2024 Publications

January 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. 
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

A tRNA-specific function for tRNA methyltransferase Trm10 is associated with a new tRNA quality control mechanism in Saccharomyces cerevisiae.
Bowles IE, Jackman JE.
RNA. 2024 Jan 16;30(2):171-187.
PMID: 38071471

 Patients' perceptions on outcomes after mechanical thrombectomy in acute ischemic stroke.
Thanki S, Pressman E, Jade KM, Skanes R, Armouti A, Guerrero WR, Vakharia K, Parthasarathy AB, Fargen K, Mistry EA, Nimjee SM, Hassan AE, Mokin M.
Interv Neuroradiol. 2024 Jan 23:15910199241227262.   
PMID: 38258391


February 2024

Characterization of ribosome stalling and no-go mRNA decay stimulated by the Fragile X protein, FMRP.
Scarpitti MR, Pastore B, Tang WKearse MG.
BioRxiv [Preprint]. 2024 Feb 3:2024.02.02.577121. 
PMID: 38352534  

Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants.
Qu P, Xu K, Faraone JN, Goodarzi N, Zheng YM, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Gumina RJ, Liu SL.
Cell. 2024 Feb 1;187(3):585-595.e6. 
PMID: 38194968  

Brief research report: impact of vaccination on antibody responses and mortality from severe COVID-19.
Adhikari B, Bednash JS, Horowitz JC, Rubinstein MP, VlasovaAN.
Front Immunol. 2024 Feb 7;15:1325243. 
PMID: 38390335  

Pre-piRNA trimming safeguards piRNAs against erroneous targeting by RNA-dependent RNA polymerase.
Pastore B, Hertz HL, Tang W. 
Cell Rep. 2024 Feb 27;43(2):113692. 
PMID: 38244197 

Corrigendum: Brief research report: impact of vaccination on antibody responses and mortality from severe COVID-19.
Adhikari B, Bednash JS, Horowitz JC, Rubinstein MP, VlasovaAN.
Front Immunol. 2024 Feb 28;15:1384209. 
PMID: 38482012  

Viral potential to modulate microbial methane metabolism varies by habitat.
Zhong ZP, Du J, Köstlbacher S, Pjevac P, Orlić S, Sullivan MB.
NatCommun. 2024 Feb 29;15(1):1857.
PMID: 38424049

Direct Versus Indirect Revascularization for Moyamoya: a Large Multicenter Study.
El Naamani K, Chen CJ, Jabre R, Saad H, Grossberg JA, Dmytriw AA, Patel AB, Khorasanizadeh M, Ogilvy CS, Thomas A, Monteiro A, Siddiqui A, Cortez GM, Hanel RA, Porto G, Spiotta AM, Piscopo AJ, Hasan DM, Ghorbani M, Weinberg J, Nimjee SM, Bekelis K, Salem MM, Burkhardt JK, Zetchi A, Matouk C, Howard BM, Lai R, Du R, Abbas R, Sioutas GS, Amllay A, Munoz A, Atallah E, Herial NA, Tjoumakaris SI, Gooch MR, Rosenwasser RH, Jabbour P.J Neurol Neurosurg Psychiatry. 2024 Feb 14;95(3):256-263. 
PMID: 37673641

 Stroke and Neurogenesis: Bridging Clinical Observations to New Mechanistic Insights from Animal Models.
Passarelli JP, Nimjee SM, Townsend KL.
Transl Stroke Res. 2024 Feb;15(1):53-68. 
PMID: 36462099 

An HTLV-1 envelope mRNA vaccine is immunogenic and protective in New Zealand rabbits.
Tu JJ, King E, Maksimova V, Smith S, Macias R, Cheng X, Vegesna T, Yu L, Ratner L, Green PL, Niewiesk S, Richner JM, Panfil AR.
J Virol. 2024 Feb 20;98(2):e0162323. 
PMID: 38193692 


March 2024

Progress in sarcomas: Highlights from the 2023 annual meetingof the Connective Tissue Oncology Society.
Cripe TP, Roberts RD, Chandler DS, Setty BA, Chen S, Shenoy A, Venkataramany AS, Ringwalt EM, Scharschmidt T, Utset-Ward T, Konieczkowski DJ, Grignol VP, Beane JD, Ruff SM, Pollock RE.
MolTher Oncol. 2024 Mar 2;32(1):200779.
PMID: 38596308  

Protein complex heterogeneity and topology revealed by electron capture charge reduction and surface induced dissociation.
Shaw J, Harvey S, Du C, Xu Z, Olmedillas E, Saphire EO, Wysocki VH.
bioRxiv [Preprint]. 2024 Mar 9:2024.03.07.583498. 
PMID: 38496594 

Distinct Patterns of SARS-CoV-2 BA.2.87.1 and JN.1 Variants in Immune Evasion, Antigenicity and Cell-Cell Fusion.
Li P, Liu Y, Faraone J, Hsu CC, Chamblee M, Zheng YM, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Li J, Gumina RJ, Liu SL.
bioRxiv [Preprint]. 2024 Mar 11:2024.03.11.583978.
PMID: 38559216  

Remote Delivery of Mindful Movement Within Healthcare Systems: Lessons Learned From the Veterans Health Administration.
Whitehead AM, Mullur R, Sullivan MB, Nicosia FM.
Glob Adv Integr Med Health. 2024 Mar 17;13:27536130241235908.  
PMID: 38501126

Macrophages derived from human induced pluripotent stem cells (iPSCs) serve as a high-fidelity cellular model for investigating HIV-1, dengue, and influenza viruses.
Yang Q, Barbachano-Guerrero A, Fairchild LM, Rowland TJ, Dowell RD, Allen MA, Warren CJ, Sawyer SL.
JVirol. 2024 Mar 19;98(3):e0156323. 
PMID: 38323811 

