Journal Club

Journal club for the summer of 2019 is being held on Friday afternoons (1:00-2:00 pm) in W565. The journal article being discussed will be announced at the beginning of the week.


August 9, 2019
Presenter: Gayatri Namala
Pickerill, E.S., Kurtz, R.P., Tharp, A., Guerrero Sanz, P., Begum, M. and Bernstein, D.A. (2019) Pseudouridine synthase 7 impacts Candida albicans rRNA processing and morphological plasticity Pus7’s role in rRNA processing and morphological plasticity. Yeast, In Press.
July 19, 2019
Presenter: Davinder Kaur
Nannenga, B.L. and Gonen, T. (2019) The cryo-EM method microcrystal electron diffraction (MicroED). Nat. Methods, 16, 369–379.
July 12, 2019
Presenter: Hope Vienneau
Hayashi, S., Mori, S., Suzuki, T., Suzuki, T. and Yoshihisa, T. (2019) Impact of intron removal from tRNA genes on Saccharomyces cerevisiae. Nucleic Acids Res., 47, 5936–5949.
July 5, 2019
Presenter: Dora Capatos
Liu, C.-X., Li, X., Nan, F., Jiang, S., Gao, X., Guo, S.-K., Xue, W., Cui, Y., Dong, K., Ding, H., et al. (2019) Structure and Degradation of Circular RNAs Regulate PKR Activation in Innate Immunity. Cell, 177, 865–880.
June 14, 2019
Presenter: Dustin Smith
Strecker, J., Ladha, A., Gardner, Z., Schmid-Burgk, J.L., Makarova, K.S., Koonin, E. V and Zhang, F. (2019) RNA-guided DNA insertion with CRISPR-associated transposases. Science, 365, 48-53.
June 7, 2019
Presenter: Dylan Girodat
Wang, J., Liu, Y., Liu, Y., Zheng, S., Wang, X., Zhao, J., Yang, F., Zhang, G., Wang, C. and Chen, P.R. (2019) Time-resolved protein activation by proximal decaging in living systems. Nature, 569, 509–513.
May 31, 2019
Presenter: Luc Roberts
Maori, E., Navarro, I.C., Boncristiani, H., Seilly, D.J., Rudolph, K.L.M., Sapetschnig, A., Lin, C.-C., Ladbury, J.E., Evans, J.D., Heeney, J.L., et al. (2019) A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal Jelly. Mol. Cell, 74, 598–608
May 24, 2019
Presenter: Taylor Sheahan
Berhanu, S., Ueda, T. and Kuruma, Y. (2019) Artificial photosynthetic cell producing energy for protein synthesis. Nat. Commun., 10, 1325.
May 17, 2019
Presenter: Jalyce Heller
Moon, S.L., Morisaki, T., Khong, A., Lyon, K., Parker, R. and Stasevich, T.J. (2019) Multicolour single-molecule tracking of mRNA interactions with RNP granules. Nat. Cell Biol., 21, 162–168.
May 10, 2019
Presenter: Justin Vigar
Alam, K.K., Jung, J.K., Verosloff, M.S., Clauer, P.R., Lee, J.W., Capdevila, D.A., Pastén, P.A., Giedroc, D.P., Collins, J.J. and Lucks, J.B. (2019) Rapid, Low-Cost Detection of Water Contaminants Using Regulated In Vitro Transcription. bioRxiv
April 26, 2019
Presenter: Dr. Jumai Abioye
Venetz, J.E., Del Medico, L., Wölfle, A., Schächle, P., Bucher, Y., Appert, D., Tschan, F., Flores-Tinoco, C.E., van Kooten, M., Guennoun, R., et al. (2019) Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality. Proc. Natl. Acad. Sci. 116, 8070-8079.
April 12, 2019
Presenter: Dr. Julie Guéguéniat
Palangat, M., Anastasakis, D.G., Fei, D.L., Lindblad, K.E., Bradley, R., Hourigan, C.S., Hafner, M. and Larson, D.R. (2019) The splicing factor U2AF1 contributes to cancer progression through a noncanonical role in translation regulation. Genes Dev. 33, 482–497.
April 5, 2019
Presenter: Tim Vos
Schuller, J.M., Falk, S., Fromm, L., Hurt, E. and Conti, E. (2018) Structure of the nuclear exosome captured on a maturing preribosome. Science (360, 219-222.
March 29, 2019 
Presenter: Harland Brandon
Hoshika, S., Leal, N.A., Kim, M.-J., Kim, M.-S., Karalkar, N.B., Kim, H.-J., Bates, A.M., Watkins, N.E., Santa Lucia, H.A., Meyer, A.J., et al. (2019) Hachimoji DNA and RNA: A genetic system with eight building blocks. Science 363, 884-887.
March 22, 2019
Presenter: Dr. Preethi Balasundaram
O’Hara, N.B., Reed, H.J., Afshinnekoo, E., Harvin, D., Caplan, N., Rosen, G., Frye, B., Woloszynek, S., Ounit, R., Levy, S., et al. (2017) Metagenomic characterization of ambulances across the USA. Microbiome, 5, 125.
