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Recent Publications by NEB Scientists
Articles Published in: 2007 | 2006 | 2005 | 2004 | Before 2004
 
2008 publications (updated 4/28/2009)
 
  • Anton, B.P., Saleh, L., Benner, J.S., Raleigh, E.A., Kasif, S. and Roberts, R.J. (2008).  RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli.  Proc Natl Acad Sci. 105(6):1826-1831.  PubMed ID: 18252828 
  • Babic, A.C., Little, E.J., Manohar, V.M., Bitinaite, J., Horton, N.C.(2008). DNA distortion and specificity in a sequence-specific endonuclease.
    J. Mol. Biol. 383(1):186-204. PubMed ID: 18762194 
  • Brammer, L.A., Bolduc, B., Kass, J.L., Felice, K.M., Noren, C.J. and Hall, M.F. (2008).  A target-unrelated peptide in an M13 phage display library traced to an advantageous mutation in the gene II ribosome-binding site.  Anal biochem. 373(1):88-98. PubMed ID: 17976366 
  • Cokus, S.J., Feng, S., Zhang, X., Chen, Z., Merriman, B., Haudenschild, C.D., Pradhan, S., Nelson, S.F., Pellegrini, M. and Jacobsen, S.E. (2008).  Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.  Nature 452(7184):215-9. PubMed ID: 18278030 
  • Crossgrove, K., Maina, C.V., Robinson-Rechavi, M. and Lochner, M.C. (2008).  Orthologues of the Drosophila melanogaster E75 molting control gene in the filarial parasites Brugia malayi and Dirofilaria immitis.  Mol Biochem Parasitol. 157(1):92-7. PubMed ID: 17942167 
  • Ding, N., Zhou, H., Esteve, P. O., Chin, H. G., Kim, S., Xu, X., Joseph, S. M., Friez, M. J., Schwartz, C. E., Pradhan, S. and Boyer, T. G. (2008). Mediator links epigenetic silencing of neuronal gene expression with X-linked mental retardation. Mol. Cell. 31(3):347-359. PubMed ID: 18691967 
  • Dunten, P.W., Little, E.J., Gregory, M.T., Manohar, V.M., Dalton, M., Hough, D., Bitinaite, J., Horton, N.C. (2008) The structure of SgrAI bound to DNA; recognition of an 8 base pair target. Nucleic Acids Res. 36(16):5405-5416. PubMed ID: 18701646 
  • Dutton, R.J., Boyd, D., Berkmen, M. and Beckwith, J. (2008). Bacterial species exhibit diversity in their mechanisms and capacity for protein disulfide bond formation. Proc Natl Acad Sci 105(33):11933-8. PubMed ID: 18695247 
  • Evans, T.C., Jr. and Nichols, N.M. (2008). DNA Repair Enzymes. Curr. Protoc. Mol. Biol. 84:3.9.1-3.9.12. PubMed ID: 18972391 
  • Formenkov, A., Too, P.H., Chan, S.H., Vaisvila, R., Cantin, B.A., Mazzola, L., Tam, V. and Xu, S.Y. (2008).  Targeting DNA (5)mCpG sites with chimeric endonucleases.  Anal Biochem. 2008 July 2. PubMed ID: 18638441 
  • Foster, J. M., Kumar, S., Ford, L., Johnston, K. L., Ben, R., Graeff-Teixeira, C. and Taylor, M. J. (2008).  Absence of Wolbachia endobacteria in the non-filariid nematodes Angiostrongylus cantonensis and A. costaricensis. Parasites & Vectors 1:31. PubMed ID: 18801163 
  • Foster, J. M., Raverdy, S., Ganatra, M.B., Colussi, P. A., Taron, C. H. and Carlow, C. K. S. (2008). The Wolbachia endosymbiont of Brugia malayi has an active phosphoglycerate mutase: a candidate target for anti-filarial therapies. Parasitology Research (in press).
  • Ghedin, E., Daehnel, K., Foster, J., Slatko, B. and Lustigman S. (2008).  The symbiotic relationship between filarial parasitic nematodes and their wolbachia endosymbionts - a resource for a new generation of control measures.  Symbiosis, 46:77-86.
