Biological, Geological, and Environmental Sciences

Published Manuscripts with Student Authors

A. Basu, D. Poddar, P. Robinet, J. Smith, M. Febbraio, W. M. Baldwin, III and B. Mazumder*. Ribosomal Protein L13a deficiency in macrophages promotes atherosclerosis by limiting translation control-dependent retardation of inflammation. Atherosclerosis, Thrombosis and Vascular Biology, 34, 533-542, 2014

A. Basu, P. Das, S. Chaudhuri, E. Bevilacqua, J. Andrews, S. Barik, M. Hatzoglou, A. A. Komar and B. Mazumder*. Requirement of rRNA methylation for 80S ribosome assembly on a cohort of cellular Internal Ribosome Entry Sites. Molecular & Cellular Biology, 31, 4482-4499, 2011

B. Mazumder*, D. Poddar, A. Basu, R. Kour, V. Verbovetskaya and S. Barik*.  Extra-ribosomal L13a is a specific innate immune factor for antiviral defense. Journal of Virology, 88, 9100-9110, 2014 (Covered as spotlight on the same issue)

Bentley AA, Merkulov SM, Peng Y, Rozmarynowycz R, Qi X, Pusztai-Carey M, Merrick WC, Yee VC, McCrae KR, Komar AA. Chimeric glutathione S-transferases containing inserts of kininogen peptides: potential novel protein therapeutics. The Journal of Biological Chemistry. 2012; 287(26):22142-50. PubMed [journal] PMID: 22577144, PMCID: PMC3381172

Buhr F, Jha S, Thommen M, Mittelstaet J, Kutz F, Schwalbe H, Rodnina MV, Komar AA. Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations. Molecular Cell. 2016; 61(3):341-51. NIHMSID: NIHMS750905 PubMed [journal] PMID: 26849192, PMCID: PMC4745992 (featured at HFSP as the frontiers science article

D. Poddar, R. Kour, W. M. Baldwin, III and B. Mazumder*. L13a-dependent translational control in macrophages limits the pathogenesis of colitis. Cellular and Molecular Immunology. Advance online publication, 13 July 2015; doi:10.1038/cmi.2015.53

D. Poddar, A. Basu, W. M. Baldwin III, R. V. Kondratov, S. Barik and B. Mazumder*. An Extraribosomal Function of Ribosomal Protein L13a in Macrophages Resolves Inflammation. Journal of Immunology, 190, 3600-3612, 2013

Dhar J, Cuevas RA, Goswami R, Zhu J, Sarkar SN, Barik S. (2015) 2'-5'-Oligoadenylate Synthetase-Like Protein Inhibits Respiratory Syncytial Virus Replication and Is Targeted by the Viral Nonstructural Protein 1. J Virol. 2015 Oct;89(19):10115-9

Dubrovsky Yu. Samsa W., & Kondratov R.V. (2010) Deficiency of circadian protein CLOCK reduces lifespan and increases age-related cataract development in mice. Aging (Albany NY).  2(12), 936-944

Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK, Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proceedings of the National Academy of Sciences of the United States of America (PNAS). 2013; 110(33):13481-6. PubMed [journal] PMID: 23901115, PMCID: PMC3746936

Gasparian AV, Neznanov N, Jha S, Galkin O, Moran JJ, Gudkov AV, Gurova KV, Komar AA. Inhibition of encephalomyocarditis virus and poliovirus replication by quinacrine: implications for the design and discovery of novel antiviral drugs. Journal of Virology. 2010; 84(18):9390-7. PubMed [journal] PMID: 20631142, PMCID: PMC2937643

Ghosh A, Jindal S, Bentley AA, Hinnebusch AG, Komar AA. Rps5-Rps16 communication is essential for efficient translation initiation in yeast S. cerevisiae. Nucleic Acids Research. 2014; 42(13):8537-55. PubMed [journal] PMID: 24948608, PMCID: PMC4117775