March 1, 2019
Presenter: Tyler Mrozowich
Shah, P.S., Link, N., Jang, G.M., Sharp, P.P., Zhu, T., Swaney, D.L., Johnson, J.R., Von Dollen, J., Ramage, H.R., Satkamp, L., et al. (2018) Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell, 175, 1931–1945.e18.
February 15, 2019
Presenter: Davinder Kaur
DeLey Cox, V.E., M.F., and Gaucher, E.A. (2019) Incorporation of Modified Amino Acids by Engineered Elongation Factors with Expanded Substrate Capabilities. ACS Synthetic Biology 8: 287–96.
February 8, 2019
Presenter: Sarah Schultz
Rapino, F., Delaunay, S., Rambow, F., Zhou, Z., Tharun, L., De Tullio, P., Sin, O., Shostak, K., Schmitz, S., Piepers, J., Ghesquière, B., Karim, L., Charloteaux, B., Jamart, D., Florin, A., Lambert, C., Rorive, A., Jerusalem, G., Leucci, E., Dewaele, M., Vooijs, M., Leidel, S.A., Georges, M., Voz, M., Peers, B., Büttner, R., Marine, J.-C., Chariot, A. and Close, P. (2018) Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature, 558, 605-609.

February 1, 2019
Presenter: Dora Capatos
Silva, D.-A., Yu, S., Ulge, U.Y., Spangler, J.B., Jude, K.M., Labão-Almeida, C., Ali, L.R., Quijano-Rubio, A., Ruterbusch, M., Leung, I., Biary, T., Crowley, S.J., Marcos, E., Walkey, C.D., Weitzner, B.D., Pardo-Avila, F., Castellanos, J., Carter, L., Stewart, L., Riddell, S.R., Pepper, M., Bernardes, G.J.L., Dougan, M., Garcia, K.C. and Baker, D. (2019) De novo design of potent and selective mimics of IL-2 and IL-15. Nature, 565, 186-191.
January 25, 2019
Presenter: Dustin Smith
Silpe, J.E. and Bassler, B.L. (2019) A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision. Cell, 176, 268-280.e213.
January 11, 2019
Presenter: Dr. Govardhan Reddy Veerareddygari
Queiroz, R.M.L., Smith, T., Villanueva, E., Marti-Solano, M., Monti, M., Pizzinga, M., Mirea, D.-M., Ramakrishna, M., Harvey, R.F., Dezi, V., Thomas, G.H., Willis, A.E. and Lilley, K.S. (2019) Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS). Nature Biotechnology.
December 7, 2018
Presenter: Luc Roberts
Kampen, K.R., Sulima, S.O., Verbelen, B., Girardi, T., Vereecke, S., Rinaldi, G., Verbeeck, J., Op de Beeck, J., Uyttebroeck, A., Meijerink, J.P.P. et al. (2018) The ribosomal RPL10 R98S mutation drives IRES-dependent BCL-2 translation in T-ALL. Leukemia.
November 30, 2018
Presenter: Taylor Sheahan
Toda, S., Blauch, L.R., Tang, S.K.Y., Morsut, L. and Lim, W.A. (2018) Programming self-organizing multicellular structures with synthetic cell-cell signaling. Science, 361, 156-162.
November 23, 2018
Presenter: Jalyce Heller
Simsek, D., Tiu, G.C., Flynn, R.A., Byeon, G.W., Leppek, K., Xu, A.F., Chang, H.Y. and Barna, M. (2017) The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity. Cell, 169, 1051-1065.e1018.
November 9, 2018
Presenter: Justin Vigar
Cambray, G., Guimaraes, J.C. and Arkin, A.P. (2018) Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coliNature Biotechnology, 36, 1005.
November 2, 2018
Presenter: Matthew Stuart-Edwards
Simpson, J.T., Workman, R.E., Zuzarte, P.C., David, M., Dursi, L.J. and Timp, W. (2017) Detecting DNA cytosine methylation using nanopore sequencing. Nature Methods, 14, 407. 
October 26, 2018
Presenter: Dr. Jumai Abioye
Halperin, S.O., Tou, C.J., Wong, E.B., Modavi, C., Schaffer, D.V. and Dueber, J.E. (2018) CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature, 560, 248-252.
October 12, 2018
Presenter: Dr. Julia Guegueniat
Chatterjee, K., Majumder, S., Wan, Y., Shah, V., Wu, J., Huang, H.-Y. and Hopper, A.K. (2017) Sharing the load: Mex67–Mtr2 cofunctions with Los1 in primary tRNA nuclear export. Genes & Development, 31, 2186-2198.
October 5, 2018
Presenter: Timothy Vos
Kornprobst, M., Turk, M., Kellner, N., Cheng, J., Flemming, D., Koš-Braun, I., Koš, M., Thoms, M., Berninghausen, O., Beckmann, R. et al. (2016) Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome. Cell, 166, 380-393.
