UFGI Publication Round-up: Week of 4/29/24

Characterizing the Palm Pathogenic Thielaviopsis Species from Florida.

Ayika MG, Rosano A, Valiente J, Chakrabarti S, Rollins JA, Dhillon B.

J Fungi (Basel). 2024 Mar 26;10(4):247. doi: 10.3390/jof10040247.

PMID: 38667918

Chemical Genetics in C. elegans Identifies Anticancer Mycotoxins Chaetocin and Chetomin as Potent Inducers of a Nuclear Metal Homeostasis Response.

Abraham E, Athapaththu AMGK, Atanasova KR, Chen QY, Corcoran TJ, Piloto J, Wu CW, Ratnayake R, Luesch H, Choe KP.

ACS Chem Biol. 2024 Apr 23. doi: 10.1021/acschembio.4c00131. Online ahead of print.

PMID: 38652683

Phylogenomics and the rise of the angiosperms.

Zuntini AR, Carruthers T, Maurin O, Bailey PC, Leempoel K, Brewer GE, Epitawalage N, Françoso E, Gallego-Paramo B, McGinnie C, Negrão R, Roy SR, Simpson L, Toledo Romero E, Barber VMA, Botigué L, Clarkson JJ, Cowan RS, Dodsworth S, Johnson MG, Kim JT, Pokorny L, Wickett NJ, Antar GM, DeBolt L, Gutierrez K, Hendriks KP, Hoewener A, Hu AQ, Joyce EM, Kikuchi IABS, Larridon I, Larson DA, de Lírio EJ, Liu JX, Malakasi P, Przelomska NAS, Shah T, Viruel J, Allnutt TR, Ameka GK, Andrew RL, Appelhans MS, Arista M, Ariza MJ, Arroyo J, Arthan W, Bachelier JB, Bailey CD, Barnes HF, Barrett MD, Barrett RL, Bayer RJ, Bayly MJ, Biffin E, Biggs N, Birch JL, Bogarín D, Borosova R, Bowles AMC, Boyce PC, Bramley GLC, Briggs M, Broadhurst L, Brown GK, Bruhl JJ, Bruneau A, Buerki S, Burns E, Byrne M, Cable S, Calladine A, Callmander MW, Cano Á, Cantrill DJ, Cardinal-McTeague WM, Carlsen MM, Carruthers AJA, de Castro Mateo A, Chase MW, Chatrou LW, Cheek M, Chen S, Christenhusz MJM, Christin PA, Clements MA, Coffey SC, Conran JG, Cornejo X, Couvreur TLP, Cowie ID, Csiba L, Darbyshire I, Davidse G, Davies NMJ, Davis AP, van Dijk KJ, Downie SR, Duretto MF, Duvall MR, Edwards SL, Eggli U, Erkens RHJ, Escudero M, de la Estrella M, Fabriani F, Fay MF, Ferreira PL, Ficinski SZ, Fowler RM, Frisby S, Fu L, Fulcher T, Galbany-Casals M, Gardner EM, German DA, Giaretta A, Gibernau M, Gillespie LJ, González CC, Goyder DJ, Graham SW, Grall A, Green L, Gunn BF, Gutiérrez DG, Hackel J, Haevermans T, Haigh A, Hall JC, Hall T, Harrison MJ, Hatt SA, Hidalgo O, Hodkinson TR, Holmes GD, Hopkins HCF, Jackson CJ, James SA, Jobson RW, Kadereit G, Kahandawala IM, Kainulainen K, Kato M, Kellogg EA, King GJ, Klejevskaja B, Klitgaard BB, Klopper RR, Knapp S, Koch MA, Leebens-Mack JH, Lens F, Leon CJ, Léveillé-Bourret É, Lewis GP, Li DZ, Li L, Liede-Schumann S, Livshultz T, Lorence D, Lu M, Lu-Irving P, Luber J, Lucas EJ, Luján M, Lum M, Macfarlane TD, Magdalena C, Mansano VF, Masters LE, Mayo SJ, McColl K, McDonnell AJ, McDougall AE, McLay TGB, McPherson H, Meneses RI, Merckx VSFT, Michelangeli FA, Mitchell JD, Monro AK, Moore MJ, Mueller TL, Mummenhoff K, Munzinger J, Muriel P, Murphy DJ, Nargar K, Nauheimer L, Nge FJ, Nyffeler R, Orejuela A, Ortiz EM, Palazzesi L, Peixoto AL, Pell SK, Pellicer J, Penneys DS, Perez-Escobar OA, Persson C, Pignal M, Pillon Y, Pirani JR, Plunkett GM, Powell RF, Prance GT, Puglisi C, Qin M, Rabeler RK, Rees PEJ, Renner M, Roalson EH, Rodda M, Rogers ZS, Rokni S, Rutishauser R, de Salas MF, Schaefer H, Schley RJ, Schmidt-Lebuhn A, Shapcott A, Al-Shehbaz I, Shepherd KA, Simmons MP, Simões AO, Simões ARG, Siros M, Smidt EC, Smith JF, Snow N, Soltis DE, Soltis PS, Soreng RJ, Sothers CA, Starr JR, Stevens PF, Straub SCK, Struwe L, Taylor JM, Telford IRH, Thornhill AH, Tooth I, Trias-Blasi A, Udovicic F, Utteridge TMA, Del Valle JC, Verboom GA, Vonow HP, Vorontsova MS, de Vos JM, Al-Wattar N, Waycott M, Welker CAD, White AJ, Wieringa JJ, Williamson LT, Wilson TC, Wong SY, Woods LA, Woods R, Worboys S, Xanthos M, Yang Y, Zhang YX, Zhou MY, Zmarzty S, Zuloaga FO, Antonelli A, Bellot S, Crayn DM, Grace OM, Kersey PJ, Leitch IJ, Sauquet H, Smith SA, Eiserhardt WL, Forest F, Baker WJ.