Ghosh A, Komar AA. Eukaryote-specific extensions in ribosomal proteins of the small subunit: Structure and function. Translation (Austin, Tex.). 2015; 3(1):e999576. PubMed [journal] PMID: 26779416, PMCID: PMC4682806

Goswami R, Majumdar T, Dhar J, Chattopadhyay S, Bandyopadhyay SK, Verbovetskaya V, Sen GC, Barik S. (2013) Viral degradasome hijacks mitochondria to suppress innate immunity. Cell Res. 2013 Aug;23(8):1025-42

I. Benmerzouga, J. Concepción-Acevedo, H.S. Kim, A.V. Vandoros, G.A.M. Cross, M.M. Klingbeil, and Bibo Li*. (2013) Trypanosoma brucei Orc1 Is Essential for Nuclear DNA Replication and Affects Both VSG Silencing and Switching. Molecular Microbiology. 87:196-210. PMID: 23216794. IF: 5.026; cited 9 times

Jha S, Komar AA. Birth, life and death of nascent polypeptide chains. Biotechnology Journal. 2011; 6(6):623-40. PubMed [journal] PMID: 21538896, PMCID: PMC3130931

Jha SS, Komar AA. Using SecM arrest sequence as a tool to isolate ribosome bound polypeptides. Journal of Visualized Experiments : JoVE. 2012; (64). PubMed [journal] PMID: 22751351, PMCID: PMC3471312

Jha SS, Komar AA. Isolation of ribosome bound nascent polypeptides in vitro to identify translational pause sites along mRNA. Journal of Visualized Experiments: JoVE. 2012; (65). PubMed [journal] PMID: 22806127, PMCID: PMC3471273

Kenega, B. A., R. A. Krebs, and W. B. Clapham, Jr. 2013. Coyote land use inside and outside urban parks. American Midland Naturalist 170: 298–310

Khapre R., Samsa W., & Kondratov R.V. (2010) Circadian regulation of cell cycle: molecular connection between circadian clock and aging. Annals of Medicine. 42(6), 404-415

Khapre R.V., Kondratova A.A., Susova O.S., & Kondratov R.V. (2011) Circadian clock protein BMAL1 regulates cellular senescence in vivo. Cell Cycle 10(23), 4162-4169

Khapre RV, Kondratova AA, Patel S, Dubrovsky Y, Wrobel M, Antoch MP, Kondratov RV. (2014) BMAL1-dependent regulation of the mTOR signaling pathway delays aging. Aging (Albany NY). Jan;6(1):48-5

Khapre RV, Patel SA, Kondratova AA, Chaudhary A, Velingkaar N, Antoch MP, Kondratov RV. (2014)  Metabolic clock generates nutrient anticipation rhythms in mTOR signaling. Aging (Albany NY). Aug;6(8):675-89

Krebs, R.A., E. M. Barkett, and M.T. Begley. 2015. The impact of dreissenid mussels on growth of Leptodea fragilis, the most abundant unionid species in Lake Erie. Canadian Journal of Zoology 93(2): 143-148, 10.1139/cjz-2014-0215

Krebs, R. A., W. C. Borden, N. M. Evans and F. P. Doerder. 2013. Differences in population structure between maternally- and paternally-inherited forms of mitochondria in Lampsilis siliquoidea (Bivalvia: Unionidae). Biological Journal of the Linnean Society 109: 229–240. Article first published online : 25 JAN 2013, DOI: 10.1111/bij.12025

Krebs, R. A., W. C. Borden, E. R. Steiner, M. S. Lyons, W. Zawiski, and B. M. Walton. 2010. Determinants of mussel diversity in Lake Erie tributaries. Journal of the North American Benthological Society 29: 506-520

