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University of Colorado Department of Biochemistry and Molecular Genetics

Biochemistry and Molecular Genetics
 

Lab Alumni


 
 ​Jennifer Pfingsten, Ph.D.
  • Completed Post-doc in the Lab of Tom Cech, UC Boulder
  • Currently at SomaLogic, Inc., Boulder, Co

Publications while in the Kieft Lab:

Pfingsten, J.S., D.A. Costantino, and J.S. Kieft, Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science, 2006. 314(5804): p. 1450-1454.

Pfingsten, J.S., D.A. Costantino, and J.S. Kieft, Conservation and divers ity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes. J Mol Biol, 2007. 370(5): p. 856-869.

Kieft, J.S., Costantino, D.A., Filbin, M.E., Hammond J., and Pfingsten, J.S. (2007) Structural methods for studying IRES function. Methods Enzymol., 430, 333-371.

Costantino, D.A., Pfingsten, J.S., Rambo, R.P. and J.S. Kieft, tRNA-mRNA mimicry drives translation initiation from a viral IRES. Nat Struct Mol Biol, 2008. 15(1): p. 57-64.

Review : Pfingsten, J.S. and J.S. Kieft, RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes. RNA, 2008. 14(7): p. 1255-1263.

Pfingsten, J.S., A.E. Castile, and J.S. Kieft, Mechanistic role of structurally dynamic regions in Dicistroviridae IGR IRESs. J Mol Biol, 2010. 395(1): p. 205-217.

 

John (J) Hammond, Ph.D.

  • Currently Post-doc in the lab of Jamie Williamson, Scripps, La Jolla, CA

Publications while in the Kieft Lab:

Kieft, J.S., Costantino, D.A., Filbin, M.E., Hammond J., and Pfingsten, J.S. (2007) Structural methods for studying IRES function. Methods Enzymol., 430, 333-371.

Hammond, J.A., et al., Comparison and functional implications of the 3D architectures of viral tRNA-like structures. RNA, 2009. 15(2): p. 294-307.

Hammond, J.A., R.P. Rambo, and J.S. Kieft, Multi-domain packing in the aminoacylatable 3' end of a plant viral RNA. J Mol Biol, 2010. 399(3): p. 450-463.

Colussi, T.M., Costantino, D.A., Hammond, J.A., Ruehle, G.M., Nix, J., & Kieft, J.S. (2014) Crystal structure of the tRNA-like sequence from TYMV: mimicry and plasticity. Nature, 511, 366-369.

 

Amanda (Aimee) Keel, Ph.D.

  • Currently an Instructor at Metropolitan State University, Denver, CO

Publications while in the Kieft Lab:

Keel, A.Y., Rambo. R.P., Batey, R.T., & Kieft, J.S. (2007) A general method to solve the phase problem in RNA crystallography. Structure 15: 761-772.

Keel, A.Y. Easton, L.E., Lukavsky, P.J., & Kieft, J.S. (2009) Large-scale native preparation of in vitro transcribed RNA, Methods Enzymol, 469: 3-25.

Keel, A.Y., Jha, B.K., and Kieft, J.S. (2011) Structural architecture of an RNA that competitively inhibits RNase L. RNA 18: 88-99.

  

Megan Filbin, Ph.D.

  • Currently an Assistant Professor in the Department of Chemistry at Metropolitan State University of Denver.

Publications while in the Kieft Lab:

Kieft, J.S., Costantino, D.A., Filbin, M.E., Hammond J., and Pfingsten, J.S. (2007) Structural methods for studying IRES function. Methods Enzymol., 430, 333-371.

Hammond, J.A., Rambo, R.P., Filbin, M.E., & Kieft, J.S. (2009) Comparison and functional implications of the 3-D architectures of viral tRNA-like structures. RNA, 15, 294-307.

Review: Filbin, M.E. & Kieft, J.S. (2009) Towards a structural understanding of IRES RNA function. Curr Opin Struct Biol, 19, 267-276.

Wallace, A., Filbin, M.E., Veo, B., McFarland, C., Stepinski, J., Jankowska-Anyszka, M., Darzynkiewicz, E., Davis, R.E. (2010) The nematode eukaryotic translation initiation factor 4E/G complex works with a trans-spliced leaer stem-loop to enable efficient translation of trimethylguanosine-capped RNAs. Mol Cell Biol, 30, 1958-1970.

Constantineau J., Greason E., West M., Filbin M., Kieft J.S., Carletti M.Z., Christenson L.K. & Rodriguez A. (2010) A synonymous variant in scavenger receptor, class B, type I gene is associated with lower SR-BI protein expression and function. Atherosclerosis, 210, 1771-1782.

Filbin, M.E. and Kieft, J.S. (2011) HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove. RNA, 17, 1258-1273.

Filbin, M.E. Vollmar, B. S., Shi, D., Gonen, T., Kieft, J.S. (2013) HCV IRES manipulates the ribosome to promote the switch from translation to elongation. Nat Struct Mol Biol, 20, 150-158.

  

James Whitehurst, M.D., Ph.D.

  • Completed Medical School, Currently Director of Research

Publications while in the Kieft Lab:

Plank, T-D.M., Whitehurst, J.T., & Kieft, J.S. (2013) Cell type specificity and structural determinants of IRES activity from the 5’ leaders of different HIV-1 transcripts. Nucleic Acids Res. 41, 6698-6714.
 
