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Publications

January 2023

Keeping development on time: Insights into post-transcriptional mechanisms driving oscillatory gene expression during vertebrate segmentation.
Blatnik MC, Gallagher TL, Amacher SL.
Wiley Interdiscip Rev RNA. 2023 Jan;14(1):e1751. 
PMID: 35851751

An enhancer-based gene-therapy strategy for spatiotemporal control of cargoes during tissue repair.
Yan R, Cigliola V, Oonk KA, Petrover Z, DeLuca S, Wolfson DW, Vekstein A, Mendiola MA, Devlin G, Bishawi M, Gemberling MP, Sinha T, Sargent MA, York AJ, Shakked A, DeBenedittis P, Wendell DC, Ou J, Kang J, Goldman JA, Baht GS, Karra R, Williams AR, Bowles DE, Asokan A, Tzahor E, Gersbach CA, Molkentin JD, Bursac N, Black BL, Poss KD.
Cell Stem Cell. 2023 Jan 5;30(1):96-111.e6. 
PMID: 36516837

Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2.
Qu P, Evans JP, Faraone JN, Zheng YM, Carlin C, Anghelina M, Stevens P, Fernandez S, Jones D, Lozanski G, Panchal A, Saif LJ, Oltz EM, Xu K, Gumina RJ, Liu SL.
Cell Host Microbe. 2023 Jan 11;31(1):9-17.e3. 
PMID: 36476380

The RNA virosphere: How big and diverse is it?
Dominguez-Huerta G, Wainaina JM, Zayed AA, Culley AI, Kuhn JH, Sullivan MB.
Environ Microbiol. 2023 Jan;25(1):209-215. 
PMID: 36511833

Novel integrative elements and genomic plasticity in ocean ecosystems.
Hackl T, Laurenceau R, Ankenbrand MJ, Bliem C, Cariani Z, Thomas E, Dooley KD, Arellano AA, Hogle SL, Berube P, Leventhal GE, Luo E, Eppley JM, Zayed AA, Beaulaurier J, Stepanauskas R, Sullivan MB, DeLong EF, Biller SJ, Chisholm SW.
Cell. 2023 Jan 5;186(1):47-62.e16. 
PMID: 36608657

Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee.
Turner D, Shkoporov AN, Lood C, Millard AD, Dutilh BE, Alfenas-Zerbini P, van Zyl LJ, Aziz RK, Oksanen HM, Poranen MM, Kropinski AM, Barylski J, Brister JR, Chanisvili N, Edwards RA, Enault F, Gillis A, Knezevic P, Krupovic M, Kurtböke I, Kushkina A, Lavigne R, Lehman S, Lobocka M, Moraru C, Moreno Switt A, Morozova V, Nakavuma J, Reyes Muñoz A, Rūmnieks J, Sarkar BL, Sullivan MB, Uchiyama J, Wittmann J, Yigang T, Adriaenssens EM.
Arch Virol. 2023 Jan 23;168(2):74. 
PMID: 36683075

A p53-TLR3 axis ameliorates pulmonary hypertension by inducing BMPR2 via IRF3.
Bhagwani AR, Ali M, Piper B, Liu M, Hudson J, Kelly N, Bogamuwa S, Yang H, Londino JD, Bednash JS, Farkas D, Mallampalli RK, Nicolls MR, Ryan JJ, Thompson AAR, Chan SY, Gomez D, Goncharova EA, Farkas L.
iScience. 2023 Jan 5;26(2):105935. 
PMID: 36685041
 

February 2023

Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae.
McNutt ZA, Roy B, Gemler BT, Shatoff EA, Moon KM, Foster LJ, Bundschuh R, Fredrick K.
Nucleic Acids Res. 2023 Feb 28;51(4):1927-1942. 
PMID: 36727479

CRISPR-Cas has a new juggling act: interplay between nuclease and protease.
Rish AD, Fu TM.
Nat Struct Mol Biol. 2023 Feb;30(2):126-128. 
PMID: 36721057

Identification of Small-Molecule Inhibitors of the Salmonella FraB Deglycase Using a Live-Cell Assay.
Sabag-Daigle A, Boulanger EF, Thirugnanasambantham P, Law JD, Bogard AJ, Behrman EJ, Gopalan V, Ahmer BMM.
Microbiol Spectr. 2023 Feb 21;11(2):e0460622. 
PMID: 36809033

Nipple fluid for breast cancer diagnosis using the nanopore of Phi29 DNA-packaging motor.
Zhang L, Burns N, Ji Z, Sun S, Deutscher SL, Carson WE 3rd, Guo P.
Nanomedicine. 2023 Feb;48:102642. 
PMID: 36581256

