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2021 NEWS

December 23, 2021 - New publication from the Watts Lab - Suppression of mutant C9orf72 expression by a potent mixed backbone antisense oligonucleotide.  Hélène Tran, Michael P. Moazami, Huiya Yang, Diane McKenna-Yasek, Catherine L. Douthwright, Courtney Pinto, Jake Metterville, Minwook Shin, Nitasha Sanil, Craig Dooley, Ajit Puri, Alexandra Weiss, Nicholas Wightman, Heather Gray-Edwards, Miklos Marosfoi, Robert M. King, Thomas Kenderdine, Daniele Fabris, Robert Bowser, Jonathan K. Watts & Robert H. Brown J.  Nat Med (2021). https://doi.org/10.1038/s41591-021-01557-6.
*Press: MassLIVE, UMass Med News

December 22, 2021 - New publication from the Khvorova Lab - Ferguson CM, Godinho BM, Alterman JF, Coles AH, Hassler M, Echeverria D, Gilbert JW, Knox EG, Caiazzi J, Haraszti RA, King RM, Taghian T, Puri A, Moser RP, Gounis MJ, Aronin N, Gray-Edwards H, Khvorova A. Comparative route of administration studies using therapeutic siRNAs show widespread gene modulation in Dorset sheep. JCI Insight. 2021 Dec 22;6(24):e152203. doi: 10.1172/jci.insight.152203. PMID: 34935646.

December 17, 2021 - New publication from the Watts Lab - Quantification of Antisense Oligonucleotides by Splint Ligation and Quantitative Polymerase Chain Reaction. Shin M, Krishnamurthy PM, Devi G, Watts JK.  Nucleic Acid Ther. 2021 Dec 17. doi: 10.1089/nat.2021.0040. Epub ahead of print. PMID: 34928745.

December 13, 2021 - New publication from the Korostelev Lab - Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP. Carbone CE, Loveland AB, Gamper HB Jr, Hou YM, Demo G, Korostelev AA.  Nat Commun. 2021 Dec 13;12(1):7236. doi: 10.1038/s41467-021-27415-0. PMID: 34903725.

December 15, 2021 - Congratulations to Adam Hedger from the Watts and Schiffer Labs for being awarded a 2022 Predoctoral Fellowship in Drug Discovery for your project titled: "Structure-based design of potent and selective chemically modified oligonucleotide inhibitors for APOBEC3 enzymes".

December 15, 2021 - Congratulations to Samuel Hildebrand from the Khvorova Lab for being awarded an an NIH F31 NRSA fellowship!

December 3, 2021 - New publication from the Grunwald Lab - Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, North AJ, Pimentel JA, Sudar D, Bajcsy P, Brown CM, Corbett AD, Faklaris O, Lacoste J, Laude A, Nelson G, Nitschke R, Farzam F, Smith CS, Grunwald D, Strambio-De-Castillia C.  Nat Methods. 2021 Dec 3. doi: 10.1038/s41592-021-01327-9. Epub ahead of print. PMID: 34862501.

December 3, 2021 - New publication from the Grunwald Lab - Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications.  Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia C.  Nat Methods. 2021 Dec 3. doi: 10.1038/s41592-021-01315-z. Epub ahead of print. PMID: 34862503.

November 26, 2021 - New publication from the Sontheimer Lab - CRISPR-enhanced human adipocyte browning as cell therapy for metabolic disease. Tsagkaraki E, Nicoloro SM, DeSouza T, Solivan-Rivera J, Desai A, Lifshitz LM, Shen Y, Kelly M, Guilherme A, Henriques F, Amrani N, Ibraheim R, Rodriguez TC, Luk K, Maitland S, Friedline RH, Tauer L, Hu X, Kim JK, Wolfe SA, Sontheimer EJ, Corvera S, Czech MP.  Nat Commun. 2021 Nov 26;12(1):6931. doi: 10.1038/s41467-021-27190-y. PMID: 34836963.