The ClC-1 chloride channel inhibitor NMD670 improves skeletal muscle function in rat models and patients with myasthenia gravis.
Skov M, Ruijs TQ, Grønnebæk TS, Skals M, Riisager A, Winther JB, Dybdahl KLT, Findsen A, Morgen JJ, Huus N, Broch-Lips M, Nielsen OB, de Cuba CMKE, Heuberger JAAC, de Kam ML, Tannemaat M, Verschuuren JJGM, Knutsen LJS, Kelly NM, Jensen KG, Arnold WD, Burghes AH, Olesen C, Bold J, Petersen TK, Quiroz JA, Hutchison J, Chin ER, Groeneveld GJ, Pedersen TH.
SciTransl Med. 2024 Mar 20;16(739):eadk9109. 
PMID: 38507469 - Clinical Trial 

Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses.
Warren CJ, Barbachano-Guerrero A, Bauer VL, Stabell AC, Dirasantha O, Yang Q, Sawyer SL.
bioRxiv [Preprint]. 2024 Mar 25:2023.11.13.566830. 
PMID: 38014262  

Metamorphic proteins and how to find them.
Porter LL, Artsimovitch I, Ramírez-Sarmiento CA.
CurrOpin Struct Biol. 2024 Mar 26;86:102807. 
PMID: 38537533  

Cell-cell communication and initial population composition shape the structure of potato spindle tuber viroid quasispecies.
Wu J, Bisaro DM.
Plant Cell. 2024 Mar 29;36(4):1036-1055.
PMID: 38252648 

Environment-specific virocell metabolic reprogramming.
Howard-Varona C, Lindback MM, Fudyma JD, Krongauz A, Solonenko NE, Zayed AA, Andreopoulos WB, Olson HM, Kim YM, Kyle JE, Del Rio TG, Adkins JN, Tfaily MM, Paul S, Sullivan MB, Duhaime MB.
ISME J. 2024 Mar 29:wrae055. 
PMID: 38552150

Preoperative prescription opioid use as an independent predictor of 90-day mortality and adverse events in craniotomy and craniectomy patients.
Shah VS, Dornbos D, Hoang NA, Cua S, Rodgers B, Pezzutti D, Duenas H, Eaton R, Kreatsoulas D, Elder JB, Prevedello DM, Lonser RR, Nimjee SM.
J Neurosurg. 2024 Mar 8;141(2):455-460.
PMID: 38457788


April 2024

Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome.
Warner BR, Fredrick K.
RNA. 2024 Apr 3:rna.079960.124. 
PMID: 38570183  

RNA three-dimensional structure drives the sequence organization of potato spindle tuber viroid quasispecies.
Wu J, Zhang Y, Nie Y, Yan F, Zirbel CL, Bisaro DM.
PLoSPathog. 2024 Apr 4;20(4):e1012142. 
PMID: 38574111 

Protein analysis using capillary electrophoresis coupled to mass spectrometry through vibrating sharp-edge spray ionization.
Witzel MT, Veltri LM, Kostelic M, Elshamy YS, Lucas JA, Lai S, Du C, Wysocki VH, Holland LA.
Electrophoresis. 2024 Apr 5.  
PMID: 38577828
  
Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.
Zuber PK, Said N, Hilal T, Wang B, Loll B, González-Higueras J, Ramírez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH.
NatCommun. 2024 Apr 8;15(1):3040. 
PMID: 38589445  

Distinct patterns of SARS-CoV-2 BA.2.87.1 and JN.1 variants in immune evasion, antigenicity, and cell-cell fusion.
Li P, Liu Y, Faraone JN, Hsu CC, Chamblee M, Zheng Y-M, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Li J, Gumina RJ, Liu S-L.
mBio. 2024 May 8;15(5):e0075124.  
PMID: 3859189

Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As.
Baek A, Lee GE, Golconda S, Rayhan A, Manganaris AA, Chen S, Tirumuru N, Yu H, Kim S, Kimmel C, Zablocki O, Sullivan MB, Addepalli B, Wu L, Kim S.
NatMicrobiol. 2024 May;9(5):1340-1355.  
PMID: 38605174

Reciprocating RNA Polymerase batters through roadblocks.
Qian J, Cartee A, Xu W, Yan Y, Wang B, Artsimovitch I, Dunlap D, Finzi L.
NatCommun. 2024 Apr 12;15(1):3193.  
PMID: 38609371  

Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation.
Said N, Finazzo M, Hilal T, Wang B, Selinger TL, Gjorgjevikj D, Artsimovitch I, Wahl MC.
NatCommun. 2024 Apr 15;15(1):3186. 
PMID: 38622114   

To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes.
Grove DJ, Russell PJ, Kearse MG.
WileyInterdiscip Rev RNA. 2024 Mar-Apr;15(2):e1833. 
PMID: 38433101

Molecular basis of Gabija anti-phage supramolecular assemblies.
Yang XY, Shen Z, Xie J, Greenwald J, Marathe I, Lin Q, Xie WJ, Wysocki VH, Fu TM.
Nat Struct Mol Biol. 2024 Apr 16.  
PMID: 38627580 

Structural Basis for the Interaction of Redβ Single-Strand Annealing Protein with Escherichia coli Single-Stranded DNA-Binding Protein.
Zakharova K, Liu M, Greenwald JR, Caldwell BC, Qi Z, Wysocki VH, Bell CE.
J Mol Biol. 2024 Apr 24;436(11):168590.  
PMID: 38663547

Native proteomics by capillary zone electrophoresis-mass spectrometry.
Wang Q, Wang Q, Qi Z, Moeller W, Wysocki VH, Sun L.
bioRxiv [Preprint]. 2024 Apr 28:2024.04.24.590970. 
PMID: 38712154

Human T-cell leukemia virus type 1 uses a specific tRNAPro isodecoder to prime reverse transcription.
Syu YC, Hatterschide J, Budding CR, Tang Y, Musier-Forsyth K.
RNA. 2024 Apr 29:rna.080006.124.  
PMID: 38684316  

Isolation of Diverse Simian Arteriviruses Causing Hemorrhagic Disease.
Shaw TM, Dettle ST, Mejia A, Hayes JM, Simmons HA, Basu P, Kuhn JH, Ramuta MD, Warren CJ, Jahrling PB, O'Connor DH, Huang L, Zaeem M, Seo J, Slukvin II, Brown ME, Bailey AL.
Emerg Infect Dis. 2024 Apr;30(4):721-731.  
PMID: 38526136  

Stroke Thrombolysis: Can You Feel the Need for Speed?