CuATSM effectively ameliorates ALS patient astrocyte-mediated motor neuron toxicity in human in vitro models of amyotrophic lateral sclerosis.
Dennys CN, Roussel F, Rodrigo R, Zhang X, Sierra Delgado A, Hartlaub A, Saelim-Ector A, Ray W, Heintzman S, Fox A, Kolb SJ, Beckman J, Franco MC, Meyer K.
Glia. 2023 Feb;71(2):350-365. 
PMID: 36213964

Determinants and Mechanisms of the Low Fusogenicity and High Dependence on Endosomal Entry of Omicron Subvariants.
Qu P, Evans JP, Kurhade C, Zeng C, Zheng YM, Xu K, Shi PY, Xie X, Liu SL.m
Bio. 2023 Feb 28;14(1):e0317622. 
PMID: 36625591

HIV-1 Gag Binds the Multi-Aminoacyl-tRNA Synthetase Complex via the EPRS Subunit.
Jin D, Zhu Y, Schubert HL, Goff SP, Musier-Forsyth K.
Viruses. 2023 Feb 8;15(2):474. 
PMID: 36851687

Four principles to establish a universal virus taxonomy.
Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N.
PLoS Biol. 2023 Feb 13;21(2):e3001922. 
PMID: 36780432

MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data.
Ayala-Ortiz C, Graf-Grachet N, Freire-Zapata V, Fudyma J, Hildebrand G, AminiTabrizi R, Howard-Varona C, Corilo YE, Hess N, Duhaime MB, Sullivan MB, Tfaily MM.
Microbiome. 2023 Feb 17;11(1):28. 
PMID: 36803638

Dissecting the Thermodynamics of ATP Binding to GroEL One Nucleotide at a Time.
Walker T, Sun HM, Gunnels T, Wysocki V, Laganowsky A, Rye H, Russell D.
ACS Cent Sci. 2023 Feb 20;9(3):466-475. 
PMID: 36968544

Single-chromosome dynamics reveals locus-dependent dynamics and chromosome territory orientation.
Chung YC, Bisht M, Thuma J, Tu LC.
J Cell Sci. 2023 Feb 15;136(4):jcs260137. 
PMID: 36718642
 

March 2023

Demonstrating the utility of sugar-phosphate phosphatases in coupled enzyme assays: galactose-1-phosphate uridylyltransferase as proof-of-concept.
Thirugnanasambantham P, Bashian E, Zaleski R, Gopalan V.
Glycobiology. 2023 Mar 6;33(2):95-98. 
PMID: 36585843

Psychometric evaluation of modified spinal muscular atrophy functional rating scale (SMAFRS) in adult patients using Rasch analysis.
Sadjadi R, Kelly K, Glanzman AM, Montes J, Linsenmayer M, Tellez M, Bartlett A, Heintzman S, Kolb SJ, Arnold WD, El-Sheikh B.
Muscle Nerve. 2023 Mar;67(3):239-243. 
PMID: 36605016

Selective suppression of de novo SARS-CoV-2 vaccine antibody responses in patients with cancer on B cell-targeted therapy.
Azar JH, Evans JP, Sikorski MH, Chakravarthy KB, McKenney S, Carmody I, Zeng C, Teodorescu R, Song NJ, Hamon JL, Bucci D, Velegraki M, Bolyard C, Weller KP, Reisinger SA, Bhat SA, Maddocks KJ, Denlinger N, Epperla N, Gumina RJ, Vlasova AN, Oltz EM, Saif LJ, Chung D, Woyach JA, Shields PG, Liu SL, Li Z, Rubinstein MP.
JCI Insight. 2023 Mar 22;8(6):e163434. 
PMID: 36749632

Aminoacylation-defective bi-allelic mutations in human EPRS1 associated with psychomotor developmental delay, epilepsy, and deafness.
Jin D, Wek SA, Cordova RA, Wek RC, Lacombe D, Michaud V, Musier-Forsyth K.
Clin Genet. 2023 Mar;103(3):358-363. 
PMID: 36411955

Advances and challenges in CRISPR-based real-time imaging of dynamic genome organization.
Thuma J, Chung YC, Tu LC.
Front Mol Biosci. 2023 Mar 31;10:1173545. 
PMID: 37065447
 