November 25, 2021 - New publication from the Khvorova Lab - Structurally constrained phosphonate internucleotide linkage impacts oligonucleotide-enzyme interaction, and modulates siRNA activity and allele specificity. Yamada K, Hildebrand S, Davis SM, Miller R, Conroy F, Sapp E, Caiazzi J, Alterman JF, Roux L, Echeverria D, Hassler MR, Pfister EL, DiFiglia M, Aronin N, Khvorova A. Nucleic Acids Res. 2021 Nov 25:gkab1126. doi: 10.1093/nar/gkab1126. Epub ahead of print. PMID: 34850120.

November 23, 2021 - New publication from the Grigorieff Lab Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation. Himes B, Grigorieff N.  IUCrJ. 2021 Sep 30;8(Pt 6):943-953. doi: 10.1107/S2052252521008538. PMID: 34804546; PMCID: PMC8562658.

November 16, 2021 - Emma RNA Saves the Day coloring & comic book is covered by WCVB Boston Channel 5 news!

November 5, 2021 - New publication from the Sontheimer Lab Orthogonal CRISPR-Cas tools for genome editing, inhibition, and CRISPR recording in zebrafish embryos.   Takasugi PR, Wang S, Truong KT, Drage EP, Kanishka SN, Higbee MA, Bamidele N, Ojelabi O, Sontheimer EJ, Gagnon JA. Genetics. 2021 Nov 4:iyab196. doi: 10.1093/genetics/iyab196. Online ahead of print. PMID: 34735006

November 2, 2021 - New publication from the Sontheimer Lab - Self-inactivating, all-in-one AAV vectors for precision Cas9 genome editing via homology-directed repair in vivo. Ibraheim R, Tai PWL, Mir A, Javeed N, Wang J, Rodríguez TC, Namkung S, Nelson S, Khokhar ES, Mintzer E, Maitland S, Chen Z, Cao Y, Tsagkaraki E, Wolfe SA, Wang D, Pai AA, Xue W, Gao G, Sontheimer EJ. Nat Commun. 2021 Nov 1;12(1):6267. doi: 10.1038/s41467-021-26518-y. PMID: 34725353

October 20, 2021 - New publication from the Mello Lab - 5'-Modifications improve potency and efficacy of DNA donors for precision genome editing. Ghanta KS, Chen Z, Mir A, Dokshin GA, Krishnamurthy PM, Yoon Y, Gallant J, Xu P, Zhang XO, Ozturk AR, Shin M, Idrizi F, Liu P, Gneid H, Edraki A, Lawson ND, Rivera-Pérez JA, Sontheimer E, Watts JK, Mello CC. Elife. 2021 Oct 19;10:e72216. doi: 10.7554/eLife.72216. Online ahead of print. PMID: 34665130

October 14, 2021 - New publication for the Xue Lab - Deletion and replacement of long genomic sequences using prime editing. Tingting Jiang, Xiao-Ou Zhang, Zhiping Weng & Wen Xue  Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-01026-y

September 29, 2021 - New publication from the Zamore LabTerminal modification, sequence, length, and PIWI-protein identity determine piRNA stability. Gainetdinov I, Colpan C, Cecchini K, Arif A, Jouravleva K, Albosta P, Vega-Badillo J, Lee Y, Özata DM, Zamore PD.  Mol Cell. 2021 Sep 29:S1097-2765(21)00746-2. doi: 10.1016/j.molcel.2021.09.012. Epub ahead of print. PMID: 34626567.

September 29, 2021 - New publication from the Korostelev Lab. Diversity and Similarity of Termination and Ribosome Rescue in Bacterial, Mitochondrial, and Cytoplasmic Translation. Korostelev AA. Biochemistry. 2021 Sep;86(9):1107-1121. doi: 10.1134/S0006297921090066.

September 17, 2021 - New publication from the Mello Lab. Caenorhabditis elegans. Ghanta KS, Ishidate T, Mello CC. Microinjection for precision genome editing in . STAR Protoc. 2021 Sep 1;2(3):100748. doi: 10.1016/j.xpro.2021.100748. PMID: 34505086; PMCID: PMC8417391.


September 16, 2021 - New publication from the Mello Lab
Cues from mRNA splicing prevent default Argonaute silencing in C. elegans. Makeyeva YV, Shirayama M, Mello CC.  Dev Cell. 2021 Sep 16:S1534-5807(21)00681-X. doi: 10.1016/j.devcel.2021.08.022. Epub ahead of print. PMID: 34547227.