Nimjee SM, Hill MD.
Neurology. 2024 Apr 9;102(7):e209253. 
PMID: 38502898
 

 May 2024

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM.
Li W, Yang H, Stachowski K, Norris AS, Lichtenthal K, Kelly S, Gollnick P, Wysocki VH, Foster MP.
bioRxiv [Preprint]. 2024 May 5:2024.05.02.592192. 
PMID: 38746386

A tribute to Sidney Altman, one of the architects of modern RNA biology.
Gopalan V, Kirsebom LA.
J Biol Chem. 2024 May 10:107364.  
PMID: 38735479

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea.
Warwick-Dugdale J, Tian F, Michelsen ML, Cronin DR, Moore K, Farbos A, Chittick L, Bell A, Zayed AA, Buchholz HH, Bolanos LM, Parsons RJ, Allen MJ, Sullivan MB, Temperton B.
NatCommun. 2024 May 14;15(1):4089.  
PMID: 38744831 

Overexpression of stress granule protein TZF1 enhances salt stress tolerance by targeting ACA11 mRNA for degradation in Arabidopsis.
He SL, Li B, Zahurancik WJ, Arthur HC, Sidharthan V, Gopalan V, Wang L, Jang JC.
Front Plant Sci. 2024 May 8;15:1375478. 
PMID: 38799098 

Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats.
Deans NC, Talbot JRB, Li M, Sáez-González C, Hövel I, Heavens D, Stam M, Hollick JB.
PLoS Genet. 2024 May 30;20(5):e1011296. 
PMID: 38814980 

Thg1 family 3'-5' RNA polymerases as tools for targeted RNA synthesis.\
Jayasinghe MI, Patel KJ, Jackman JE.
RNA. 2024 Sep 16;30(10):1315-1327. 
PMID: 3899712

Characteristics of JN.1-derived SARS-CoV-2 subvariants SLip, FLiRT, and KP.2 in neutralization escape, infectivity and membrane fusion.
Li P, Faraone JN, Hsu CC, Chamblee M, Zheng YM, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Li J, Gumina RJ, Xu K, Liu SL.
bioRxiv [Preprint]. 2024 May 21:2024.05.20.595020. 
PMID: 38826376 
 

June 2024

  Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis.
McElroy CA, Ihms EC, Kumar Yadav D, Holmquist ML, Wadhwa V, Wysocki VH, Gollnick P, Foster MP.
J Struct Biol X. 2024 Jun 11;10:100103. 
PMID: 39035014  

Contribution of an alternative 16S rRNA helix to biogenesis of the 30S subunit of the ribosome.
Warner BR, Fredrick K.
RNA. 2024 Jun 17;30(7):770-778. 
PMID: 38570183   

KDM2B is required for ribosome biogenesis and its depletion unequally affects mRNA translation.
Anastas V, Chavdoula E, La Ferlita A, Soysal B, Cosentini I, Nigita G, Kearse MG, Tsichlis PN.
bioRxiv [Preprint]. 2024 Jun 6:2024.05.22.595403.
PMID: 38826406 

Nucleolin acute degradation reveals novel functions in cell cycle progression and division in TNBC.
Mills J, Tessari A, Anastas V, Kumar DS, Rad NS, Lamba S, Cosentini I, Reers A, Zhu Z, Miles WO, Coppola V, Cocucci E, Magliery TJ, Shive H, Davies AE, Rizzotto L, Croce CM, Palmieri D.
bioRxiv [Preprint]. 2024 Jun 22:2024.06.17.599429. 
PMID: 38948867 

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle.
McGivern BB, Cronin DR, Ellenbogen JB, Borton MA, Knutson EL, Freire-Zapata V, Bouranis JA, Bernhardt L, Hernandez AI, Flynn RM, Woyda R, Cory AB, Wilson RM, Chanton JP, Woodcroft BJ, Ernakovich JG, Tfaily MM, Sullivan MB, Tyson GW, Rich VI, Hagerman AE, Wrighton KC.
Nat Microbiol. 2024 Jun;9(6):1454-1466. 
PMID: 38806673 


 July 2024

Targeted degradation of extracellular mitochondrial aspartyl-tRNA synthetase modulates immune responses.
Johnson BS, Farkas D, El-Mergawy R, Adair JA, Elhance A, Eltobgy M, Coan FM, Chafin L, Joseph JA, Cornwell A, Johns FJ, Rosas L, Rojas M, Farkas L, Bednash JS, Londino JD, Ray P, Ray A, Kagan V, Lee JS, Chen BB, Mallampalli RK.
Nat Commun. 2024 Jul 22;15(1):6172. 
PMID: 39039092 

Mutation of the conserved late element in geminivirus CP promoters abolishes Arabidopsis TCP24 transcription factor binding and decreases H3K27me3 levels on viral chromatin.
Williams J, Regedanz E, Lucinda N, Nava Fereira AR, Lacatus G, Berger M, O'Connell N, Coursey T, Ruan J, Bisaro DM, Sunter G.
PLoS Pathog. 2024 Jul 18;20(7):e1012399.
PMID: 39024402 

A-to-I Editing Is Subtype-Specific in Non-Hodgkin Lymphomas.
Chen C, Bundschuh R.
Genes (Basel). 2024 Jul 1;15(7):864.
PMID: 39062643 

DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.
Yang XY, Shen Z, Wang C, Nakanishi KFu TM.
bioRxiv [Preprint]. 2024 Jul 20:2024.07.20.604412. 
Update in:  Cell. 2024 Sep 19;187(19):5253-5266.e16.
PMID: 39071313 

Trypanosoma brucei multi-aminoacyl-tRNA synthetase complex formation limits promiscuous tRNA proofreading.
Watkins RR, Vradi A, Shulgina I, Musier-Forsyth K.
Front Microbiol. 2024 Jul 16;15:1445687. 
PMID: 39081885  

Defined folding pattern of poly(rG) supports inherent ability to encode biological information.
Kankia N, Lomidze L, Stevenson S, Musier-Forsyth K, Kankia B.
Biopolymers. 2024 Nov;115(6):e23615. 
PMID: 39004945 

Human T-cell leukemia virus type 1 uses a specific tRNAPro isodecoder to prime reverse transcription.
Syu YC, Hatterschide J, Budding CR, Tang Y, Musier-Forsyth K.
RNA. 2024 Jul 16;30(8):967-976.
PMID: 38684316 

Polyethylene Glycol Impacts Conformation and Dynamics of Escherichia coliProlyl-tRNA Synthetase Via Crowding and Confinement Effects.
Liebau J, Laatsch BF, Rusnak J, Gunderson K, Finke B, Bargender K, Narkiewicz-Jodko A, Weeks K, Williams MT, Shulgina I, Musier-Forsyth K, Bhattacharyya S, Hati S.
Biochemistry. 2024 Jul 2;63(13):1621-1635. 
PMID: 38607680 

Decompressive craniectomy in symptomatic intracerebral hemorrhage after ischemic stroke: a multicenter retrospective cohort study.
Pressman E, Gersey ZC, Jonzzon SB, Weinberg JH, Fogg DN, Flaherty EG, Gross BA, Chitale RV, Fusco MR, Froehler MT, Vignolles-Jeong J, Nimjee SM, Hanel RA, Cortez GM, Ravi S, Desai SK, Hassan AE, Monteiro A, Siddiqui AH, Matsoukas S, Majidi S, Smith T, Vakharia K, Mokin M.
J Neurosurg. 2024 Jul 26;142(1):52-61.
PMID: 39059427

The Venous System of the Central Nervous System: Anatomy, Diseases, Treatments, and Pathway to Innovation.
Nimjee SM.
Neurosurg Clin N Am. 2024 Jul;35(3):xi-xii. 
PMID: 38782532

circPCMTD1 : A protein-coding circular RNA that regulates DNA damage response in BCR/ABL -positive leukemias.
Papaioannou D, Urs AP, Buisson R, Petri A, Kulkarni R, Nicolet D, Woodward L, Goda C, Mrózek K, Behbehani GK, Kauppinen S, Eisfeld AK, Aifantis I, Singh G, Dorrance AM, Garzon R.
bioRxiv [Preprint]. 2024 Jul 2:2024.06.27.601046.  
PMID: 39005285  

Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient.
Sun CL, Pratama AA, Gazitúa MC, Cronin D, McGivern BB, Wainaina JM, Vik DR, Zayed AA, Bolduc B; IsoGenie Project Field Teams 2010‐2017, the IsoGenie and EMERGE Projects Coordinators; Wrighton KC, Rich VI, Sullivan MB.
Environ Microbiol. 2024 Jul;26(8):e16665. 
PMID: 39101434
 

August 2024

Neutralization escape, infectivity, and membrane fusion of JN.1-derived SARS-CoV-2 SLip, FLiRT, and KP.2 variants.
Li P, Faraone JN, Hsu CC, Chamblee M, Zheng YM, Carlin C, Bednash JS, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Li J, Gumina RJ, Xu K, Liu SL.
Cell Rep. 2024 Aug [SG1] 27;43(8):114520.  
PMID: 39024099 
 
Force and the α-C-terminal domains bias RNA polymerase recycling.
Qian J, Wang B, Artsimovitch I, Dunlap D, Finzi L.
Nat Commun. 2024 Aug 30;15(1):7520.  
PMID: 39214958 

Longitudinal transcriptomic analysis reveals persistent enrichment of iron homeostasis and erythrocyte function pathways in severe COVID-19 ARDS.
Eltobgy M, Johns F, Farkas D, Leuenberger L, Cohen SP, Ho K, Karow S, Swoope G, Pannu S, Horowitz JC, Mallampalli RK, Englert JA, Bednash JS.
Front Immunol. 2024 Aug 5;15:1397629.  
PMID: 39161760  

Transmembrane channel-like 4 and 5 proteins at microvillar tips are potential ion channels and lipid scramblases.
Ebrahim S, Ballesteros A, Zheng WS, Mukherjee S, Hu G, Weng WH, Montgomery JS, Agyemang Y, Cui R, Sun W, Krystofiak E, Foster MP, Sotomayor M, Kachar B.
bioRxiv [Preprint]. 2024 Aug 23:2024.08.22.609173.  
PMID: 39229161 

DdmDE eliminates plasmid invasion by DNA-guided DNA targeting.
Yang XY, Shen Z, Wang C, Nakanishi KFu TM.
Cell. 2024 Sep 19;187(19):5253-5266.e16. 
PMID: 39173632 

Use of the 'double diamond' design framework to nurture creativity in life sciences research.
Shen Y, Bosch G, Pino L, Gopalan V. 
Trends Biochem Sci. 2024 Aug;49(8):654-657. 
PMID: 38777701 

Environmentally dependent interactions shape patterns in gene content across natural microbiomes.
Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S.
Nat Microbiol. 2024 Aug;9(8):2022-2037. 
PMID: 38977908

The Brain Injury Guidelines (BIG) and emergency department observation and admission rates: A retrospective cohort study.
Southerland LT, Alnemer A, Laufenberg C, Nimjee SM, Bischof JJ.
Am J Emerg Med. 2024 Aug;82:37-41.
PMID: 3878178