April 2023

Base editing rescue of spinal muscular atrophy in cells and in mice.
Arbab M, Matuszek Z, Kray KM, Du A, Newby GA, Blatnik AJ, Raguram A, Richter MF, Zhao KT, Levy JM, Shen MW, Arnold WD, Wang D, Xie J, Gao G, Burghes AHM, Liu DR.
Science. 2023 Apr 21;380(6642):eadg6518. 
PMID: 36996170 

NaV1.6 dysregulation within myocardial T-tubules by D96V calmodulin enhances proarrhythmic sodium and calcium mishandling.
Tarasov M, Struckman HL, Olgar Y, Miller A, Demirtas M, Bogdanov V, Terentyeva R, Soltisz AM, Meng X, Min D, Sakuta G, Dunlap I, Duran AD, Foster MP, Davis JP, Terentyev D, Györke S, Veeraraghavan R, Radwański PB.
J Clin Invest. 2023 Apr 3;133(7):e152071. 
PMID: 36821382

Targeted delivery of RNAi to cancer cells using RNA-ligand displaying exosome.
Uddin N, Binzel DW, Shu D, Fu TM, Guo P.
Acta Pharm Sin B. 2023 Apr;13(4):1383-1399. 
PMID: 37139430

STING Agonist-Derived LNP-mRNA Vaccine Enhances Protective Immunity Against SARS-CoV-2.
Zhang Y, Yan J, Hou X, Wang C, Kang DD, Xue Y, Du S, Deng B, McComb DW, Liu SL, Zhong Y, Dong Y.
Nano Lett. 2023 Apr 12;23(7):2593-2600. 
PMID: 36942873

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase.
Shaffer M, Borton MA, Bolduc B, Faria JP, Flynn RM, Ghadermazi P, Edirisinghe JN, Wood-Charlson EM, Miller CS, Chan SHJ, Sullivan MB, Henry CS, Wrighton KC.
Bioinformatics. 2023 Apr 3;39(4):btad110. 
PMID: 36857575

DJ-1 Molecular Chaperone Activity Depresses Tau Aggregation Propensity through Interaction with Monomers.
Jimenez-Harrison D, Huseby CJ, Hoffman CN, Sher S, Snyder D, Seal B, Yuan C, Fu H, Wysocki V, Giorgini F, Kuret J.
Biochemistry. 2023 Mar 7;62(5):976-988. 
PMID: 36813261
 

May 2023

Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA.
Liang Y, Willey S, Chung YC, Lo YM, Miao S, Rundell S, Tu LC, Bong D.
Nat Commun. 2023 May 24;14(1):2987. 
PMID: 37225690

Structural basis of tRNAPro acceptor stem recognition by a bacterial trans-editing domain.
Ma X, Bakhtina M, Shulgina I, Cantara WA, Kuzmishin Nagy AB, Goto Y, Suga H, Foster MP, Musier-Forsyth K.
Nucleic Acids Res. 2023 May 8;51(8):3988-3999. 
PMID: 36951109

Structural basis for the self-recognition of sDSCAM in Chelicerata.
Cheng J, Yu Y, Wang X, Zheng X, Liu T, Hu D, Jin Y, Lai Y, Fu TM, Chen Q.
Nat Commun. 2023 May 2;14(1):2522. 
PMID: 37130844

An outreach activity to enhance biochemistry pedagogy.
Roth KS, Bannerman T, Gopalan V.
Trends Biochem Sci. 2023 May;48(5):410-413. 
PMID: 36925316

Revolving hexameric ATPases as asymmetric motors to translocate double-stranded DNA genome along one strand.
Bohmer M, Bhullar AS, Weitao T, Zhang L, Lee JH, Guo P.
iScience. 2023 May 19;26(6):106922. 
PMID: 37305704

In Vivo Cross-Linking and Co-Immunoprecipitation Procedure to Analyze Nuclear tRNA Export Complexes in Yeast Cells.
Chatterjee K, Hopper AK.
Methods Mol Biol. 2023;2666:115-136. 
PMID: 37166661

A Simple Method for the Detection of Wybutosine-Modified tRNAPheGAA as a Readout of Retrograde tRNA Nuclear Import and Re-export: HCl/Aniline Cleavage and Nonradioactive Northern Hybridization.
Nostramo RT, Hopper AK.
Methods Mol Biol. 2023;2666:1-14. 
PMID: 37166653

Neutralization escape of Omicron XBB, BR.2, and BA.2.3.20 subvariants.
Faraone JN, Qu P, Evans JP, Zheng YM, Carlin C, Anghelina M, Stevens P, Fernandez S, Jones D, Lozanski G, Panchal A, Saif LJ, Oltz EM, Gumina RJ, Liu SL.
Cell Rep Med. 2023 May 16;4(5):101049. 
PMID: 37148877