September 21, 2018
Presenter: Harland Brandon
Peselis, A. and Serganov, A. (2018) ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands. Nature Chemical Biology, 14, 887-894.
September 14, 2018
Presenter: Chris Isaac
Dwidar, M. and Yokobayashi, Y. (2017) Controlling Bdellovibrio bacteriovorus Gene Expression and Predation Using Synthetic Riboswitches. ACS Synthetic Biology, 6, 2035-2041.
September 7, 2018
Presenter: Dominic Czekay
De Zoysa, M.D., Wu, G., Katz, R. and Yu, Y.-T. (2018) Guide-substrate base-pairing requirement for box H/ACA RNA-guided RNA pseudouridylation. RNA, 24, 1106-1117.
August 24, 2018
Presenter: Cristina Carvalho Barbosa de Souza
Crowe-McAuliffe, C., Graf, M., Huter, P., Takada, H., Abdelshahid, M., Nováček, J., Murina, V., Atkinson, G.C., Hauryliuk, V. and Wilson, D.N. (2018) Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. Proceedings of the National Academy of Sciences, 115, 8978-8983.
August 17, 2018
Presenter: Davinder Kaur
Ovchinnikov, V., Stone, T.A., Deber, C.M. and Karplus, M. (2018) Structure of the EmrE multidrug transporter and its use for inhibitor peptide design. Proceedings of the National Academy of Sciences, 115, E7932-E7941.
August 10, 2018
Presenter: Sarah Schultz
Shao, Y., Lu, N., Wu, Z., Cai, C., Wang, S., Zhang, L.-L., Zhou, F., Xiao, S., Liu, L., Zeng, X. et al. (2018) Creating a functional single-chromosome yeast. Nature, 560, 331-335.
August 3, 2018
Presenter: Chris Lindgren
Allan, C., Ker, A., Smith, C.-A., Tsimbouri, P.M., Borsoi, J., O’Neill, S., Gadegaard, N., Dalby, M.J. and Dominic Meek, R.M. (2018) Osteoblast response to disordered nanotopography. Journal of Tissue Engineering, 9, 2041731418784098.
July 27, 2018
Presenter: Dora Capatos
Gupta, R., Somyajit, K., Narita, T., Maskey, E., Stanlie, A., Kremer, M., Typas, D., Lammers, M., Mailand, N., Nussenzweig, A. et al. (2018) DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity. Cell, 173, 972-988
July 20, 2018
Presenter: Dr. Govardhan Reddy Veerareddygari
van de Waterbeemd, M., Tamara, S., Fort, K.L., Damoc, E., Franc, V., Bieri, P., Itten, M., Makarov, A., Ban, N. and Heck, A.J.R. (2018) Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods. Nature Communications, 9, 2493.
July 13, 2018
Presenter: Justin Vigar
Mao, N., Cubillos-Ruiz, A., Cameron, D.E. and Collins, J.J. (2018) Probiotic strains detect and suppress cholera in mice. Science Translational Medicine, 10.
July 6, 2018
Presenter: Dustin Smith
Mimee, M., Nadeau, P., Hayward, A., Carim, S., Flanagan, S., Jerger, L., Collins, J., McDonnell, S., Swartwout, R., Citorik, R.J. et al. (2018) An ingestible bacterial-electronic system to monitor gastrointestinal health. Science, 360, 915-918.
June 22, 2018
Presenter: Dr. Soumya Deo
Lei, R., Hou, J., Chen, Q., Yuan, W., Cheng, B., Sun, Y., Jin, Y., Ge, L., Ben-Sasson, S.A., Chen, J. et al. (2018) Self-Assembling Myristoylated Human α-Defensin 5 as a Next-Generation Nanobiotics Potentiates Therapeutic Efficacy in Bacterial Infection. ACS Nano, 12, 5284-5296.
June 8, 2018
Presenter: Harland Brandon
Valero, J., Pal, N., Dhakal, S., Walter, N.G. and Famulok, M. (2018) A bio-hybrid DNA rotor–stator nanoengine that moves along predefined tracks. Nature Nanotechnology, 13, 496-503.
June 1, 2018
Presenter: Dylan Girodat
Lu, P., Min, D., DiMaio, F., Wei, K.Y., Vahey, M.D., Boyken, S.E., Chen, Z., Fallas, J.A., Ueda, G., Sheffler, W. et al. (2018) Accurate computational design of multipass transmembrane proteins. Science, 359, 1042-1046.
May 18, 2018
Presenter: Taylor Sheahan
Sedlmayer, F., Hell, D., Müller, M., Ausländer, D. and Fussenegger, M. (2018) Designer cells programming quorum-sensing interference with microbes. Nature Communications, 9, 1822.
May 11, 2018
Presenter: Hope Vienneau
Leppik, M., Liiv, A. and Remme, J. (2017) Random pseuoduridylation in vivo reveals critical region of Escherichia coli 23S rRNA for ribosome assembly. Nucleic Acids Research, 45, 6098-6108.