Diffusion-Weighted Imaging Fluid-Attenuated Inversion Recovery Mismatch on Portable, Low-Field Magnetic Resonance Imaging Among Acute Stroke Patients.
Sorby-Adams A, Guo J, de Havenon A, Payabvash S, Sze G, Pinter NK, Jaikumar V, Siddiqui A, Baldassano S, Garcia-Guarniz AL, Zabinska J, Lalwani D, Peasley E, Goldstein JN, Nelson OK, Schaefer PW, Wira CR 3rd, Pitts J, Lee V, Muir KW, Nimjee SM, Kirsch J, Iglesias JE, Rosen MS, Sheth KN, Kimberly WT.
Ann Neurol. 2024 Aug;96(2):321-331.
PMID: 38738750

Technical and clinical success after venous sinus stenting for treatment of idiopathic intracranial hypertension using a novel guide catheter for access: Case series and initial multi-center experience.
Zyck S, Malik M, Webb M, Mohammed M, Powers CJ, Birnbaum L, Hawk H, Brinjikji W, Nimjee SM.
Interv Neuroradiol. 2024 Aug;30(4):524-528. 
PMID: 36397725

Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.
Tian F, Wainaina JM, Howard-Varona C, Domínguez-Huerta G, Bolduc B, Gazitúa MC, Smith G, Gittrich MR, Zablocki O, Cronin DR, Eveillard D, Hallam SJ, Sullivan MB.
Microbiome. 2024 Aug 29;12(1):159. 
PMID: 39198891 

Characterization of ribosome stalling and no-go mRNA decay stimulated by the fragile X protein, FMRP.
Scarpitti MR, Pastore B, Tang W, Kearse MG.
J Biol Chem. 2024 Aug;300(8):107540. 
PMID: 38971316  

The neonatal Fc receptor (FcRn) is a pan-arterivirus receptor.
Shaw TM, Huey D, Mousa-Makky M, Compaleo J, Nennig K, Shah AP, Jiang F, Qiu X, Klipsic D, Rowland RRR, Slukvin II, Sullender ME, Baldridge MT, Li H, Warren CJ, Bailey AL.
Nat Commun. 2024 Aug 7;15(1):6726.
PMID: 39112502 

KDM5A/B contribute to HIV-1 latent infection and survival of HIV-1 infected cells.
Li TW, Park Y, Watters EG, Wang X, Zhou D, Fiches GN, Wu Z, Badley AD, Sacha JB, Ho WZ, Santoso NG, Qi J, Zhu J.
Antiviral Res. 2024 Aug;228:105947. 
PMID: 38925368


September 2024

Fast-twitch myofibrils grow in proportion to Mylpf dosage in the zebrafish embryo.
Adekeye TE, Teets EM, Tomak EA, Waterman SL, Sprague KA, White A, Coffin ML, Varga SM, Easterbrooks TE, Shepherd SJ, Austin JD, Krivorotko D, Hupper TE, Kelley JB, Amacher SL, Talbot JC. 
bioRxiv [Preprint]. 2024 Sep 23:2024.09.18.613721. 
PMID: 39345555 

Antiterminator LoaP loads onto RNA to chase a runaway RNA polymerase.
Wang B, Artsimovitch I. 
Structure. 2024 Sep 5;32(9):1298-1300.  
PMID: 39241762

Neutralization and Stability of JN.1-derived LB.1, KP.2.3, KP.3 and KP.3.1.1 Subvariants.
Li P, Faraone JN, Hsu CC, Chamblee M, Liu Y, Zheng YM, Xu Y, Carlin C, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Li J, Gumina RJ, Bednash JS, Xu K, Liu SL
bioRxiv [Preprint]. 2024 Sep 5:2024.09.04.611219.  
PMID: 39282390 
 
Potato spindle tuber viroid (PSTVd) loop 27 mutants promote cell-to-cell movement and phloem unloading of the wild type: Insights into RNA-based viroid interactions.
Wu J, Bisaro DM.
Virology. 2024 Sep;597:110137.
PMID: 38897019 

Identification of leader-trailer helices of precursor ribosomal RNA in all phyla of bacteria and archaea.
Gemler BT, Warner BR, Bundschuh R, Fredrick K.
RNA. 2024 Sep 16;30(10):1264-1276.  
PMID: 39043438  

Structural analysis of noncanonical translation initiation complexes.
Mattingly JM, Nguyen HA, Roy B, Fredrick K, Dunham CM.
J Biol Chem. 2024 Oct;300(10):107743.
PMID: 39222680 

Structures and functions of short argonautes.
Wang C, Shen Z, Yang XY, Fu TM.
RNA Biol. 2024 Jan;21(1):1-7. 
PMID: 39219231 

Thg1 family 3'-5' RNA polymerases as tools for targeted RNA synthesis.
Jayasinghe MI, Patel KJ, Jackman JE.
RNA. 2024 Sep 16;30(10):1315-1327. |PMID: 3899712

Machine learning-enhanced electrical impedance myography to diagnose and track spinal muscular atrophy progression.
Sonbas Cobb B, Kolb SJ, Rutkove SB.
Physiol Meas. 2024 Sep 6;45(9):10.1088/1361-6579/ad74d5. 
PMID: 39197472  

The impact of hypertension on clinical outcomes in moyamoya disease: a multicenter, propensity score-matched analysis.
Musmar B, Roy JM, Abdalrazeq H, Atallah E, Naamani KE, Chen CJ, Jabre R, Saad H, Grossberg JA, Dmytriw AA, Patel AB, Khorasanizadeh M, Ogilvy CS, Thomas AJ, Monteiro A, Siddiqui A, Cortez GM, Hanel RA, Porto G, Spiotta AM, Piscopo AJ, Hasan DM, Ghorbani M, Weinberg J, Nimjee SM, Bekelis K, Salem MM, Burkhardt JK, Zetchi A, Matouk C, Howard BM, Lai R, Du R, Abbas R, Sioutas GS, Amllay A, Munoz A, Herial NA, Tjoumakaris SI, Gooch MR, Rosenwasser RH, Jabbour P.
Acta Neurochir (Wien). 2024 Sep 13;166(1):366.
PMID: 39269654 