Nature. 2024 Apr 24. doi: 10.1038/s41586-024-07324-0. Online ahead of print.

PMID: 38658746

Leveraging QSP Models for MIPD: A Case Study for Warfarin/INR.

Falkenhagen U, Cavallari LH, Duarte JD, Kloft C, Schmidt S, Huisinga W.

Clin Pharmacol Ther. 2024 Apr 24. doi: 10.1002/cpt.3274. Online ahead of print.

PMID: 38655898

Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas.

Pena MM, Bhandari R, Bowers RM, Weis K, Newberry E, Wagner N, Pupko T, Jones JB, Woyke T, Vinatzer BA, Jacques MA, Potnis N.

Genome Biol Evol. 2024 Apr 2;16(4):evae074. doi: 10.1093/gbe/evae074.

PMID: 38648506

Xanthomonas as a model system for studying pathogen emergence and evolution.

Timilsina S, Kaur A, Sharma A, Ramamoorthy S, Vallad GE, Wang N, White FF, Potnis N, Goss EM, Jones JB.

Phytopathology. 2024 Apr 22. doi: 10.1094/PHYTO-03-24-0084-RVW. Online ahead of print.

PMID: 38648116

Spaceflight impacts xyloglucan oligosaccharide abundance in Arabidopsis thaliana root cell walls.

Diao X, Haveman N, Califar B, Dong X, Prentice B, Paul AL, Ferl RJ.

Life Sci Space Res (Amst). 2024 May;41:110-118. doi: 10.1016/j.lssr.2024.02.004. Epub 2024 Feb 16.

PMID: 38670637

Ctenophora: Illustrated Guide and Taxonomy.

Moroz LL, Collins R, Paulay G.

Methods Mol Biol. 2024;2757:27-102. doi: 10.1007/978-1-0716-3642-8_2.

PMID: 38668962

Toxic effects of local anesthetics on rat fibroblasts: An in-vitro study.

