, Wu, F, Huso, DL, Hamad, AR, Chakravarti, S. Extracellular matrix protein lumican regulates inflammation in a mouse model of colitis. Inflamm Bowel Diseases, 2011 Apr 11. doi: 10.1002/ibd.21713. [Epub ahead of print] | PMID: 21484968


44. Shao, H, Chaerkady, R, Chen, S, Sneha, Pintoc, M, Sharma, R, Delanghe,B, Birk, D, Pandey, A  and Chakravarti, S. Proteome profiling of wild type and lumican-deficient mouse corneas. J Proteomics. 2011 May 17. [Epub ahead of print] | PMID: 21616181


45. Zuoxiang Xiao Z, Mohamood AS, Sophia Uddin S, Hiroaki Kimura H, Caturegli P, Womer KL, Huang Y,  Jie C, Chakravarti S, Schneck JP, Yagita H and Hamad AR. Inhibition of Fas ligand unmasks a potent role for IL-10 in restricting the ability of diabetogenic T cells to cause insulitis. The American J. Patholology, 2011 Aug;179(2):725-32. | PMID: 21718680


46. Delalande A, Bouakaz A, Renault G, Tabareau F, Kotopoulis S, Midoux P, Arbeille B, Uzbekov R, Chakravarti S, Postema M, Pichon C. Ultrasound and microbubble-assisted gene delivery in Achilles tendons: Long lasting gene expression and restoration of fibromodulin KO phenotype. J Control Release. 2011 Aug 23. [Epub ahead of print] | PMID: 21888933


47. Kelliher C, Chakravarti S, Vij N, Mazur S, Stahl PJ, Engler C, Matthaei M, Yu SM, Jun AS. A Cellular Model for the Investigation of Fuchs' Endothelial Corneal Dystophy. Experimental Eye Research, 2011 Dec;93(6):880-8. Epub 2011 Oct 18. | PMID: 22020132


48. Jun AS, Meng H, Ramanan N, Matthaei M, Chakravarti S, Bonshek R, Black GCM, Grebe R, Kimos M. An Alpha 2 Collagen VIII Transgenic Knock-in Model of Fuchs Endothelial Corneal Dystrophy Shows Early Endothelial Cell Unfolded Protein Response and Apoptosis. Hum. Mol. Gen., 2012 Jan 15;21(2):384-93. Epub 2011 Oct 14. | PMID: 22002996


49. Scott S-G,  Jun AS and Chakravarti S. Sphere formation from corneal keratocytes and phenotype specific markers. Experimental Eye Research, 2011 Dec;93(6):898-905. Epub 2011 Oct 21. | PMID: 22032988


50. Shao H, Lee S, Gae-Scott S, Nakata C, Chen S, Hamad AR, Chakravarti S. Extracellular matrix lumican promotes bacterial phagocytosis and Lum-/- mice show increased Pseudomonas aeruginosa lung infection severity. J Biol Chem. 2012 Aug 3. [Epub ahead of print] | PMID: 22865855

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