May 4, 2018
Presenter: Yubo Cheng
Magistri, M., Velmeshev, D., Makhmutova, M. and Faghihi, M.A. (2015) Transcriptomics Profiling of Alzheimer’s Disease Reveal Neurovascular Defects, Altered Amyloid-β Homeostasis, and Deregulated Expression of Long Noncoding RNAs. Journal of Alzheimer's Disease, 48, 647-665.
April 27, 2018
Presenter: Tyler Mrozowich
Razew, M., Warkocki, Z., Taube, M., Kolondra, A., Czarnocki-Cieciura, M., Nowak, E., Labedzka-Dmoch, K., Kawinska, A., Piatkowski, J., Golik, P. et al. (2018) Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components. Nature Communications, 9, 97.
April 20, 2018
Presenter: Julia Guegueniat
Guzzi, N., Cieśla, M., Ngoc, P.C.T., Lang, S., Arora, S., Dimitriou, M., Pimková, K., Sommarin, M.N.E., Munita, R., Lubas, M. et al. (2018) Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells. Cell.
April 13, 2018
Presenter: Chris Isaac
Chavez, A., Pruitt, B.W., Tuttle, M., Shapiro, R.S., Cecchi, R.J., Winston, J., Turczyk, B.M., Tung, M., Collins, J.J. and Church, G.M. (2018) Precise Cas9 targeting enables genomic mutation prevention. Proceedings of the National Academy of Sciences, 115, 3669-3673.
April 6, 2018
Presenter: Jalyce Heller
Segall-Shapiro, T.H., Sontag, E.D. and Voigt, C.A. (2018) Engineered promoters enable constant gene expression at any copy number in bacteria. Nature Biotechnology, 36, 352.
March 23, 2018
Presenter: Rhys Hakstol
Einfalt, T., Witzigmann, D., Edlinger, C., Sieber, S., Goers, R., Najer, A., Spulber, M., Onaca-Fischer, O., Huwyler, J. and Palivan, C.G. (2018) Biomimetic artificial organelles with in vitro and in vivo activity triggered by reduction in microenvironment. Nature Communications, 9, 1127.
March 16, 2018
Presenter: Cristina Carvalho Barbosa de Souza
Li, S., Jiang, Q., Liu, S., Zhang, Y., Tian, Y., Song, C., Wang, J., Zou, Y., Anderson, G.J., Han, J.-Y. et al. (2018) A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo. Nature Biotechnology, 36, 258.
March 9, 2018
Presenter: Sarah Schultz
Franzmann, T.M., Jahnel, M., Pozniakovsky, A., Mahamid, J., Holehouse, A.S., Nüske, E., Richter, D., Baumeister, W., Grill, S.W., Pappu, R.V. et al. (2018) Phase separation of a yeast prion protein promotes cellular fitness. Science, 359.
March 2, 2018
Presenter: Dominic Czekay
Kim, W.K., Yun, S., Kwon, Y., You, K.T., Shin, N., Kim, J. and Kim, H. (2017) mRNAs containing NMD-competent premature termination codons are stabilized and translated under UPF1 depletion. Scientific Reports, 7, 15833.
February 23, 2018
Presenter: Davinder Kaur
Ferruz, N., Doerr, S., Vanase-Frawley, M.A., Zou, Y., Chen, X., Marr, E.S., Nelson, R.T., Kormos, B.L., Wager, T.T., Hou, X. et al. (2018) Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs. Scientific Reports, 8, 897.
February 16, 2018
Presenter: Erin Kelly
Angrisani, A., Matrone, N., Belli, V., Vicidomini, R., Di Maio, N., Turano, M., Scialò, F., Netti, P.A., Porcellini, A. and Furia, M. (2018) A functional connection between dyskerin and energy metabolism. Redox Biology14, 557-565.
February 9, 2018
Presenter: Dora Capatos
Arribere, J.A., Cenik, E.S., Jain, N., Hess, G.T., Lee, C.H., Bassik, M.C. and Fire, A.Z. (2016) Translation readthrough mitigation. Nature534, 719.
February 2, 2018
Presenter: Dr. Govardhan Reddy Veerareddygari
Morscher, R.J., Ducker, G.S., Li, S.H.-J., Mayer, J.A., Gitai, Z., Sperl, W. and Rabinowitz, J.D. (2018) Mitochondrial translation requires folate-dependent tRNA methylation. Nature.
January 19, 2018
Presenter: Dustin Smith
Collins, J., Robinson, C., Danhof, H., Knetsch, C.W., van Leeuwen, H.C., Lawley, T.D., Auchtung, J.M. and Britton, R.A. (2018) Dietary trehalose enhances virulence of epidemic Clostridium difficile. Nature 553: 291-294.
January 12, 2018
Presenter: Dr. Senthil Kumar Duraikannu Kailasam
Najafabadi, H.S., Garton, M., Weirauch, M.T., Mnaimneh, S., Yang, A., Kim, P.M. and Hughes, T.R. (2017) Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding. Genome Biol 18: 167.