Lumsden T, Bentley AA, Beutler W, Ghosh A, Galkin O, Komar AA. Yeast strains with N-terminally truncated ribosomal protein S5: implications for the evolution, structure and function of the Rps5/Rps7 proteins. Nucleic Acids Research. 2010; 38(4):1261-72. PubMed [journal] PMID: 19969550, PMCID: PMC2831326

Majumdar T, Chattopadhyay S, Ozhegov E, Dhar J, Goswami R, Sen GC, Barik S. (2015) Induction of interferon-stimulated genes by IRF3 promotes replication of Toxoplasma gondii. PLoS Pathog. 2015 Mar 26;11(3):e1004779

Mazumder B, Poddar D, Basu A, Kour R, Verbovetskaya V, Barik S.(2014) Extraribosomal L13a is a specific innate immune factor for antiviral defense. J Virol. 2014 Aug;88(16):9100-10

P. Das, A. Basu, A. Biswas, D. Poddar, J. Andrews, S. Barik, A. A. Komar and B. Mazumder*. Insights into the mechanism of ribosomal incorporation of mammalian L13a protein during ribosome biogenesis. Molecular & Cellular Biology, 33, 2829-2842, 2013

Patel S.A, Velingkaar N, Kondratov R.V. (2014) Transcriptional control of antioxidant defense by the circadian clock Antioxid Redox Signal. 2014 Jun 20;20(18):2997-3006, Jan 4. [Epub ahead of print] PMID: 24111970

Patel SA, Chaudhari A, Gupta R, Velingkaar N, Kondratov RV. (2015) Circadian clocks govern calorie restriction-mediated life span extension through BMAL1- and IGF-1-dependent mechanisms. FASEB J. Apr; 30(4), 1634-42, pii: fj.15-282475 [Epub ahead of print]

Patel SA, Velingkaar N, Makwana K, Chaudhari A, Kondratov R. (2016) Calorie restriction regulates circadian clock gene expression through BMAL1 dependent and independent mechanisms. Sci Rep. May 12;6:25970. doi: 10.1038/srep25970

R. Lama, R. Sandhu, B. Zhong, Bibo Li*, and Bin Su* (2012) Identification of selective tubulin inhibitors as potential anti-trypanosomal agents. Bioorg Med Chem Lett. 22:5508-5516. PMID: 22850214. IF: 2.331; cited once

R. Sandhu and Bibo Li* (2011) Examination of the Telomere G-overhang Structure in Trypanosoma brucei. JoVE. PMID: 21307825. IF not available; cited 1 time

R. Sandhu, S. Sanford, S. Basu, M. Park, U. M. Pandya, K. Chakrabarti*, Bibo Li*. (2013) A Trans-spliced Telomerase RNA Dictates Telomere Synthesis in Trypanosoma brucei. Cell Research. 23:537-551. PMID: 23478302. IF: 11.981; cited 2 times

S. Jehi, F. Wu, and Bibo Li*. (2014) Trypanosoma brucei TIF2 suppresses VSG switching by maintaining subtelomere integrity. Cell Research. 24:870-885. PMID: 24810301. IF: 11.981

S. Jehi, X. Li, R. Sandhu, F. Ye, I. Benmerzouga, M. Zhang, Y. Zhao*, and Bibo Li*. (2014) Suppression of subtelomeric VSG switching by Trypanosoma brucei TRF requires its TTAGGG repeat-binding activity. Nucleic Acid Research. 42:12899-12911. PMID: 25313155. IF: 8.808

S. Jehi, V. Nanavaty, Bibo Li*. (2016) Trypanosoma brucei TIF2 and TRF Suppress VSG Switching Using Overlapping and Independent Mechanisms. PLoS One. 11(6): e0156746. IF: 3.234

Sampson, D. A. and R. A. Krebs. 2013. Developmental variation and distyly in Hedyotis caerulea (Rubiaceae). SpringerPlus 2(1) http://dx.doi.org/10.1186/2193-1801-2-383

