Lab Alumni

Matthew Szucs, Ph.D.

New England Biolabs

Publications while in the Kieft Lab:

Jones RA, Steckelberg AL, Vicens Q, Szucs MJ, Akiyama BM, Kieft JS. Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA. RNA. 2021 Jan;27(1):54-65.

Szucs MJ, Nichols PJ, Jones RA, Vicens Q, Kieft JS. A New Subclass of Exoribonuclease-Resistant RNA Found in Multiple Genera of Flaviviridae. mBio. 2020 Sep 29;11(5).

*Steckelberg A.-L., *Vicens Q., Costantino D.A., Nix J.C., Kieft J.S. (2020) The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold. RNA 26, 1767-1776. *These authors contributed equally 

 Rachel Jones, Ph.D.

Post-Doc at Sandia National Labs

Publications while in the Kieft Lab:

Szucs MJ, Nichols PJ, Jones RA, Vicens Q, Kieft JS. A New Subclass of Exoribonuclease-Resistant RNA Found in Multiple Genera of Flaviviridae. mBio. 2020 Sep 29;11(5).

Jones RA, Steckelberg AL, Vicens Q, Szucs MJ, Akiyama BM, Kieft JS. Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA. RNA. 2021 Jan;27(1):54-65.

 Jillian Ramos, Ph.D.

Sales Account Manager at Genscript

Publications while in the Kieft Lab:

Ramos J. RNA modifications: an overview of select web-based tools. RNA. 2022 Nov 28;(11):1440-1445.

 Daniel Eiler, Ph.D.

Senior Scientist in Drug Design at Schrodinger

Publications while in the Kieft Lab:

Akiyama, B.M., Eiler, D. & Kieft, J.S. (2015) Structured RNAs that evade or confound exonucleases: function follows form. Curr Opin Struct Biol 36, 40-47.

Eiler, D.R., Wimberly, B.T., Bilodeau, D.Y., Rissland, O.R., Kieft, J.S. The Giardia lamblia ribosome structure reveals divergences in translation and quality control pathways. BioRxiv. [Preprint]. Available at: doi: https://doi.org/10.1101/2020.09.30.321331 (Cell Reports, in revision)

 Ben Akiyama, Ph.D.

Scientist II, Meso Scale Discovery

Publications while in the Kieft Lab:

Akiyama, B.M., Eiler, D. & Kieft, J.S. (2015) Structured RNAs that evade or confound exonucleases: function follows form. Curr Opin Struct Biol 36, 40-47.

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.

Steckelberg, A.-L., Akiyama, B.A., Costantino, D.A., Sit, T.A., Nix, J.C., & Kieft, J.S. (2018) A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure. Proc. Natl. Acad. Sci. 115, 6404-6409.

Sparks, H., Monogue, B., Akiyama, B.M., Kieft, J.S. & Beckham, J.D. (2020) Disruption of Zika Virus xrRNA1-dependent sfRNA production results in tissue-specific attenuated viarl replication. Viruses, 12, 1177, doi: 10.3390/v12101177.

Jones R.A., Steckelberg A.-L., Szucs M.J., Akiyama B.M., Vicens Q., & Kieft J.S. (2021) Different tertiary interactions create the same important 3-D features in divergent flavivirus xrRNAs. RNA 27, 54-65.

Akiyama, B.M., Graham, M.E., O’Donoghue, Z.G., Beckham, J.D. & Kieft, J.S. (2021) Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. Nucleic Acids Res., 49, 7122-7138.

 Zoe O’Donoghue, Ph.D.

AAAS Science and Technology Policy Fellow, USAID

Publications while in the Kieft Lab:

*MacFadden, A., *O’Donoghue, Z., Silva, Patricia A.G.C, Chapman. E.G., Olsthoom, R.C., Sterken, M.G., Pijlman, G.P., Bredenbeek, P.J., & Kieft, J.S. (2018) Mechanism and structural diversity of exoribonuclease resistant RNA structures in flaviviral RNAs. Nat. Commun. 9, 119.*These authors contributed equally 

More on the way!