January 5, 2018
Presenter: Elijah Dueck
Poole, A.R., Vicino, I., Adachi, H., Yu, Y.-T. and Hebert, M.D. (2017) Regulatory RNPs: a novel class of ribonucleoproteins that potentially contribute to ribosome heterogeneity. Biology Open 6: 1342-1354.
December 8, 2017
Presenter: Dr. Soumya Deo
Sivaramakrishnan, P., Sepúlveda, L.A., Halliday, J.A., Liu, J., Núñez, M.A.B., Golding, I., Rosenberg, S.M. and Herman, C. (2017) The transcription fidelity factor GreA impedes DNA break repair. Nature, 550: 214-218.
December 1, 2017
Presenter: William Reid
Tang, T.Y.D., Cecchi, D., Fracasso, G., Accardi, D., Coutable-Pennarun, A., Mansy, S.S., Perriman, A.W., Anderson, J.L.R. and Mann, S. (2017) Gene-Mediated Chemical Communication in Synthetic Protocell Communities. ACS Synthetic Biology.
November 17, 2017
Presenter: Harland Brandon
Ljubetič, A., Lapenta, F., Gradišar, H., Drobnak, I., Aupič, J., Strmšek, Ž., Lainšček, D., Hafner-Bratkovič, I., Majerle, A., Krivec, N. et al. (2017) Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo. Nature Biotechnology, 35, 1094.
November 10, 2017
Presenter: Taylor Sheahan
Gaudelli, N.M., Komor, A.C., Rees, H.A., Packer, M.S., Badran, A.H., Bryson, D.I. and Liu, D.R. (2017) Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature.
November 3, 2017
Presenter: Luc Roberts
Shepherd, T.R., Du, L., Liljeruhm, J., Samudyata, Wang, J., Sjödin, M.O.D., Wetterhall, M., Yomo, T. and Forster, A.C. (2017) De novo design and synthesis of a 30-cistron translation-factor module. Nucleic Acids Research, 45, 10895-10905.
October 27, 2017
Presenter: Justin Vigar
Moor, A.E., Golan, M., Massasa, E.E., Lemze, D., Weizman, T., Shenhav, R., Baydatch, S., Mizrahi, O., Winkler, R., Golani, O. et al. (2017) Global mRNA polarization regulates translation efficiency in the intestinal epithelium. Science, 357, 1299-1303.
October 13, 2017
Presenter: Jalyce Heller
Chevalier, A., Silva, D.-A., Rocklin, G.J., Hicks, D.R., Vergara, R., Murapa, P., Bernard, S.M., Zhang, L., Lam, K.-H., Yao, G. et al. (2017) Massively parallel de novo protein design for targeted therapeutics. Nature, 550, 74.
October 6, 2017
Presenter: Erin Kelly
Ma, H., Marti-Gutierrez, N., Park, S.-W., Wu, J., Lee, Y., Suzuki, K., Koski, A., Ji, D., Hayama, T., Ahmed, R. et al. (2017) Correction of a pathogenic gene mutation in human embryos. Nature, 548, 413.
September 29, 2017
Presenter: Cristina Carvalho Barbosa de Souza
Temmel, H., Müller, C., Sauert, M., Vesper, O., Reiss, A., Popow, J., Martinez, J. and Moll, I. (2017) The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli. Nucleic Acids Research, 45, 4708-4721.
September 22, 2017
Presenter: Rhys Hakstol
Thubagere, A.J., Li, W., Johnson, R.F., Chen, Z., Doroudi, S., Lee, Y.L., Izatt, G., Wittman, S., Srinivas, N., Woods, D. et al. (2017) A cargo-sorting DNA robot. Science357.
September 15, 2017
Presenter: Dominic Czekay
Harrington, L.B., Doxzen, K.W., Ma, E., Liu, J.-J., Knott, G.J., Edraki, A., Garcia, B., Amrani, N., Chen, J.S., Cofsky, J.C. et al. (2017) A Broad-Spectrum Inhibitor of CRISPR-Cas9. Cell, 170, 1224-1233.
September 1, 2017
Presenter: Davinder Kaur
Ingles-Prieto, A., Ibarra-Molero, B., Delgado-Delgado, A., Perez-Jimenez, R., Fernandez, Julio M., Gaucher, Eric A., Sanchez-Ruiz, Jose M. and Gavira, Jose A. (2013) Conservation of Protein Structure over Four Billion Years. Structure, 21, 1690-1697.
August 25, 2017
Presenter: Sarah Schultz
Kazlauskiene, M., Kostiuk, G., Venclovas, Č., Tamulaitis, G. and Siksnys, V. (2017) A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems. Science, 357, 605-609.
August 18, 2017
Presenter: Dora Capatos
Sendoel, A., Dunn, J.G., Rodriguez, E.H., Naik, S., Gomez, N.C., Hurwitz, B., Levorse, J., Dill, B.D., Schramek, D., Molina, H. et al. (2017) Translation from unconventional 5′ start sites drives tumour initiation. Nature, 541, 494-499.