Prime-Pull Immunization of Mice with a BcfA-Adjuvanted Vaccine Elicits Sustained Mucosal Immunity That Prevents SARS-CoV-2 Infection and Pathology.
Shamseldin MM, Kenney A, Zani A, Evans JP, Zeng C, Read KA, Hall JM, Chaiwatpongsakorn S, Mahesh KC, Lu M, Eltobgy M, Denz P, Deora R, Li J, Peeples ME, Oestreich KJ, Liu SL, Corps KN, Yount JS, Dubey P.
J Immunol. 2023 May 1;210(9):1257-1271. 
PMID: 36881867

Slit2/Robo1 signaling inhibits small-cell lung cancer by targeting β-catenin signaling in tumor cells and macrophages.
Ahirwar DK, Peng B, Charan M, Misri S, Mishra S, Kaul K, Sassi S, Gadepalli VS, Siddiqui J, Miles WO, Ganju RK.
Mol Oncol. 2023 May;17(5):839-856. 
PMID: 35838343

Structural basis of tRNAPro acceptor stem recognition by a bacterial trans-editing domain.
Ma X, Bakhtina M, Shulgina I, Cantara WA, Kuzmishin Nagy AB, Goto Y, Suga H, Foster MP, Musier-Forsyth K.
Nucleic Acids Res. 2023 May 8;51(8):3988-3999. 
PMID: 36951109

Probing differences among Aβ oligomers with two triangular trimers derived from Aβ.
Kreutzer AG, Guaglianone G, Yoo S, Parrocha CMT, Ruttenberg SM, Malonis RJ, Tong K, Lin YF, Nguyen JT, Howitz WJ, Diab MN, Hamza IL, Lai JR, Wysocki VH, Nowick JS.
Proc Natl Acad Sci U S A. 2023 May 30;120(22):e2219216120. 
PMID: 37216514

Inhibiting the Deubiquitinase UCHL1 Reduces SARS-CoV-2 Viral Uptake by ACE2.
Bednash JS, Johns F, Farkas D, Elhance A, Adair J, Cress K, Yount JS, Kenney AD, Londino JD, Mallampalli RK.
Am J Respir Cell Mol Biol. 2023 May;68(5):566-576. 
PMID: 36730646
 

June 2023

Roles of the leader-trailer helix and antitermination complex in biogenesis of the 30S ribosomal subunit.
Warner BR, Bundschuh R, Fredrick K.
Nucleic Acids Res. 2023 Jun 9;51(10):5242-5254. 
PMID: 37102690

Molecular mechanisms of Holliday junction branch migration catalyzed by an asymmetric RuvB hexamer.
Rish AD, Shen Z, Chen Z, Zhang N, Zheng Q, Fu TM.
Nat Commun. 2023 Jun 15;14(1):3549. 
PMID: 37322069

Ligand-displaying-exosomes using RNA nanotechnology for targeted delivery of multi-specific drugs for liver cancer regression.
Ellipilli S, Wang H, Binzel DW, Shu D, Guo P.
Nanomedicine. 2023 Jun;50:102667. 
PMID: 36948369

Captured: the elusive eukaryotic tRNA splicing enzyme.
Hopper AK, Zhang J.
Nat Struct Mol Biol. 2023 Jun;30(6):711-713. 
PMID: 37231155

Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay.
Russell PJ, Slivka JA, Boyle EP, Burghes AHM, Kearse MG.
RNA. 2023 Jun;29(6):735-744. 
PMID: 36878710

Evaluation of the orally bioavailable 4-phenylbutyrate-tethered trichostatin A analogue AR42 in models of spinal muscular atrophy.
Lumpkin CJ, Harris AW, Connell AJ, Kirk RW, Whiting JA, Saieva L, Pellizzoni L, Burghes AHM, Butchbach MER.
Sci Rep. 2023 Jun 26;13(1):10374. 
PMID: 37365234

Impaired motor unit recovery and maintenance in a knock-in mouse model of ALS-associated Kif5a variant.
Rich KA, Pino MG, Yalvac ME, Fox A, Harris H, Balch MHH, Arnold WD, Kolb SJ.
Neurobiol Dis. 2023 Jun 15;182:106148. 
PMID: 37164288

Discovery of novel papain-like protease inhibitors for potential treatment of COVID-19.
Hersi F, Sebastian A, Tarazi H, Srinivasulu V, Mostafa A, Allayeh AK, Zeng C, Hachim IY, Liu SL, Abu-Yousef IA, Majdalawieh AF, Zaher DM, Omar HA, Al-Tel TH.
Eur J Med Chem. 2023 Jun 5;254:115380. 
PMID: 37075625