  • Gissendanner, C.R., Kelley, K., Nguyen, T.Q., Hoener, M.C., Sluder, A.E. and Maina, C.V. (2008).  The Caenorhabditis elegans NR4A nuclear receptor is required for spermatheca morphogenesis.  Developmental Biology 313:767-786.   PubMed ID: 18096150  
  • Hillebrecht, J.R. and Chong, S. (2008). A comparative study of protein synthesis in in vitro systems: from the prokaryotic reconstituted to the eukaryotic extract-based.  BMC Biotechnol. 8(1):58. PubMed ID: 18664286 
  • Jiang, W., Saleh, L., Barr, E.W., Xie, J., Gardner, M.M., Krebs, C. and Bollinger, J.M. Jr. (2008)
    Branched Activation- and Catalysis-Specific Pathways for Electron Relay to the Manganese/Iron Cofactor in Ribonucleotide Reductase from Chlamydia trachomatis.
    Biochemistry 47(33):8477-84.  PubMed ID: 18656954 
  • Kim JK, Samaranayake M, Pradhan S. (2008). Epigenetic mechanisms in mammals. Cell Mol Life Sci. Nov 3. [Epub ahead of print]. PubMed ID: 18985277 
  • Koutsioulis, D., Landry, D. and Guthrie E.P. (2008). Novel endo-alpha-N-acetylgalactosaminidases with broader substrate specificity. Glycobiology, 18(10):799-805. PubMed ID: 18635885 
  • Kucera, R.B. and Nichols, N.M. (2008). DNA-Dependent DNA Polymerases. Curr. Protoc. Mol. Biol. 84:3.5.1-3.5.19. PubMed ID: 18972387 
  • Laget, S. and Defossez, P.A.(2008). Le double jeu de l’épigénétique: Cible et acteur du cancer [Master and servant: epigenetic deregulations as a cause and a consequence of cancer.]Med Sci (Paris). 2008 Aug-Sep;24(8-9):725-30. French. PubMed ID: 18789219 
  • Lambert, A.R., Sussman, D., Shen, b., Maunus, R., Nix, J., Samuelson, J., Xu, S.Y. and Stoddard, B.L. (2008). Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Strucutre 16(4):558-569. PubMed ID: 18400177 
  • Merritt, R., Bierwort, L., Slatko, B., Weiner, M., Weiner, E., Ingram, J. and Sciarra, K. (2008).  Tasting Phenylthiocarbamide (PTC): A New Lab With an Old Flavor.  Am. Biol. Teacher, Online publication, May 2008.  http://www.nabt.org/sites/S1/File/pdf/070-05-0023.pdf
  • Morgan, R.D.,  Bhatia, T.K., Lovasco, L. and Davis, T.B. (2008). MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection. Nucleic Acids Res. 2008 Oct. 17 [Epub ahead of print]. PubMed ID: 18931376 
  • Neely, R.K. and Roberts, R.J. (2008) The BsaHI restriction-modification system: Cloning, sequencing and characterisation of DNA recognising motifs. BMC Molecular Biology 9: 48.  PubMed ID: 18479503 
  • Nichols, N.M., and Yue, D. (2008).  Ribonucleases. Curr. Protoc. Mol. Biol. 84:3.13.1-3.13.8. PubMed ID: 18972385  
  • Nichols, N.M., Tabor, S. and McReynolds, L.A. (2008). RNA ligases.  Curr. Protoc. Mol. Biol. 84:3.15.1-3.15.4 PubMed ID: 18972386  
  • Niv, M.Y., Skrabanek, L., Roberts, R.J., Scheraga, H.A. and Weinstein, H. (2008).  Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.  Proteins 71(2):631-640.  PubMed ID: 17972284  
  • Paschal, B.M., McReynolds, L.A., Noren, C.J. and Nichols, N.M. (2008). RNA Polymerases. Curr. Protoc. Mol. Biol. 84:3.8.1-3.8.8.  PubMed ID: 18972390  
  • Pedamallu, C.S., Ozdamar, L., Csendes, T. and Vinko, T. (2008). Efficient interval partitioning approach for global optimization.  Journal of Global Optimization, 42:369-384.