Scientists' call to action: Microbes, planetary health, and the Sustainable Development Goals.
Crowther TW, Rappuoli R, Corinaldesi C, Danovaro R, Donohue TJ, Huisman J, Stein LY, Timmis JK, Timmis K, Anderson MZ, Bakken LR, Baylis M, Behrenfeld MJ, Boyd PW, Brettell I, Cavicchioli R, Delavaux CS, Foreman CM, Jansson JK, Koskella B, Milligan-McClellan K, North JA, Peterson D, Pizza M, Ramos JL, Reay D, Remais JV, Rich VI, Ripple WJ, Singh BK, Smith GR, Stewart FJ, Sullivan MB, van den Hoogen J, van Oppen MJH, Webster NS, Zohner CM, van Galen LG.
Cell. 2024 Sep 19;187(19):5195-5216. 
PMID: 39303686 

 

October 2024

Synergy Between NK Cells and Monocytes in Potentiating Cardiovascular Disease Risk in Severe COVID-19.
Gunasena M, Alles M, Wijewantha Y, Mulhern W, Bowman E, Gabriel J, Kettelhut A, Kumar A, Weragalaarachchi K, Kasturiratna D, Horowitz JC, Scrape S, Pannu SR, Liu SL, Vilgelm A, Wijeratne S, Bednash JS, Demberg T, Funderburg NT, Liyanage NPM.
Arterioscler Thromb Vasc Biol. 2024 Oct;44(10):e243-e261. 
PMID: 38989579  

Sm-site containing mRNAs can accept Sm-rings and are downregulated in Spinal Muscular Atrophy.
Blatnik AJ, Sanjeev M, Slivka J, Pastore B, Embree CM, Tang W, Singh GBurghes AHM.
bioRxiv [Preprint]. 2024 Oct 9:2024.10.09.617433.  
PMID: 39416143  

Dynamics in Cre-loxP site-specific recombination.
Foster MP, Benedek MJ, Billings TD, Montgomery JS.
Curr Opin Struct Biol. 2024 Oct;88:102878. 
PMID: 39029281 

Topological rearrangements activate the HerA-DUF anti-phage defense system.
Rish AD, Fosuah E, Shen Z, Marathe IA, Wysocki VHFu TM.
bioRxiv [Preprint]. 2024 Oct 24:2024.10.24.620088. 
PMID: 39484427  

RNA-driven phase transitions in biomolecular condensates.
Wadsworth GM, Srinivasan S, Lai LB, Datta M, Gopalan V, Banerjee PR.
Mol Cell. 2024 Oct 3;84(19):3692-3705.  
PMID: 39366355              

HDAC7 promotes cardiomyocyte proliferation by suppressing Myocyte Enhancer Factor 2.
Jang J, Bentsen M, Bu J, Chen L, Campos AR, Looso M, Li D.
J Mol Cell Biol. 2024 Oct 11:mjae044. 
PMID: 39394661

Antagonistic roles of cGAS/STING signaling in colorectal cancer chemotherapy.
Liang B, Xing X, Storts H, Ye Z, Claybon H, Austin R, Ding R, Liu B, Wen H, Miles WO, Fishel R, Wang JJ.
Front Oncol. 2024 Oct 14;14:1441935.|
PMID: 39469633 

Translation of HIV-1 unspliced RNA is regulated by 5' untranslated region structure.
Cheng Z, Islam S, Kanlong JG, Sheppard M, Seo H, Nikolaitchik OA, Kearse MG, Pathak VK, Musier-Forsyth K, Hu W-S.
J Virol. 2024 Oct 22;98(10):e0116024.  
PMID: 39315813 

Transcription start site choice regulates HIV-1 RNA conformation and function.
Musier-Forsyth K, Rein A, Hu WS.
Curr Opin Struct Biol. 2024 Oct;88:102896.
PMID: 39146887 Review.

Target cleavage and gene silencing by Argonautes with cityRNAs.
Zhang H, Sim G, Kehling AC, Adhav VA, Savidge A, Pastore B, Tang WNakanishi K.
Cell Rep. 2024 Oct 22;43(10):114806. 
PMID: 39368090  

Comparative Outcomes of Unilateral vs Bilateral Revascularization in Moyamoya Disease: A Multicenter Retrospective Study.
Musmar B, Roy JM, Abdalrazeq H, Kaul A, Atallah E, El Naamani K, Chen CJ, Jabre R, Saad H, Grossberg JA, Dmytriw AA, Patel AB, Khorasanizadeh M, Ogilvy CS, Thomas AJ, Monteiro A, Siddiqui A, Cortez GM, Hanel RA, Porto G, Spiotta AM, Piscopo AJ, Hasan DM, Ghorbani M, Weinberg J, Nimjee SM, Bekelis K, Salem MM, Burkhardt JK, Zetchi A, Matouk C, Howard BM, Lai R, Du R, Abbas R, Sioutas GS, Amllay A, Munoz A, Herial NA, Tjoumakaris SI, Gooch MR, Rosenwasser RH, Jabbour P.
Neurosurgery. 2024 Oct 28.  
PMID: 39465938  

Von Willebrand factor targeted thrombolysis in canine basilar artery occlusion.
Carfora A, Holthaus B, Yacoub S, Franceschelli D, Joseph M, Milks MW, Mandybur I, Anderson C, Lee C, Huttinger A, Shujaat M, Wheeler DG, Sullenger B, Nimjee SM.
Front Neurol. 2024 Oct 9;15:1436291. 
PMID: 39445200 