Hones KM, Hao KA, Wright JO, Wright TW, Hartzell J, Myara DA, Levings PP, Badman B, Ghivizzani SC, Watson Levings RS.

J Orthop Sci. 2024 Apr 25:S0949-2658(24)00060-5. doi: 10.1016/j.jos.2024.04.003. Online ahead of print.

PMID: 38670825

Bioinformatic Prohormone Discovery in Basal Metazoans: Insights from Trichoplax.

Nikitin MA, Romanova DY, Moroz LL.

Methods Mol Biol. 2024;2757:531-581. doi: 10.1007/978-1-0716-3642-8_22.

PMID: 38668982

Long-Term Culturing of Placozoans (Trichoplax and Hoilungia).

Romanova DY, Varoqueaux F, Eitel M, Yoshida MA, Nikitin MA, Moroz LL.

Methods Mol Biol. 2024;2757:509-529. doi: 10.1007/978-1-0716-3642-8_21.

PMID: 38668981

Parallel Evolution of Transcription Factors in Basal Metazoans.

Mukherjee K, Moroz LL.

Methods Mol Biol. 2024;2757:491-508. doi: 10.1007/978-1-0716-3642-8_20.

PMID: 38668980

Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution.

Hsiao J, Deng LC, Moroz LL, Chalasani SH, Edsinger E.

Methods Mol Biol. 2024;2757:461-490. doi: 10.1007/978-1-0716-3642-8_19.

PMID: 38668979

DNA Methylation in Ctenophores.

Dabe EC, Kohn AB, Moroz LL.

Methods Mol Biol. 2024;2757:447-460. doi: 10.1007/978-1-0716-3642-8_18.

PMID: 38668978

Analysis and Visualization of Single-Cell Sequencing Data with Scanpy and MetaCell: A Tutorial.

Li Y, Sun C, Romanova DY, Wu DO, Fang R, Moroz LL.

Methods Mol Biol. 2024;2757:383-445. doi: 10.1007/978-1-0716-3642-8_17.

PMID: 38668977

Gap Junctions in Ctenophora.

Kohn AB, Moroz LL.

Methods Mol Biol. 2024;2757:361-381. doi: 10.1007/978-1-0716-3642-8_16.

PMID: 38668976

Recording Cilia Activity in Ctenophores.

Norekian TP, Moroz LL.

Methods Mol Biol. 2024;2757:307-313. doi: 10.1007/978-1-0716-3642-8_14.

PMID: 38668974

Gene Expression Patterns in the Ctenophore Pleurobrachia bachei: In Situ Hybridization.

Kohn AB, Bobkova Y, Moroz LL.

Methods Mol Biol. 2024;2757:215-237. doi: 10.1007/978-1-0716-3642-8_9.

PMID: 38668969

RNA Isolation from Ctenophores.

Kohn AB, Bobkova Y, Moroz LL.

Methods Mol Biol. 2024;2757:201-214. doi: 10.1007/978-1-0716-3642-8_8.

PMID: 38668968

DNA Isolation Long-Read Genomic Sequencing in Ctenophores.

Moraga Amador D, Kohn AB, Bobkova Y, Panayotova NG, Moroz LL.

Methods Mol Biol. 2024;2757:185-200. doi: 10.1007/978-1-0716-3642-8_7.

PMID: 38668967

Scanning Electron Microscopy of Ctenophores: Illustrative Atlas.

Norekian TP, Moroz LL.

Methods Mol Biol. 2024;2757:163-184. doi: 10.1007/978-1-0716-3642-8_6.

PMID: 38668966

Illustrated Neuroanatomy of Ctenophores: Immunohistochemistry.

Norekian TP, Moroz LL.

Methods Mol Biol. 2024;2757:147-161. doi: 10.1007/978-1-0716-3642-8_5.

PMID: 38668965

Brief History of Placozoa.

Romanova DY, Moroz LL.

Methods Mol Biol. 2024;2757:103-122. doi: 10.1007/978-1-0716-3642-8_3.