August 11, 2017
resenter: Abeer Ogailan
Aguado, L.C., Schmid, S., May, J., Sabin, L.R., Panis, M., Blanco-Melo, D., Shim, J.V., Sachs, D., Cherry, S., Simon, A.E. et al. (2017) RNase III nucleases from diverse kingdoms serve as antiviral effectors. Nature, 547, 114-117.
August 4, 2017
Presenter: Dylan Girodat
Guixà-González, R., Albasanz, J.L., Rodriguez-Espigares, I., Pastor, M., Sanz, F., Martí-Solano, M., Manna, M., Martinez-Seara, H., Hildebrand, P.W., Martín, M. et al. (2017) Membrane cholesterol access into a G-protein-coupled receptor. Nature Communications 8, 14505.
July 28, 2017
Presenter:Dr. Govardhan Reddy Veerareddygari
Safra, M., Nir, R., Farouq, D., Vainberg Slutskin, I. and Schwartz, S. (2017) TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code. Genome Research, 27, 393-406.
July 21, 2017
Presenter: Tim Vos
Fayet‐Lebaron, E., Atzorn, V., Henry, Y. and Kiss, T. (2009) 18S rRNA processing requires base pairings of snR30 H/ACA snoRNA to eukaryote‐specific 18S sequences. The EMBO Journal28, 1260-1270.
July 14, 2017
Presenter: Hope Vienneau
Chen, Y., Cao, J., Xiong, M., Petersen, Andrew J., Dong, Y., Tao, Y., Huang, Cindy T.-L., Du, Z. and Zhang, S.-C. (2015) Engineering Human Stem Cell Lines with Inducible Gene Knockout using CRISPR/Cas9. Cell Stem Cell, 17, 233-244.
July 7, 2017
Presenter: Dustin Smith
Ostrov, N., Landon, M., Guell, M., Kuznetsov, G., Teramoto, J., Cervantes, N., Zhou, M., Singh, K., Napolitano, M.G., Moosburner, M. et al. (2016) Design, synthesis, and testing toward a 57-codon genome. Science, 353, 819-822.
June 30, 2017
Presenter: Dr. Senthil Kumar Duraikannu Kailasam
Sinturel, F., Gerber, A., Mauvoisin, D., Wang, J., Gatfield, D., Stubblefield, J.J., Green, C.B., Gachon, F. and Schibler, U. (2017) Diurnal Oscillations in Liver Mass and Cell Size Accompany Ribosome Assembly Cycles. Cell169, 651-663.e614.
June 23, 2017
Presenter: Fan Mo
Italia, J.S., Addy, P.S., Wrobel, C.J.J., Crawford, L.A., Lajoie, M.J., Zheng, Y., and Chatterjee, A. (2017). An orthogonalized platform for genetic code expansion in both bacteria and eukaryotes. Nat Chem Biol 13, 446-450.
June 16, 2017
Presenter: Hossein Hosseini
Frieda, K.L., Linton, J.M., Hormoz, S., Choi, J., Chow, K.-H.K., Singer, Z.S., Budde, M.W., Elowitz, M.B., and Cai, L. (2017). Synthetic recording and in situ readout of lineage information in single cells. Nature 541, 107-111.
June 9, 2017
Presenter: Harland Brandon
Fernandez-Rodriguez, J., Moser, F., Song, M., and Voigt, C.A. (2017). Engineering RGB color vision into Escherichia coliNat Chem Biol advance online publication.
June 2, 2017
Presenter: Jeremy Quiroga
Wang, X., Li, S.-H., Zhu, L., Nian, Q.-G., Yuan, S., Gao, Q., Hu, Z., Ye, Q., Li, X.-F., Xie, D.-Y., et al. (2017). Near-atomic structure of Japanese encephalitis virus reveals critical determinants of virulence and stability. Nature Communications 8, 14.
May 26, 2017
Presenter: Zak Stinson
Liscovitch-Brauer, N., Alon, S., Porath, H.T., Elstein, B., Unger, R., Ziv, T., Admon, A., Levanon, E.Y., Rosenthal, J.J.C., and Eisenberg, E. (2017). Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods. Cell 169, 191-202.
May 19, 2017
Presenter: Justin Vigar
Gootenberg, J.S., Abudayyeh, O.O., Lee, J.W., Essletzbichler, P., Dy, A.J., Joung, J., Verdine, V., Donghia, N., Daringer, N.M., Freije, C.A., et al. (2017). Nucleic acid detection with CRISPR-Cas13a/C2c2. Science.
May 12, 2017
Presenter: Luc Roberts
Allen, S.E., Hug, I., Pabian, S., Rzeszutek, I., Hoehener, C., and Nowacki, M. (2017). Circular Concatemers of Ultra-Short DNA Segments Produce Regulatory RNAs. Cell 168, 990-999.
May 5, 2017
Presenter: Taylor Sheahan
van de Waterbeemd, M., Fort, K.L., Boll, D., Reinhardt-Szyba, M., Routh, A., Makarov, A., and Heck, A.J.R. (2017). High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles. Nat Meth 14, 283-286.