Rerupture of an Aneurysmal Subarachnoid Hemorrhage.
Franceschelli D, Nimjee SM.
N Engl J Med. 2024 Oct 3;391(13):e27. 
PMID: 39348672  

HTLV-1 infected T cells cause bone loss via small extracellular vesicles.
Pokhrel NK, Panfil AR, Habib H, Seeniraj S, Joseph A, Rauch D, Cox L, Sprung R, Gilmore PE, Zhang Q, Townsend RR, Yu L, Yilmaz AS, Aurora R, Park W, Ratner L, Weilbaecher KN, Veis DJ.
J Extracell Vesicles. 2024 Oct;13(10):e12516. 
PMID: 39385703   
 
Forward genetic approach identifies a phylogenetically conserved serine residue critical for the catalytic activity of UBIQUITIN-SPECIFIC PROTEASE 12 in Arabidopsis.
Hajdu A, Nyári DV, Ádám É, Kim YJ, Somers DE, Silhavy D, Nagy F, Kozma-Bognár L.
Sci Rep. 2024 Oct 25;14(1):25273. 
PMID: 39455703 

Polyphenol rewiring of the microbiome reduces methane emissions.
McGivern BB, Ellenbogen JB, Hoyt DW, Bouranis JA, Stemple BP, Daly RA, Bosman SH, Sullivan MB, Hagerman AE, Chanton JP, Tfaily MM, Wrighton KC.
bioRxiv [Preprint]. 2024 Oct 22:2024.10.22.619724.
PMID: 39484614 

Widespread regulation of the maternal transcriptome by Nanos in Drosophila.
Marhabaie M, Wharton TH, Kim SY, Wharton RP.
PLoS Biol. 2024 Oct 14;22(10):e3002840. 
PMID: 39401257 
 

November 2024

A Biochemical and Biophysical Analysis of the Interaction of nsp9 with nsp12 from SARS-CoV-2-Implications for Future Drug Discovery Efforts.
Baker DL, Wang B, Wilkinson-White LE, El-Kamand S, Allport TA, Ataide SF, Kwan AH, Artsimovitch I, Cubeddu L, Gamsjaeger R.
Proteins. 2024 Nov;92(11):1308-1317.
PMID: 38958516

Pseudomonas aeruginosa- mediated cardiac dysfunction is driven by extracellular vesicles released during infection.
Kumar N, Mattoo SS, Sanghvi S, Ellendula MP, Mahajan S, Planner C, Bednash JS, Khan M, Ganesan LP, Singh H, Lafuse WP, Wozniak DJ, Rajaram MVS.
bioRxiv [Preprint]. 2024 Nov 25:2024.11.22.624948. 
PMID: 39651123   

Immune Evasion, Cell-Cell Fusion, and Spike Stability of the SARS-CoV-2 XEC Variant: Role of Glycosylation Mutations at the N-terminal Domain.
Li P, Faraone JN, Hsu CC, Chamblee M, Liu Y, Zheng YM, Xu Y, Carlin C, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Li J, Gumina RJ, Bednash JS, Xu K, Liu SL.
bioRxiv [Preprint]. 2024 Nov 13:2024.11.12.623078. 
PMID: 39605558  

Insights into Ligand-Mediated Activation of an Oligomeric Ring-Shaped Gene-Regulatory Protein from Solution- and Solid-State NMR.
Muzquiz R, Jamshidi C, Conroy DW, Jaroniec CP, Foster MP.
J Mol Biol. 2024 Nov 15;436(22):168792. 
PMID: 39270971    

RNA Nanotechnology for Codelivering High-Payload Nucleoside Analogs to Cancer with a Synergetic Effect.
Li X, Jin K, Liao YC, Lee WJ, Chen LC, Cheng TC, Ho YS, Guo P.
Mol Pharm. 2024 Nov 4;21(11):5690-5702.
PMID: 39388598

The Answer ALS return of results study: Answering the duty to disclose.
Roggenbuck J, Kaschalk M, Eustace R, Vicini L, Gokun Y, Harms MB, Kolb SJ.
Amyotroph Lateral Scler Frontotemporal Degener. 2024 Nov;25(7-8):743-750.
PMID: 39091255 

Endovascular intervention for carotid blowout syndrome and predictors of recurrence: A retrospective and multicenter cohort study.
Weinberg JH, Liu K, Asada AM, Bahri M, El Naamani K, Zakeri A, Zakeri J, Tjoumakaris S, Jabbour P, Rocco JW, VanKoevering K, Yang S, Old M, Powers C, Nimjee S, Youssef P.
Clin Neurol Neurosurg. 2024 Nov;246:108584. 
PMID: 39368393

ROTEM and von Willebrand Factor in COVID patients presenting with acute ischemic stroke: A case series: ROTEM and von Willebrand Factor in COVID-19 Related Stroke.
Salas JR, Jacob C, Ibekwe E, Zakeri AS, Nimjee SM, Strohm T.
J Stroke Cerebrovasc Dis. 2024 Nov;33(11):107894
PMID: 39106921

 Author Correction: Forward genetic approach identifies a phylogenetically conserved serine residue critical for the catalytic activity of UBIQUITIN-SPECIFIC PROTEASE 12 in Arabidopsis.
Hajdu A, Nyári DV, Ádám É, Kim YJ, Somers DE, Silhavy D, Nagy F, Kozma-Bognár L.
Sci Rep. 2024 Nov 20;14(1):28722. 
PMID: 39567646 

HOS15-mediated turnover of PRR7 enhances freezing tolerance.
Kim YJ, Kim WY, Somers DE.
New Phytol. 2024 Nov;244(3):798-810.  
PMID: 39155726