Sept 6, 2021 - New publication from the Khvorova Lab - AIM2 regulates anti-tumor immunity and is a viable therapeutic target for melanoma. Fukuda K, Okamura K, Riding RL, Xueli Fan X, Khashayar Afshari K, Haddadi NS, McCauley SM, Guney MH, Luban J, Funakoshi T, Yaguchi T, Kawakami Y, Khvorova A, A Fitzgerald KA, Harris JE. J Exp Med. 2021 Sep 6;218(9):e20200962. doi: 10.1084/jem.20200962. Epub 2021 Jul 29. PMID: 34325468

July 30, 2021 - New publication from the Korostelev Lab - Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation.  Demo, G, Gamper, HB, Loveland, AB et al. Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation. Nat Commun 12, 4644 (2021). https://doi.org/10.1038/s41467-021-24911-1

May 21, 2021 - New publication from the Grunwald Lab - REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A. Nat Methods. 2021 May 21. doi: 10.1038/s41592-021-01166-8. Online ahead of print. PMID: 34021280 

May 18, 2021 - New publication from the Mello Lab - PIE-1 SUMOylation promotes germline fates and piRNA-dependent silencing in C. elegans. Kim H, Ding YH, Lu S, Zuo MQ, Tan W, Conte D Jr, Dong MQ, Mello CC. Elife. 2021 May 18;10:e63300. doi: 10.7554/eLife.63300. PMID: 34003111

May 18, 2021 - New publication from the Mello Lab - HDAC1 SUMOylation promotes Argonaute-directed transcriptional silencing in C. elegans. Kim H, Ding YH, Zhang G, Yan YH, Conte D Jr, Dong MQ, Mello CC. Elife. 2021 May 18;10:e63299. doi: 10.7554/eLife.63299. PMID: 34003109

May 1, 2021 - Craig Mello, PhD was featured on the Nature Magazine First Rounders podcast.  

April 21, 2021, Congratulations to the RTI's Nikolaus Grigorieff for his election into The National Academy of Sciences!
When Niko is not using his gadget of choice, a 300,000 volt electron microscope, he is taking gorgeous images of the night sky.  Well deserved, Niko!

April 21, 2021 - New publication from the Grigorieff Lab. Locating Macromolecular Assemblies in Cells by 2D Template Matching with cisTEM.  Bronwyn A. Lucas, Benjamin A. Himes, Liang Xue, Timothy Grant, Julia Mahamid, Nikolaus Grigorieff  bioRxiv 2021.04.20.440648; doi: https://doi.org/10.1101/2021.04.20.440648

April 9, 2021 - New publication from the Xue Lab - Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice.  Liu, P., Liang, SQ., Zheng, C. et al. Nat Commun 122121 (2021). https://doi.org/10.1038/s41467-021-22295-w

April 9, 2021 - New publication from the Sontheimer Lab - The NIH Somatic Cell Genome Editing program. Saha K, Sontheimer EJ, Brooks PJ, Dwinell MR, Gersbach CA, Liu DR, Murray SA, Tsai SQ, Wilson RC, Anderson DG, Asokan A, Banfield JF, Bankiewicz KS, Bao G, Bulte JWM, Bursac N, Campbell JM, Carlson DF, Chaikof EL, Chen ZY, Cheng RH, Clark KJ, Curiel DT, Dahlman JE, Deverman BE, Dickinson ME, Doudna JA, Ekker SC, Emborg ME, Feng G, Freedman BS, Gamm DM, Gao G, Ghiran IC, Glazer PM, Gong S, Heaney JD, Hennebold JD, Hinson JT, Khvorova A, Kiani S, Lagor WR, Lam KS, Leong KW, Levine JE, Lewis JA, Lutz CM, Ly DH, Maragh S, McCray PB Jr, McDevitt TC, Mirochnitchenko O, Morizane R, Murthy N, Prather RS, Ronald JA, Roy S, Roy S, Sabbisetti V, Saltzman WM, Santangelo PJ, Segal DJ, Shimoyama M, Skala MC, Tarantal AF, Tilton JC, Truskey GA, Vandsburger M, Watts JK, Wells KD, Wolfe SA, Xu Q, Xue W, Yi G, Zhou J; SCGE Consortium. Nature. 2021 Apr;592(7853):195-204. doi: 10.1038/s41586-021-03191-1. Epub 2021 Apr 7. PMID: 33828315 Review.