HIV-1 usurps transcription start site heterogeneity of host RNA polymerase II to maximize replication fitness.
Nikolaitchik OA, Islam S, Kitzrow JP, Duchon A, Cheng Z, Liu Y, Rawson JMO, Shao W, Nikolaitchik M, Kearney MF, Maldarelli F, Musier-Forsyth K, Pathak VK, Hu WS.
Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2305103120. 
PMID: 37252967

Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems.
Lombard F, Bourdin G, Pesant S, Agostini S, Baudena A, Boissin E, Cassar N, Clampitt M, Conan P, Da Silva O, Dimier C, Douville E, Elineau A, Fin J, Flores JM, Ghiglione JF, Hume BCC, Jalabert L, John SG, Kelly RL, Koren I, Lin Y, Marie D, McMinds R, Mériguet Z, Metzl N, Paz-García DA, Pedrotti ML, Poulain J, Pujo-Pay M, Ras J, Reverdin G, Romac S, Rouan A, Röttinger E, Vardi A, Voolstra CR, Moulin C, Iwankow G, Banaigs B, Bowler C, de Vargas C, Forcioli D, Furla P, Galand PE, Gilson E, Reynaud S, Sunagawa S, Sullivan MB, Thomas OP, Troublé R, Thurber RV, Wincker P, Zoccola D, Allemand D, Planes S, Boss E, Gorsky G.
Sci Data. 2023 Jun 1;10(1):324. 
PMID: 37264023

Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean.
Armstrong EJ, Lê-Hoang J, Carradec Q, Aury JM, Noel B, Hume BCC, Voolstra CR, Poulain J, Belser C, Paz-García DA, Cruaud C, Labadie K, Da Silva C, Moulin C, Boissin E, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Zoccola D, Planes S, Allemand D, Wincker P.
Nat Commun. 2023 Jun 1;14(1):3056. 
PMID: 37264036

Pervasive tandem duplications and convergent evolution shape coral genomes.
Noel B, Denoeud F, Rouan A, Buitrago-López C, Capasso L, Poulain J, Boissin E, Pousse M, Da Silva C, Couloux A, Armstrong E, Carradec Q, Cruaud C, Labadie K, Lê-Hoang J, Tambutté S, Barbe V, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Allemand D, Planes S, Gilson E, Zoccola D, Wincker P, Voolstra CR, Aury JM.
Genome Biol. 2023 Jun 1;24(1):123. 
PMID: 37264421

 

July 2023

Insights into the catalytic mechanism of a bacterial deglycase essential for utilization of fructose-lysine.
Kovvali S, Gao Y, Cool A, Lindert S, Wysocki VH, Bell CE, Gopalan V.
Protein Sci. 2023 Jul;32(7):e4695. 
PMID: 37289023

Targeting oncogenic KRAS in non-small cell lung cancer with EGFR aptamer-conjugated multifunctional RNA nanoparticles.
Yang L, Li Z, Binzel DW, Guo P, Williams TM.
Mol Ther Nucleic Acids. 2023 Jul 28;33:559-571. 
PMID: 37637206

Tumor targeting and therapeutic assessments of RNA nanoparticles carrying α9-nAChR aptamer and anti-miR-21 in triple-negative breast cancers.
Liao YC, Cheng TC, Tu SH, Chang J, Guo P, Chen LC, Ho YS.
Mol Ther Nucleic Acids. 2023 Jul 15;33:351-366. 
PMID: 37547295

The life and times of a tRNA.
Phizicky EM, Hopper AK.
RNA. 2023 Jul;29(7):898-957. 
PMID: 37055150

SARS-CoV-2 Serological Investigation of White-Tailed Deer in Northeastern Ohio.
Boley PA, Dennis PM, Faraone JN, Xu J, Liu M, Niu X, Gibson S, Hale V, Wang Q, Liu SL, Saif LJ, Kenney SP.
Viruses. 2023 Jul 22;15(7):1603. 
PMID: 37515289

Molecular Genetics of Retrovirus Replication.
Levin JG, Musier-Forsyth K, Rein A.
Viruses. 2023 Jul 14;15(7):1549. 
PMID: 37515235 

Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification.
Adriaenssens EM, Roux S, Brister JR, Karsch-Mizrachi I, Kuhn JH, Varsani A, Yigang T, Reyes A, Lood C, Lefkowitz EJ, Sullivan MB, Edwards RA, Simmonds P, Rubino L, Sabanadzovic S, Krupovic M, Dutilh BE.
Nat Biotechnol. 2023 Jul;41(7):898-902. 
PMID: 37430074
 