 A functional microbiome catalogue crowdsourced from North American rivers.
Borton MA, McGivern BB, Willi KR, Woodcroft BJ, Mosier AC, Singleton DM, Bambakidis T, Pelly A, Daly RA, Liu F, Freiburger A, Edirisinghe JN, Faria JP, Danczak R, Leleiwi I, Goldman AE, Wilkins MJ, Hall EK, Pennacchio C, Roux S, Eloe-Fadrosh EA, Good SP, Sullivan MB, Wood-Charlson EM, Miller CS, Ross MRV, Henry CS, Crump BC, Stegen JC, Wrighton KC.
Nature. 2024 Nov 20.  
PMID: 39567690 

Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.
Freire-Zapata V, Holland-Moritz H, Cronin DR, Aroney S, Smith DA, Wilson RM, Ernakovich JG, Woodcroft BJ, Bagby SC; EMERGE 2012 Field Team; EMERGE Biology Integration Coordinators; Rich VI, Sullivan MB, Stegen JC, Tfaily MM.
Nat Microbiol. 2024 Nov;9(11):2892-2908.  
PMID: 39354152 

 Employing splice-switching oligonucleotides and AAVrh74.U7 snRNA to target insulin receptor splicing and cancer hallmarks in osteosarcoma.
Khurshid S, Venkataramany AS, Montes M, Kipp JF, Roberts RD, Wein N, Rigo F, Wang PY, Cripe TP, Chandler DS.
Mol Ther Oncol. 2024 Nov 23;32(4):200908.
PMID: 39720325

 
December 2024

Protein and DNA Conformational Changes Contribute to Specificity of Cre Recombinase.
Montgomery JS, Judson ME, Foster MP.
bioRxiv [Preprint]. 2024 Dec 11:2024.12.11.627928.  
PMID: 39713331 

 Use of a small molecule microarray screen to identify inhibitors of the catalytic RNA subunit of Methanobrevibacter smithii RNase P.
Sidharthan V, Sibley CD, Dunne-Dombrink K, Yang M, Zahurancik WJ, Balaratnam S, Wilburn DB, Schneekloth JS Jr, Gopalan V.
Nucleic Acids Res. 2024 Dec 16:gkae1190. 
PMID: 39676671

Author Correction: Environmentally dependent interactions shape patterns in gene content across natural microbiomes.
Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S.
Nat Microbiol. 2024 Dec 2.
PMID: 39623069 

Engineered extracellular vesicles for combinatorial TNBC therapy: SR-SIM-guided design achieves substantial drug dosage reduction.
Bhullar AS, Jin K, Shi H, Jones A, Hironaka D, Xiong G, Xu R, Guo P, Binzel DW, Shu D.
Mol Ther. 2024 Dec 4;32(12):4467-4481.
PMID: 39369270

Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase.
Devarkar SC, Budding CR, Pathirage C, Kavoor A, Herbert C, Limbach PA, Musier-Forsyth K, Xiong Y.
bioRxiv [Preprint]. 2024 Dec 8:2024.12.07.627298. 
PMID: 39677689 

NMR-based solution structure of the Caulobacter crescentus ProXp-ala trans-editing enzyme.\
Duran AD, Danhart EM, Ma X, Nagy ABK, Musier-Forsyth K, Foster MP.\
Biomol NMR Assign. 2024 Dec;18(2):233-238.
PMID: 39214936 

Evolving treatment paradigms of cerebral aneurysm stasis in flow diversion.
Weinberg JH, Gruber M, Ritchey N, Ehlers L, Cua S, Zakeri A, Powers C, Nimjee S, Youssef P.\
J Clin Neurosci. 2024 Dec 24;132:110996. 
PMID: 39721118

Pretreatment factors associated with symptomatic stroke in Moyamoya disease patients: A multicenter study.
Musmar B, Roy JM, Salim HA, Kaul A, Atallah E, Naamani KE, Chen CJ, Jabre R, Saad H, Grossberg JA, Dmytriw AA, Patel AB, Khorasanizadeh M, Ogilvy CS, Thomas AJ, Monteiro A, Siddiqui A, Cortez GM, Hanel RA, Porto G, Spiotta AM, Piscopo AJ, Hasan DM, Ghorbani M, Weinberg J, Nimjee SM, Bekelis K, Salem MM, Burkhardt JK, Zetchi A, Matouk C, Howard BM, Lai R, Du R, Abbas R, Sioutas GS, Amllay A, Munoz A, Herial NA, Tjoumakaris SI, Gooch MR, Rosenwasser RH, Jabbour P.
J Clin Neurosci. 2024 Dec;130:110922. 
PMID: 39571479

Oncogenic Functions of Alternatively Spliced MDM2-ALT2 Isoform in Retroperitoneal Liposarcoma.
de Faria FCC, Khurshid S, Sarchet P, Tahara S, Casadei L, Grignol V, Karna R, Rentsch S, Sp N, Beane JD, Mazzoccoli L, Montes M, Nigita G, Sharick JT, Leight JL, Calore F, Chandler DS, Pollock RE. 
Int J Mol Sci
PMID: 39769278

Utilizing a portable magnetic resonance imaging (MRI) in the setting of an acute ischemic stroke in a patient with a cardiac implantable electronic device.
Patel MS, Mannix N, Carfora A, Nimjee SM.
Interv Neuroradiol. 2024 Dec;30(6):862-865. 
PMID: 39340468 

Direct and indirect effects of spliceosome disruption compromise gene regulation by Nonsense-Mediated mRNA Decay.
Embree CM, Stephanou A, Singh G.
bioRxiv [Preprint]. 2024 Dec 27:2024.12.27.630533. 
PMID: 39763844  
 
Regulation of human interferon signaling by transposon exonization.
Pasquesi GIM, Allen H, Ivancevic A, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen LL, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB.
Cell. 2024 Dec 26;187(26):7621-7636.e19
PMID: 39672162 

Regulation of human interferon signaling by transposon exonization.
Pasquesi GIM, Allen H, Ivancevic A, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen L, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB.
bioRxiv [Preprint]. 2023 Sep 15:2023.09.11.557241.
Update in:  Cell. 2024 Dec 26;187(26):7621-7636.e19.
PMID: 37745311