April 7, 2021 - Erik Sontheimer co-leading efforts to develop gene editing toolkit by NIH Somatic Cell Genome Editing Consortium.

April 6, 2021 - New publication from the Khvorova Lab. Kinetics of HTT lowering in brain of YAC 128 mice following single and repetitive intranasal dosing of siRNA packaged in chitosan-based nanoparticle. Sava V, Fihurka O, Khvorova A, Sanchez-Ramos J. J Drug Deliv Sci Technol. 2021 Jun;63:102517. doi: 10.1016/j.jddst.2021.102517. Epub 2021 Apr 

March 24, 2021 New publication from the Watts Lab. Hybrid Aptamer-Molecularly Imprinted Polymer (aptaMIP) Nanoparticles from Protein Recognition-A Trypsin Model. Sullivan MV, Clay O, Moazami MP, Watts JK, Turner NW. Macromol Biosci. 2021 Mar 24:e2100002. doi: 10.1002/mabi.202100002. Online ahead of print. PMID: 33760365

March 10, 2021 Congratulations, Khvorova lab! The Khvorova lab’s 2019 publication: ‘A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system’ was selected as one of Nature Biotech’s 25 landmark papers of the last 25 years!

March 3, 2021 New publication from the Mello lab. Germ granule dysfunction is a hallmark and mirror of Piwi mutant sterility.  Spichal M, Heestand B, Billmyre KK, Frenk S, Mello CC, Ahmed S. Nat Commun. 2021 Mar 3;12(1):1420. doi: 10.1038/s41467-021-21635-0. PMID: 33658512

February 19, 2021 Dr. Craig Mello was featured on WBZ Channel 4 Boston Next  - 
Local Nobel Prize Winner Hopes COVID Vaccine RNA Technology Can Fight Other Diseases

January 30, 2021 Please join us in congratulating former RTI faculty member Melissa J. Moore for being selected as the recipient of the 2021 Lifetime Achievement in Science Award from the RNA Society.  Melissa J. Moore is well known for her mechanistic and structural analyses of spliceosomes and mRNPs, co-discovery of the exon junction complex (EJC), and studies of intracellular RNA transport and quality control pathways. She was also instrumental in developing multiple enabling technologies for the field, including methods for introducing site-specific modifications into long RNA molecules and single molecule methods for observing the dynamics of RNP complex assembly and disassembly. Following a nineteen-year run as an HHMI Investigator (1997-2016), Melissa resigned from HHMI to become the Chief Scientific Officer of Platform Research at Moderna Therapeutics, where she leads the translation of RNA biology to drug development. By designing new strategies to increase the functional output and longevity of therapeutic mRNAs, Melissa´s insights were key for the success of the Covid-19 vaccine. One overarching piece of advice Melissa offers women looking to advance their career: No fear. “Fear holds you back and prevents you from taking the types of risks that can pay off with huge rewards”, she said. ​ 

January 22, 2021 New publication from the Zamore Lab. Defining the functions of PIWI-interacting RNAsWu PH, Zamore PD. Nat Rev Mol Cell Biol. 2021 Jan 22. doi: 10.1038/s41580-021-00336-y. Online ahead of print. PMID: 33483697 No abstract available.

January 21, 2021 New publication from the Zamore Lab. To Degrade a MicroRNA, Destroy Its Argonaute Protein. Pei-Hsuan We, Phillip D. Zamore, Molecular Cell, Col 81 Iss 2, 21 Jan 2021, Pages 223-225. https://doi.org/10.1016/j.molcel.2020.12.043

January 4, 2021 New publication from the Zamore Lab. Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes. Tianxiong Yu, Kaili Fan, Deniz M. Özata Gen Zhang, Yu Fu, William E. Theurkauf, Phillip D. Zamore & Zhiping Weng NATURE COMMUNICATIONS | (2021)12:73 | https://doi.org/10.1038/s41467-020-20345-3