Aug 2023

Making nucleic acid structures and schematics.
Lai LB, Gopalan V, Jansson MD, Chen Q, Zhang X, Wolfram-Schauerte M, Höfer K.
Trends Biochem Sci. 2023 Aug;48(8):655-658. 
PMID: 37451237

In vitro Analysis of Stalled Ribosomes Using Puromycin Incorporation.
Scarpitti MR, Kearse MG.
Bio Protoc. 2023 Aug 20;13(16):e4744. 
PMID: 37638299

The Pleiotropic Effects of YBX1 on HTLV-1 Transcription.
Smith S, Seth J, Midkiff A, Stahl R, Syu YC, Shkriabai N, Kvaratskhelia M, Musier-Forsyth K, Jain P, Green PL, Panfil AR.
Int J Mol Sci. 2023 Aug 23;24(17):13119. 
PMID: 37685922

HSP90 in morphogenesis: taking the heat and keeping the dark.
Somers DE.
New Phytol. 2023 Aug;239(4):1157-1159. 
PMID: 37292049

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines.
Zhong ZP, Vik D, Rapp JZ, Zablocki O, Maughan H, Temperton B, Deming JW, Sullivan MB.
Microbiome. 2023 Aug 7;11(1):174. 
PMID: 37550784

Ocean-wide comparisons of mesopelagic planktonic community structures.
Rigonato J, Budinich M, Murillo AA, Brandão MC, Pierella Karlusich JJ, Soviadan YD, Gregory AC, Endo H, Kokoszka F, Vik D, Henry N, Frémont P, Labadie K, Zayed AA, Dimier C, Picheral M, Searson S, Poulain J, Kandels S, Pesant S, Karsenti E; Tara Oceans coordinators; Bork P, Bowler C, de Vargas C, Eveillard D, Gehlen M, Iudicone D, Lombard F, Ogata H, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Chaffron S, Jaillon O.
ISME Commun. 2023 Aug 18;3(1):83. 
PMID: 37596349 

MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets.
Vik D, Bolduc B, Roux S, Sun CL, Pratama AA, Krupovic M, Sullivan MB.
ISME Commun. 2023 Aug 24;3(1):87. 
PMID: 37620369

Interrogating the viral dark matter of the rumen ecosystem with a global virome database.
Yan M, Pratama AA, Somasundaram S, Li Z, Jiang Y, Sullivan MB, Yu Z.
Nat Commun. 2023 Aug 29;14(1):5254. 
PMID: 37644066
 

Sept 2023

Adeno-associated virus serotype 9 antibody seroprevalence for patients in the United States with spinal muscular atrophy.
Day JW, Mendell JR, Burghes AHM, van Olden RW, Adhikary RR, Dilly KW.
Mol Ther Methods Clin Dev. 2023 Sep 20;31:101117. 
PMID: 37822718

Oligomerization-mediated activation of a short prokaryotic Argonaute.
Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi KFu TM.
Nature. 2023 Sep;621(7977):154-161. 
PMID: 37494956

A novel auxin-inducible degron system for rapid, cell cycle-specific targeted proteolysis.
Capece M, Tessari A, Mills J, Vinciguerra GLR, Louke D, Lin C, McElwain BK, Miles WO, Coppola V, Davies AE, Palmieri D, Croce CM.
Cell Death Differ. 2023 Sep;30(9):2078-2091. 
PMID: 37537305

Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation.
Sanz-Sáez I, Sánchez P, Salazar G, Sunagawa S, de Vargas C, Bowler C, Sullivan MB, Wincker P, Karsenti E, Pedrós-Alió C, Agustí S, Gojobori T, Duarte CM, Gasol JM, Sánchez O, Acinas SG.
ISME Commun. 2023 Sep 2;3(1):92. 
PMID: 37660234

Four additional natural 7-deazaguanine derivatives in phages and how to make them.
Cui L, Balamkundu S, Liu CF, Ye H, Hourihan J, Rausch A, Hauß C, Nilsson E, Hoetzinger M, Holmfeldt K, Zhang W, Martinez-Alvarez L, Peng X, Tremblay D, Moinau S, Solonenko N, Sullivan MB, Lee YJ, Mulholland A, Weigele PR, de Crécy-Lagard V, Dedon PC, Hutinet G.
Nucleic Acids Res. 2023 Sep 22;51(17):9214-9226. 
PMID: 37572349