PMID: 38668963

Brief History of Ctenophora.

Moroz LL.

Methods Mol Biol. 2024;2757:1-26. doi: 10.1007/978-1-0716-3642-8_1.

PMID: 38668961

Molecular, behavioral, and growth responses of juvenile yellow catfish (Tachysurus fulvidraco) exposed to carbamazepine.

Chen H, Gu X, Mao Z, Zeng Q, Jin M, Wang W, Martyniuk CJ.

Aquat Toxicol. 2024 Apr 20;271:106929. doi: 10.1016/j.aquatox.2024.106929. Online ahead of print.

PMID: 38663201

Bringing the Genomic Revolution to Comparative Oncology: Human and Dog Cancers.

Cahill JA, Smith LA, Gottipati S, Torabi TS, Graim K.

Annu Rev Biomed Data Sci. 2024 Apr 22. doi: 10.1146/annurev-biodatasci-102423-111936. Online ahead of print.

PMID: 38648188

Radiation Biological Toximetry Using Circulating Cell-Free DNA (cfDNA) for Rapid Radiation/Nuclear Triage.

Okunieff P, Swarts SG, Fenton B, Zhang SB, Zhang Z, Rice L, Zhou D, Carrier F, Zhang L.

Radiat Res. 2024 Apr 25. doi: 10.1667/RADE-23-00159.1. Online ahead of print.

PMID: 38661544

Deep learning modeling of rare noncoding genetic variants in human motor neurons defines CCDC146 as a therapeutic target for ALS.

Zhang S, Moll T, Rubin-Sigler J, Tu S, Li S, Yuan E, Liu M, Butt A, Harvey C, Gornall S, Alhalthli E, Shaw A, Souza CDS, Ferraiuolo L, Hornstein E, Shelkovnikova T, van Dijk CH, Timpanaro IS, Kenna KP, Zeng J, Tsao PS, Shaw PJ, Ichida JK, Cooper-Knock J, Snyder MP.

medRxiv [Preprint]. 2024 Apr 1:2024.03.30.24305115. doi: 10.1101/2024.03.30.24305115.

PMID: 38633814

A group of L-type lectin receptor kinases function redundantly in mediating extracellular NAD(P) signaling in Arabidopsis.

Li Q, Zhou M, Harris F, Mou Z.

Plant Physiol. 2024 Apr 23:kiae224. doi: 10.1093/plphys/kiae224. Online ahead of print.

PMID: 38652702

Subcutaneous injection of adipose stromal cell-secretome improves renal function and reduces inflammation in established acute kidney injury.

Ullah MM, Collett JA, Monroe JC, Traktuev D, Coleman M, March KL, Basile DP.

Stem Cell Res Ther. 2024 Apr 24;15(1):119. doi: 10.1186/s13287-024-03736-x.

PMID: 38659070

Diet-induced metabolic and immune impairments are sex-specifically modulated by soluble TNF signaling in the 5xFAD mouse model of Alzheimer’s disease.

Rodrigues MES, Bolen ML, Blackmer-Raynolds L, Schwartz N, Chang J, Tansey MG, Sampson TR.

Neurobiol Dis. 2024 Apr 24:106511. doi: 10.1016/j.nbd.2024.106511. Online ahead of print.

PMID: 38670277

Periparturient Mineral Metabolism: Implications to Health and Productivity.

Vieira-Neto A, Lean IJ, Santos JEP.

Animals (Basel). 2024 Apr 19;14(8):1232. doi: 10.3390/ani14081232.

PMID: 38672379

Short-Term Dietary Restriction Potentiates an Anti-Inflammatory Circulating Mucosal-Associated Invariant T-Cell Response.

Fazzone B, Anderson EM, Rozowsky JM, Yu X, O’Malley KA, Robinson S, Scali ST, Cai G, Berceli SA.

Nutrients. 2024 Apr 22;16(8):1245. doi: 10.3390/nu16081245.

PMID: 38674935