April 28, 2017
Presenter: Dora Capatos
Razi, A., Guarné, A., and Ortega, J. (2017). The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly. Proceedings of the National Academy of Sciences 114, E3396-E3403.
April 7, 2017
Presenter: Sarah Schultz
Rubio, M.A.T., Gaston, K.W., McKenney, K.M., Fleming, I.M.C., Paris, Z., Limbach, P.A., and Alfonzo, J.D. (2017). Editing and methylation at a single site by functionally interdependent activities. Nature 542, 494-497.
March 31, 2017
Presenter: Rhys Hakstol
Weinberg, B.H., Pham, N.T.H., Caraballo, L.D., Lozanoski, T., Engel, A., Bhatia, S., and Wong, W.W. (2017). Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells. Nat Biotech advance online publication.
March 24, 2017
Presenter: Cristina Carvalho Barbosa de Souza
Priye, A., Bird, S.W., Light, Y.K., Ball, C.S., Negrete, O.A., and Meagher, R.J. (2017). A smartphone-based diagnostic platform for rapid detection of Zika, chikungunya, and dengue viruses. Scientific Reports 7, 44778.
March 17, 2017
Presenter: Erin Kelly
Chikne, V., Doniger, T., Rajan, K.S., Bartok, O., Eliaz, D., Cohen-Chalamish, S., Tschudi, C., Unger, R., Hashem, Y., Kadener, S., et al. (2016). A pseudouridylation switch in rRNA is implicated in ribosome function during the life cycle of Trypanosoma brucei. Scientific Reports 6, 25296.
March 10, 2017
Presenter: Jalyce Heller
Shalev-Benami, M., Zhang, Y., Matzov, D., Halfon, Y., Zackay, A., Rozenberg, H., Zimmerman, E., Bashan, A., Jaffe, Charles L., Yonath, A., et al. 2.8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania. Cell Reports 16, 288-294.
March 3, 2017
Presenter: Dominic Czekay
Zander, G., Hackmann, A., Bender, L., Becker, D., Lingner, T., Salinas, G., and Krebber, H. (2016). mRNA quality control is bypassed for immediate export of stress-responsive transcripts. Nature 540, 593-596.
February 24, 2017
Presenter: Abeer Ogailan
Bhamla, M.S., Benson, B., Chai, C., Katsikis, G., Johri, A., and Prakash, M. (2017). Hand-powered ultralow-cost paper centrifuge. Nature Biomedical Engineering 1, 0009.
February 17, 2017
Presenter: Davinder Kaur
Yoshida, T., Kakizuka, A., and Imamura, H. (2016) BTeam, a Novel BRET-based Biosensor for the Accurate Quantification of ATP Concentration within Living Cells. Scientific Reports 6, 39618.
February 10, 2017
Presenter: Dr. Raja Kamalampeta
Desai, N., Brown, A., Amunts, A., and Ramakrishnan, V. (2017) The structure of the yeast mitochondrial ribosome. Science 355, 528-531.
January 20, 2017
Presenter: Harland Brandon
Katoh, T., Tajima, K., and Suga, H. (2016) Consecutive elongation of D-amino acids in translation. Cell Chemical Biology 24, 46-54.
January 13, 2017
Presenter: Dylan Girodat
Koenig, P., Lee, C. V., Walters, B. T., Janakiraman, V., Stinson, J., Patapoff, T. W., and Fuh, G. (2017) Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding. Proceedings of the National Academy of Sciences 114, E486-E495.
December 16, 2016
Presenter: Rhys Hakstol
Watters, K. E., Strobel, E. J., Yu, A. M., Lis, J. T., and Lucks, J. B. (2016) Cotranscriptional folding of a riboswitch at nucleotide resolution. Nature Structural & Molecular Biology 23, 1124-1131.
December 2, 2016
Presenter: Dora Capatos
Perli, S. D., Cui, C. H., and Lu, T. K. (2016) Continuous genetic recording with self-targeting CRISPR-Cas in human cells. Science.
November 25, 2016
Presenter: Taylor Sheahan
Quick, J., et al. (2016) Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228-232.
November 18, 2016
Presenter: Sarah Schultz
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., and Kieft, J. S. (2016) Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease. Science 354, 1148-1152.
November 4, 2016
Presenter: Cristina Carvalho Barbosa de Souza
Smirnov, A., Förstner, K. U., Holmqvist, E., Otto, A., Günster, R., Becher, D., Reinhardt, R., and Vogel, J. (2016) Grad-seq guides the discovery of ProQ as a major small RNA-binding protein. Proceedings of the National Academy of Sciences 113, 11591-11596.
October 28, 2016
Presenter: Elijah Dueck
Li, X., Zhu, P., Ma, S., Song, J., Bai, J., Sun, F., and Yi, C. (2015) Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nature Chemical Biology 11, 592-597.
October 21, 2016
Presenter: Jalyce Heller
Zoued, A., Durand, E., Brunet, Y. R., Spinelli, S., Douzi, B., Guzzo, M., Flaugnatti, N., Legrand, P., Journet, L., Fronzes, R., Mignot, T., Cambillau, C., and Cascales, E. (2016) Priming and polymerization of a bacterial contractile tail structure. Nature 531, 59-63.