Predicting global distributions of eukaryotic plankton communities from satellite data.
Kaneko H, Endo H, Henry N, Berney C, Mahé F, Poulain J, Labadie K, Beluche O, El Hourany R; Tara Oceans Coordinators; Chaffron S, Wincker P, Nakamura R, Karp-Boss L, Boss E, Bowler C, de Vargas C, Tomii K, Ogata H.ISME Commun. 2023 Sep 22;3(1):101. 
  PMID: 37740029

C. elegans germ granules sculpt both germline and somatic RNAome.
Price IF, Wagner JA, Pastore B, Hertz HL, Tang W.
Nat Commun. 2023 Sep 25;14(1):5965. 
PMID: 37749091

Combining Surface-Induced Dissociation and Charge Detection Mass Spectrometry to Reveal the Native Topology of Heterogeneous Protein Complexes.
Du C, Cleary SP, Kostelic MM, Jones BJ, Kafader JO, Wysocki VH.
Anal Chem. 2023 Sep 19;95(37):13889-13896. 
PMID: 37672632
 

Oct 2023

TMEM63 proteins function as monomeric high-threshold mechanosensitive ion channels.
Zheng W, Rawson S, Shen Z, Tamilselvan E, Smith HE, Halford J, Shen C, Murthy SE, Ulbrich MH, Sotomayor M, Fu TM, Holt JR.
Neuron. 2023 Oct 18;111(20):3195-3210.e7. 
PMID: 37543036

The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration.
Rao A, Lyu B, Jahan I, Lubertozzi A, Zhou G, Tedeschi F, Jankowsky E, Kang J, Carstens B, Poss KD, Baskin K, Goldman JA.
Development. 2023 Oct 15;150(20):dev201376. 
PMID: 37306388

Transfer RNAs: A treasure trove that keeps on giving.
Gopalan V, Musier-Forsyth K.
J Biol Chem. 2023 Oct;299(10):105170. 
PMID: 37769358 

Increased levels of eIF2A inhibit translation by sequestering 40S ribosomal subunits.
Grove DJ, Levine DJ, Kearse MG.
Nucleic Acids Res. 2023 Oct 13;51(18):9983-10000. 
PMID: 37602404

A next-generation intranasal trivalent MMS vaccine induces durable and broad protection against SARS-CoV-2 variants of concern.
Xu J, Zhang Y, Qu P, Shamseldin MM, Yoo SJ, Misny J, Thongpan I, Kc M, Hall JM, Evans JP, Eltobgy M, Lu M, Ye C, Chamblee M, Liang X, Martinez-Sobrido L, Amer AO, Yount JS, Boyaka PN, Peeples ME, Liu SL, Dubey P, Li J.
Proc Natl Acad Sci U S A. 2023 Oct 10;120(41):e2220403120. 
PMID: 37796985

Oxidized and Reduced Dimeric Protein Complexes Illustrate Contrasting CID and SID Charge Partitioning.
Jia M, Song Y, Du C, Wysocki VH.
J Am Soc Mass Spectrom. 2023 Oct 4;34(10):2166-2175. 
PMID: 37590530
 

Nov 2023

A structural analysis of the nsp9 protein from the coronavirus MERS CoV reveals a conserved RNA binding interface.
Mani G, El-Kamand S, Wang B, Baker DL, Ataide SF, Artsimovitch I, Cubeddu L, Gamsjaeger R.
Proteins. 2023 Nov 6. doi: 10.1002/prot.26630. 
PMID: 37929701

Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range.
Wang B, Finazzo M, Artsimovitch I.
Genes (Basel). 2023 Nov 5;14(11):2044. 
PMID: 38002987

Analysis of programmed frameshifting during translation of prfB in Flavobacterium johnsoniae.
Naeem FM, Gemler BT, McNutt ZA, Bundschuh R, Fredrick K.
RNA. 2023 Nov 10:rna.079721.123. 
PMID: 37949662

Heterogeneous splicing patterns resulting from KIF5A variants associated with amyotrophic lateral sclerosis.
Pino MG, Rich KA, Hall NJ, Jones ML, Fox A, Musier-Forsyth K, Kolb SJ.
Hum Mol Genet. 2023 Nov 3;32(22):3166-3180. 
PMID: 37593923

Evidence-based consensus guidelines for ALS genetic testing and counseling.
Roggenbuck J, Eubank BHF, Wright J, Harms MB, Kolb SJ; ALS Genetic Testing and Counseling Guidelines Expert Panel.
Ann Clin Transl Neurol. 2023 Nov;10(11):2074-2091. 
PMID: 37691292

