UFGI Publication Round-up: Week of 6/10/24

Li Y, Tang H, Guo Y, Shao H, Kimmel SE, Bian J, Schatz DA, Guo J.

Front Pharmacol. 2024 May 23;15:1379251. doi: 10.3389/fphar.2024.1379251. eCollection 2024.

PMID: 38846094

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez Martinez JM, Hunt T, Lagarde J, Liang CE, Li H, Meade MJ, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Çelik MH, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Li JL, Lienhard M, Mikheenko A, Mulligan D, Nip KM, Pertea M, Ritchie ME, Sim AD, Tang AD, Wan YK, Wang C, Wong BY, Yang C, Barnes I, Berry AE, Capella-Gutierrez S, Cousineau A, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Götz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Ren X, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Smith ML, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Maehr R, Shen Y, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Au KF, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN.

Nat Methods. 2024 Jun 7. doi: 10.1038/s41592-024-02298-3. Online ahead of print.

PMID: 38849569

Genome evolution of the ancient hexaploid Platanus × acerifolia (London planetree).

Yan X, Shi G, Sun M, Shan S, Chen R, Li R, Wu S, Zhou Z, Li Y, Liu Z, Hu Y, Liu Z, Soltis PS, Zhang J, Soltis DE, Ning G, Bao M.

Proc Natl Acad Sci U S A. 2024 Jun 11;121(24):e2319679121. doi: 10.1073/pnas.2319679121. Epub 2024 Jun 3.

PMID: 38830106

Expression of mitochondrial oxidative stress response genes in muscle is associated with mitochondrial respiration, physical performance, and muscle mass in the Study of Muscle, Mobility, and Aging.

Tranah GJ, Barnes HN, Cawthon PM, Coen PM, Esser KA, Hepple RT, Huo Z, Kramer PA, Toledo FGS, Zhang X, Wu K, Wolff CA, Evans DS, Cummings SR.

Aging Cell. 2024 Jun 3:e14114. doi: 10.1111/acel.14114. Online ahead of print.

PMID: 38831629

Higher expression of denervation-responsive genes is negatively associated with muscle volume and performance traits in the study of muscle, mobility, and aging (SOMMA).

Lukasiewicz CJ, Tranah GJ, Evans DS, Coen PM, Barnes HN, Huo Z, Esser KA, Zhang X, Wolff C, Wu K, Lane NE, Kritchevsky SB, Newman AB, Cummings SR, Cawthon PM, Hepple RT.

Aging Cell. 2024 Jun 3:e14115. doi: 10.1111/acel.14115. Online ahead of print.

PMID: 38831622

Bigger isn’t always better: Challenging assumptions about the associations between diapause, body weight, and overwintering survival.

Short CA, Walters JL, Hahn DA.

Ecol Evol. 2024 Jun 3;14(6):e11511. doi: 10.1002/ece3.11511. eCollection 2024 Jun.

PMID: 38835525

Amplified and distinctive genotoxicity of titanium dioxide nanoparticles in transformed yeast reporters with human cytochrome P450 (CYP) genes.

Jiang T, Hou L, Rahman SM, Gong Z, Bai X, Vulpe C, Fasullo M, Gu AZ.

J Hazard Mater. 2024 Jun 6;474:134850. doi: 10.1016/j.jhazmat.2024.134850. Online ahead of print.

PMID: 38850947

Impaired islet function and normal exocrine enzyme secretion occur with low inter-regional variation in type 1 diabetes.

Drotar DM, Mojica-Avila AK, Bloss DT, Cohrs CM, Manson CT, Posgai AL, Williams MD, Brusko MA, Phelps EA, Wasserfall CH, Speier S, Atkinson MA.

Cell Rep. 2024 Jun 7;43(6):114346. doi: 10.1016/j.celrep.2024.114346. Online ahead of print.

PMID: 38850534

High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive TE superfamilies in the clonal Lombardy poplar.

Peña-Ponton C, Diez-Rodriguez B, Perez-Bello P, Becker C, McIntyre LM, van der Putten WH, De Paoli E, Heer K, Opgenoorth L, Verhoeven KJF.

J Exp Bot. 2024 Jun 5:erae262. doi: 10.1093/jxb/erae262. Online ahead of print.

PMID: 38836523

Genetic relationships between behavioral traits and feed efficiency traits in lactating Holstein cows.

Nascimento BM, Cavani L, Caputo MJ, Marinho MN, Borchers MR, Wallace RL, Santos JEP, White HM, Peñagaricano F, Weigel KA.

J Dairy Sci. 2024 May 31:S0022-0302(24)00835-X. doi: 10.3168/jds.2023-24526. Online ahead of print.

PMID: 38825121

Genome-wide determinants of mortality and motor progression in Parkinson’s disease.

Tan MMX, Lawton MA, Pollard MI, Brown E, Real R, Carrasco AM, Bekadar S, Jabbari E, Reynolds RH, Iwaki H, Blauwendraat C, Kanavou S, Hubbard L, Malek N, Grosset KA, Bajaj N, Barker RA, Burn DJ, Bresner C, Foltynie T, Wood NW, Williams-Gray CH, Andreassen OA, Toft M, Elbaz A, Artaud F, Brice A, Corvol JC, Aasly J, Farrer MJ, Nalls MA, Singleton AB, Williams NM, Ben-Shlomo Y, Hardy J, Hu MTM, Grosset DG, Shoai M, Pihlstrøm L, Morris HR.

NPJ Parkinsons Dis. 2024 Jun 7;10(1):113. doi: 10.1038/s41531-024-00729-8.

PMID: 38849413

Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases.

Zhang S, Shu H, Zhou J, Rubin-Sigler J, Yang X, Liu Y, Cooper-Knock J, Monte E, Zhu C, Tu S, Li H, Tong M, Ecker JR, Ichida JK, Shen Y, Zeng J, Tsao PS, Snyder MP.

bioRxiv [Preprint]. 2024 May 14:2024.05.14.594252. doi: 10.1101/2024.05.14.594252.

PMID: 38798507

The Effects of Simulated and Real Microgravity on Vascular Smooth Muscle Cells.

Ludtka C, Allen JB.

Gravit Space Res. 2024 Jan;12(1):46-59. doi: 10.2478/gsr-2024-0003. Epub 2024 May 25.

PMID: 38846256

Status of single-cell RNA sequencing for reproductive toxicology in zebrafish and the transcriptomic trade-off.

Connell ML, Meyer DN, Haimbaugh A, Baker TR.

Curr Opin Toxicol. 2024 Jun;38:100463. doi: 10.1016/j.cotox.2024.100463. Epub 2024 Jan 26.

PMID: 38846809