  • Pedamallu, C. S., Kumar, A., Csendes, T., and Posfai, J. (2008). An interval partitioning algorithm for constraint satisfaction problems, IJMIC special issue on "Nonlinear Optimization with Engineering and Scientific Applications. Accepted, 2008.
  • Pedamallu, R., Pedamallu, S. B., Rama Rao, K. V., and Pedamallu, C. S. (2008) Incidence of occult carcinoma in multinodular goiter using histopathological findings. Internet journal of surgery TM 1528-8242, 17:1.
  • Pedamallu, S.B., Reddy, K.S., Pedamallu, R. and Pedamallu, C.S. (2008).  Reliability of Cycloplegic Autorefractor Measurements to determine Spherical and Astigmatic Refractive Errors in Young Children, The Internet Journal of Ophthalmology and Visual Science, 6:1 2008.
  • Porte, M. and Chong, S. (2008).  Single-process expression and purification of multiple recombinant protein through cocultivation and affinity purification. Anal Biochem. 2008 Jun 18. [Epub ahead of print]. PubMed ID: 18602361  
  • Pradhan, M., Estève, P. O., Chin, H. G., Samaranayke, M., Kim, G. D. and Pradhan, S. (2008). CXXC domain of human DNMT1 is essential for enzymatic activity. Biochemistry, 47(38):10000-10009. PubMed ID: 18754681 
  • Raverdy, S., Foster, J.M., Roopenian, E. and Carlow, C.K. (2008).  The Wolbachia endosymbiont of Brugia malayi has an active pyruvate phosphate dikinase.  Mol Biochem Parasitol. 160(2):163-166.  PubMed ID: 18539347  
  • Roberts, R.J. (2008).  Restriction and modification enzymes and their recognition sequences.  In Life Illuminated.  Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.  pp 215 -216.
  • Roberts, R.J. (2008).  HhaI methyltransferase flips its target base out of the DNA helix.  In Life Illuminated.  Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.  pp 51-53.
  • Smallwood, A., Black, J.C., Tanese, N., Pradhan, S. and Carey, M. (2008).  HP1-mediated silencing targets Pol II coactivator complexes.  Nat Struct Mol Biol. 15(3):318-20.  PubMed ID: 18264112  
  • Swaim, C., Anton, B., Sharma, S., Taron, C. and Benner, J. (2008).  Physical and computational analysis of the yeast Kluyveromyces lactis secreted proteome.  Proteomics 8(13):2714-2723.  PubMed ID: 18601269 
  • Teichert, A.M., Scott, J.A., Robb, G.B., Zhou, Y.Q., Zhu, S.N., Lem, M., Keightley, A., Steer, B.M.,
    Schuh, A.C., Adamson, S.L., Cybulsky, M.I. and Marsden, P.A. (2008). Endothelial nitric oxide synthase gene expression during murine embryogenesis: commencement of expression in the embryo occurs with the establishment of a unidirectional circulatory system.  Circ Res. 103(1):24-33.  PubMed ID: 18556578 
  • Tzertzinis, G., Tabor, S., and Nichols, N.M. 2008.  RNA-Dependent DNA Polymerases. Curr. Protoc. Mol. Biol. 84:3.7.1-3.7.4.  PubMed ID: 18972389  
  • Wei, H., Therrien, C., Blanchard, A., Guan, S. and Zhu, Z. (2008).  The fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases.  Nucleic Acids Res. 36. PubMed ID: 18413342 
  • Weiner, M. and Slatko, B. (2008).  Kits and their unique role in molecular biology: a brief retrospective. Biotechniques.  Apr;44(5):701-704. PubMed ID: 18474048 
  • Yue, D., Tabor, S. and Nichols, N.M. (2008). Template-Independent DNA Polymerases. Curr. Protoc. Mol. Biol. 84:3.6.1-3.6.3.   PubMed ID: 18972388 
  • Zimmermann, J., Hajibabaei, M., Blackburn, D.C., Hanken, J., Cantin, E., Posfai, J. and Evans, T.C. (2008). DNA damage in preserved specimens and tissue samples: a molecular assessment. Frontiers in Zoology 2008, 5:18.  PubMed ID: 18947416