Continued evasion of neutralizing antibody response by Omicron XBB.1.16.
Faraone JN, Qu P, Zheng YM, Carlin C, Jones D, Panchal AR, Saif LJ, Oltz EM, Gumina RJ, Liu SL.
Cell Rep. 2023 Oct 31;42(10):113193. 
PMID: 37777967

Immune imprinting as a barrier to effective COVID-19 vaccines.
Faraone JN, Liu SL.
Cell Rep Med. 2023 Nov 21;4(11):101291. 
PMID: 37992689

Challenges and Prospects in Developing Future SARS-CoV-2 Vaccines: Overcoming Original Antigenic Sin and Inducing Broadly Neutralizing Antibodies.
Evans JP, Liu SL.
J Immunol. 2023 Nov 15;211(10):1459-1467. 
PMID: 37931210

When Argonaute takes out the ribonuclease sword.
Nakanishi K.
J Biol Chem. 2023 Nov 27;300(1):105499. 
PMID: 38029964

Determining the defining lengths between mature microRNAs/small interfering RNAs and tinyRNAs.
Sim G, Kehling AC, Park MS, Divoky C, Zhang H, Malhotra N, Secor J, Nakanishi K.
Sci Rep. 2023 Nov 13;13(1):19761. 
PMID: 37957252
 

Dec 2023

Assembly-mediated activation of the SIR2-HerA supramolecular complex for anti-phage defense.
Shen Z, Lin Q, Yang XY, Fosuah E, Fu TM.
Mol Cell. 2023 Dec 21;83(24):4586-4599.e5. 
PMID: 38096827

RNAs undergo phase transitions with lower critical solution temperatures.
Wadsworth GM, Zahurancik WJ, Zeng X, Pullara P, Lai LB, Sidharthan V, Pappu RV, Gopalan V, Banerjee PR. 
Nat Chem. 2023 Dec;15(12):1693-1704. 
PMID: 37932412

RNA four-way junction (4WJ) for spontaneous cancer-targeting, effective tumor-regression, metastasis suppression, fast renal excretion and undetectable toxicity.
Li X, Jin K, Cheng TC, Liao YC, Lee WJ, Bhullar AS, Chen LC, Rychahou P, Phelps MA, Ho YS, Guo P.
Biomaterials. 2023 Dec 21;305:122432. 
PMID: 38176263

Differential impact on motor unit characteristics across severities of adult spinal muscular atrophy.
Kelly KM, Mizell J, Bigdeli L, Paul S, Tellez MA, Bartlett A, Heintzman S, Reynolds JE, Sterling GB, Rajneesh KF, Kolb SJ, Elsheikh B, Arnold WD.
Ann Clin Transl Neurol. 2023 Dec;10(12):2208-2222. 
PMID: 37735861

Immune evasion and membrane fusion of SARS-CoV-2 XBB subvariants EG.5.1 and XBB.2.3.
Faraone JN, Qu P, Goodarzi N, Zheng YM, Carlin C, Saif LJ, Oltz EM, Xu K, Jones D, Gumina RJ, Liu SL.
Emerg Microbes Infect. 2023 Dec;12(2):2270069. 
PMID: 37819267

Human lysyl-tRNA synthetase phosphorylation promotes HIV-1 proviral DNA transcription.
Tang Y, Behrens RT, St Gelais C, Wu S, Vivekanandan S, Razin E, Fang P, Wu L, Sherer N, Musier-Forsyth K.
Nucleic Acids Res. 2023 Dec 11;51(22):12111-12123. 
PMID: 37933844

Interplay of dynamic genome organization and biomolecular condensates.
Chung YC, Tu LC.
Curr Opin Cell Biol. 2023 Dec;85:102252. 
PMID: 37806293
 

Jan 2024

PtuA and PtuB assemble into an inflammasome-like oligomer for anti-phage defense.
Li Y, Shen Z, Zhang M, Yang XY, Cleary SP, Xie J, Marathe IA, Kostelic M, Greenwald J, Rish AD, Wysocki VH, Chen C, Chen Q, Fu TM, Yu Y.
Nat Struct Mol Biol. 2024 Jan 4. doi: 10.1038/s41594-023-01172-8. 
PMID: 38177683

NUA positively regulates plant immunity by coordination with ESD4 to deSUMOylate TPR1 in Arabidopsis.
Xie B, Luo M, Li Q, Shao J, Chen D, Somers DE, Tang D, Shi H.
New Phytol. 2024 Jan;241(1):363-377. 
PMID: 37786257