October 7, 2016
Presenter: Erin Kelly
Dar, D., Shamir, M., Mellin, J. R., Koutero, M., Stern-Ginossar, N., Cossart, P., and Sorek, R. (2016) Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria. Science 352, aad9822.
September 23, 2016
Presenter: Dominic Czekay
Xu, S., Cao, S., Zou, B., Yue, Y., Gu, C., Chen, X., Wang, P., Dong, X., Xiang, Z., Li, K., Zhu, M., Zhao, Q., and Zhou, G. (2016) An alternative novel tool for DNA editing without target sequence limitation: the structure-guided nuclease. Genome Biology 17, 186.
September 16, 2016
Presenter: Luc Roberts
Horning, D. P., and Joyce, G. F. (2016) Amplification of RNA by an RNA polymerase ribozyme. Proceedings of the National Academy of Sciences 113, 9786-9791.
September 9, 2016
Presenter: Dr. Senthil Kumar Duraikannu Kailasam
Aw, J. G. A., Shen, Y., Wilm, A., Sun, M., Lim, X. N., Boon, K.-L., Tapsin, S., Chan, Y.-S., Tan, C.-P., and Sim, A. Y. (2016) In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation. Molecular Cell 62, 603-617.
August 26, 2016
Presenter: Dora Capatos
Reimer, J. M., Aloise, M. N., Harrison, P. M., and Martin Schmeing, T. (2016) Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase. Nature 529, 239-242.
August 12, 2016
Presenter: Rhys Hakstol
Fernandez-Rodriguez, J., and Voigt, C. A. (2016) Post-translational control of genetic circuits using Potyvirus proteases. Nucleic Acids Research 44, 6493-6502.
August 5, 2016
Presenter: Justin Vigar
Din, M. O., Danino, T., Prindle, A., Skalak, M., Selimkhanov, J., Allen, K., Julio, E., Atolia, E., Tsimring, L. S., Bhatia, S. N., and Hasty, J. (2016) Synchronized cycles of bacterial lysis for in vivo delivery. Nature 536, 81-85.
July 29, 2016
Presenter: Dr. Andy Hudson
Bird, J. G., Zhang, Y., Tian, Y., Panova, N., Barvík, I., Greene, L., Liu, M., Buckley, B., Krásný, L., Lee, J. K., Kaplan, C. D., Ebright, R. H., and Nickels, B. E. (2016) The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA. Nature 535, 444-447.
July 22, 2016
Presenter: Dr. Senthil Kumar Duraikannu Kailasam
Wang, C., Han, B., Zhou, R., and Zhuang, X. Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells. Cell 165, 990-1001.
July 15, 2016
Presenter: Jalyce Heller
Oakes, B. L., Nadler, D. C., Flamholz, A., Fellmann, C., Staahl, B. T., Doudna, J. A., and Savage, D. F. (2016) Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Nature Biotechnology 34, 646-651.
July 8, 2016
Presenter: Laura Keffer-Wilkes
Pardee, K., Green, Alexander A., Takahashi, Melissa K., Braff, D., Lambert, G., Lee, Jeong W., Ferrante, T., Ma, D., Donghia, N., Fan, M., Daringer, Nichole M., Bosch, I., Dudley, Dawn M., O’Connor, David H., Gehrke, L., and Collins, James J. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell 165, 1255-1266.
June 24, 2016
Presenter: Dr. Raja Kamalampeta
Wood, T. L., Guha, R., Tang, L., Geitner, M., Kumar, M., and Wood, T. K. (2016) Living biofouling-resistant membranes as a model for the beneficial use of engineered biofilms. Proceedings of the National Academy of Sciences 113, E2802-E2811.
June 17, 2016
Presenter: Harland Brandon
Amiram, M., Haimovich, A. D., Fan, C., Wang, Y.-S., Aerni, H.-R., Ntai, I., Moonan, D. W., Ma, N. J., Rovner, A. J., Hong, S. H., Kelleher, N. L., Goodman, A. L., Jewett, M. C., Soll, D., Rinehart, J., and Isaacs, F. J. (2015) Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nature Biotechnology 33, 1272-1279.
June 10, 2016
Presenter: Taylor Sheahan
Abudayyeh, O. O., Gootenberg, J. S., Konermann, S., Joung, J., Slaymaker, I. M., Cox, D. B. T., Shmakov, S., Makarova, K. S., Semenova, E., Minakhin, L., Severinov, K., Regev, A., Lander, E. S., Koonin, E. V., and Zhang, F. (2016) C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science.
May 27, 2016
Presenter: Evan Caton
Sarkisyan, K. S. et al. (2016) Local fitness landscape of the green fluorescent protein. Nature 533, 397-401.
May 20, 2016
Presenter: Dylan Girodat
Wang, Z., Xu, W., Liu, L., and Zhu, T. F. (2016) A synthetic molecular system capable of mirror-image genetic replication and transcription. Nature Chemistry 8, 698-704.