 Anna-Lena Steckelberg, Ph.D.

Assistant Professor at Columbia University

Publications while in the Kieft Lab:

Steckelberg, A.-L., Akiyama, B.A., Costantino, D.A., Sit, T.A., Nix, J.C., & Kieft, J.S. (2018) A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure. Proc. Natl. Acad. Sci. 115, 6404-6409.

*Steckelberg, A.-L., *#Vicens, Q., & #Kieft, J.S. (2018) Exoribonuclease-resistant RNAs exist in both coding and non-coding subgenomic RNAs. MBio  9,(6):e02461-18. doi: 10.1128/mBio.02461-18. *These authors contributed equally #Joint corresponding authors

*Steckelberg A.-L., *Vicens Q., Costantino D.A., Nix J.C., Kieft J.S. (2020) The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold. RNA 26, 1767-1776. *These authors contributed equally 

Jones R.A., Steckelberg A.-L., Szucs M.J., Akiyama B.M., Vicens Q., & Kieft J.S. (2021) Different tertiary interactions create the same important 3-D features in divergent flavivirus xrRNAs. RNA 27, 54-65.

 Erik Hartwick, Ph.D.

Post-Doc in the lab of Ruben Gonzalez, Columbia University

Publications while in the Kieft Lab:

Hartwick, E.W., Costantino, D.A., MacFadden, A. Nix, J.C., Tian, S,. Das, R., Kieft, J.S. (2018) Ribosome-induced RNA conformational changes in a viral 3 ¢UTR sense and regulated translation levels. Nature Communications 29, 5074-.​

Thulson, E., Hartwick, E.W., Cooper-Sansone, A., Williams, M.A., soliman, M.E., Robinson, L.K., Kieft, J.S., & Mouzakis, K.D. An RNA pseudoknot stimulates HTLV-1 pro-pol programmed -1 ribosomal frameshifting. RNA 26, 512-528.

More in preparation!

 Hannah Laurence

Earned DVM in 2018. Now doing a combined veterinary anatomical pathology residency/PhD program at Colorado State University

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.

 Zane Jaafar, Ph.D.

Research Scientist at Watchmaker Genomics

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

Jaafar, Z. A. & Kieft, J.S. (2018) Viral RNA structure-based strategies to manipulate translation. Nat. Rev. Microbiol. 17, 110-123.

 Erich Chapman, Ph.D.

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

*MacFadden, A., *O'Donoghue, Z., Silva, Patricia A.G.C., Chapman, E.G., Olsthoom, R.C., Sterken, M.G., Pijlman, G.P., Bredenbeek, P.J., & Kieft, J.S. (2018) Mechanism and structural diversity of exonuclease resistant RNA structures in flaiviviral RNAs. Nature Communicationa, 9, 119. *These authors contributed equally.

 Marisa Ruehle, Ph.D.

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

 Yumeng Hao, Ph.D.

Senior Scientist at FL70, Inc

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 the self-association of phage packaging RNAs. RNA Biol. 13, 635-645.

 Terra-Dawn Plank, Ph.D.

Variant Scientist at Ambry Genetics

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

 Tim Colussi, Ph.D.

Data Scientist at Enko

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

 Megan Filbin-Wong, Ph.D.

Tenured Associate 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.

Director of Research at Aalto Scientific

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.

 Amanda (Aimee) Keel, Ph.D.

Instructor 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., 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.

 John (J) Hammond, Ph.D.

Senior Scientist at 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.

 Jennifer Pfingsten, Ph.D.

Communications Specialist at SomaLogic, Inc., Boulder, CO

Publications while in the Kieft Lab:

Pfingsten, J.S., D.A. Costantino, and J.S. Kieft, (2006) Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science, 314(5804):1450-4.

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.NA. Science, 2006. 314(5804): p. 1450-1454.

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.