Sampson, D. A. and R. A. Krebs. 2012. Quantitative evaluation of reciprocal herkogamy in the distylous species, Hedyotis caerulea (Rubiaeceae). Plant Systematics and Evolution 298: 1361-1370

Samsa WE, Amit Vasanji, Midura RJ, Kondratov RV. (2016) Deficiency of Circadian Clock Protein BMAL1 in Mice Results in a Low Bone Mass Phenotype. Bone. March; 84, 194-203

Scott, M. W., M. T. Begley, R. A. Krebs, and D. T. Zanatta. 2014. Mitochondrial DNA variation in the Eastern Pondmussel, Ligumia nasuta (Bivalvia: Unionoida) in the Great Lakes region. Walkerana, 17: 60-67

Simhadri VL, Hamasaki-Katagiri N, Tseng SC, Bentley AA, Zichel R, Hershko AY, Komar AA, Kimchi-Sarfaty C. Factor IX oligomerization underlies reduced activity upon disruption of physiological conditions. Haemophilia : the official journal of the World Federation of Hemophilia. 2014; 20(2):e157-63. PubMed [journal] PMID: 24417758

T. Mazumdar, R. Sandhu, M. Qadan, J. DeVecchio, V. Magloire, A. Agyeman, Bibo Li, and J. A. Houghton. (2013) Hedgehog signaling regulates telomerase reverse transcriptase in human cancer cells. PLoS One. 10.1371/journal.pone.0075253. PMID: 24086482. IF: 3.534; cited once

U. M. Pandya, R. Sandhu, and Bibo Li*. (2013) Silencing subtelomeric VSG by Trypanosoma brucei RAP1 at the insect stage involves chromatin structure changes. Nucleic Acid Research. 41:7673-7682. PMID: 23804762. IF: 8.808; cited 5 times

V. Nanavaty, R. Lama, R. Sandhu, B. Zhong, D. Kulman, V. Bobba, A. Zhao, B. Li*, B. Su*. (2016) Orally active and selective tubulin inhibitors as anit-trypanosome agents. PLoS One. 11:e0146289. IF: 3.234

Yasick, A.L., Krebs, R.A. and Wolin, J.A. 2015. Colonization of Lake Erie Tributaries by Allocapnia recta(Capniidae). International Journal of Stonefly Research 11(5):41-50. 

Yuan, F., M. Koran, and A. Valdez (2013), Late Glacial and Holocene record of climatic change in the southern Rocky Mountains from sediments in San Luis Lake, Colorado, Palaeogeography, Palaeoclimatology, Palaeoecology,392(12):146 160,doi:10.1016/j.palaeo.2013.09.016

Yuan, F., J. A. Quellos, and C. Fan (2013), Controls of phosphorus loading and transport in the Cuyahoga River, northeast Ohio, USA, Applied Geochemistry, 38(11):59-69, doi: 10.1016/j.apgeochem.2013.08.011

Zanatta, D. T. , J. Bossenbroek, L. E. Burlakova, T. Crail, F. de Szalay, T. A. Griffith, D. Kapusinski, A.Y. Karateyev, R. A. Krebs, E. S. Meyer, W. L. Paterson, T. J. Prescott, M.T. Rowe, D. W. Schloesser, M. C. Walsh. 2015. Distribution of native mussel (Unionidae) assemblages in coastal Lake Erie, Lake St. Clair, and Connecting Channels, twenty-five years after a dreissenid invasion. Northeastern Naturalist 22: 223-235. DOI: 10.1656/045.022.0115

Zhu J, Zhang Y, Ghosh A, Cuevas RA, Forero A, Dhar J, Ibsen MS, Schmid-Burgk JL, Schmidt T, Ganapathiraju MK, Fujita T, Hartmann R, Barik S, Hornung V, Coyne CB, Sarkar SN. (2014) Antiviral activity of human OASL protein is mediated by enhancing signaling of the RIG-I RNA sensor. Immunity. 2014 Jun 19;40(6):936-48