Plank, T-D.M., Whitehurst, J.T., Cencic, R., Pelletier, J. & Kieft, J.S. (2014) Internal translation initiation from HIV-1 transcripts is conferred by a common RNA structure. Translation, 2, e27694; DOI:10.4161/trla.27694.

 

  

Tim Colussi, Ph.D.

  • Currently a Research Scientist and Boston Biomedical, Inc.

Publications while in the Kieft Lab:

Colussi, T.M., Costantino, D.A., Hammond, J.A., Ruehle, G.M., Nix, J., & Kieft, J.S. (2014) The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA. Nature, 511, 366-369.

Colussi, T.M., Costantino, D.A., Zhu, J., Donohue, J.P., Korostelev, A.A., Jaafar, Z.A., Plank, T-D.M., Noller, H.F., & Kieft, J.S. (2015) Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Nature, 519: 110-113

   
 ​Terra-Dawn Plank, Ph.D.
  • Currently Post-doc in the lab of Miles Wilkinson, Univ. of California, San Diego
Publications while in the Kieft Lab:
 
Vallejos M., Deforges J., Plank T-D., Letelier A., Ramdohr P., Abraham C.G., Valiente-Echeverria F., Kieft J.S., Sargueil B., &Lopez-Lastra M. (2011). Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors. Nucleic Acids Res, 39, 6186-6200.
 
Plank, T-D. & Kieft, J.S. (2012) The structures of nonprotein-coding RNAs that drive internal ribosome entry site function. Wiley Interdiscip Rev RNA. 3, 195-212.
 
Plank, T-D.M., Whitehurst, J.T., & Kieft, J.S. (2013) Cell type specificity and structural determinants of IRES activity from the 5’ leaders of different HIV-1 transcripts. Nucleic Acids Res. 41, 6698-6714.
 
Plank, T-D.M., Whitehurst, J.T., Cencic, R., Pelletier, J. & Kieft, J.S. (2014) Internal translation initiation from HIV-1 transcripts is conferred by a common RNA structure. Translation, 2, e27694; DOI:10.4161/trla.27694.
 
Colussi, T.M., Costantino, D.A., Zhu, J., Donohue, J.P., Korostelev, A.A., Jaafar, Z.A., Plank, T-D.M., Noller, H.F., & Kieft, J.S. (2015). Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Nature, 519: 110-113
  
 ​Yumeng Hao, Ph.D.
  • Currently Post-doc in the lab of Sarah Woodson,  Johns Hopkins School of Medicine.
Publications while in the Kieft Lab:
Hao, Y., & Kieft, J.S. (2014) Diverse self-association properties within a family of phage packaging RNAs RNA, 20:1759-1774
 
Hao, Y. & Kieft, J.S. (2016) Three-way junction conformation dictates self-association of phage packaging RNAs. RNA Biol. 13, 635-645.
 

Marisa Ruehle, Ph.D.chapmanphoto.jpg

      • Currently a Post-Doc in the lab of Chad Pearson, University of Colorado School of Medicine

Publications while in the Kieft Lab:

Ruehle, M.D., Zhang, H., Sheridan, R.M., Somdeb, M. Chen, Y. Gonzalez, R.G., Cooperman, B.S., & Kieft, J.S. (2015) A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation. eLife, Nov 2;4. pii: e08146. doi: 10.7554/eLife.08146.
 
Ruehle, M.D. & Kieft, J.S. (2015) Molecular prejudice: RNA discrimination against purines allows response to a cellular alarm (News and Views). Nat. Struct. Biol., 22, 754-756
 

Erich Chapman, Ph.D.chapmanphoto.jpg

    • Currently an Assistant Professor in the Department of Chemistry at the University of Denver.

Publications while in the Kieft Lab:
Chapman, E.G., Costantino, D.A., Rabe, J.L., Moon, S.L., Wilusz, J., Nix, J., & Kieft, J.S. (2014) The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production. Science, 344, 307-31.

Chapman, E.G., Moon, S.L., Wilusz, J. & Kieft, J.S. (2014) RNA Structures that Resist Degradation by Xrn1 Produce a Pathogenic Dengue Virus RNA. eLife, April 1,  DOI: 10.7554/eLife.01892

Kieft, J.S., Rabe, J.L., & Chapman, E.G. (2015) New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: conservation, folding, and host adaptation. RNA Biol., 12, 1169-1177

 

Zane Jaafar, Ph.D. HL UCD ID photo.PNG

    • Currently a  Post-Doc in the lab of Onn Brandman, Stanford University

Publications while in the Kieft Lab:

Jaafar, Z.A. & Kieft, J.S. A unified mechanism for the HCV IRES in stressed and unstressed cells: Implications for RNA-Based translational control. eLife, Dec 23;5. pii: e21198. doi: 10.7554/eLife.21198

More coming soon.

 

 
Hannah Laurence HL UCD ID photo.PNG
  • Currently a veterinary student at University of California, Davis

Publications while in the Kieft Lab:

Akiyama, B.M., Laurence, H.M., Massey, A.R., Costantino, D.A., Xie, X., Yang, Y., Shi, P-Y., Nix, J.C., Beckham, J.D., & Kieft, J.S. (2016) Zika virus produces non-coding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease. Science, 354, 1148-1152.