Publications

2024 Publications

June 2024

Genotype-specific nonphotochemical quenching responses to nitrogen deficit are linked to chlorophyll a to b ratios.

Sahay S, Grzybowski M, Schnable JC, Głowacka K. J Plant Physiol. 2024 Jun;297:154261. doi: 10.1016/j.jplph.2024.154261. Epub 2024 May 1. PMID: 38705078

Brown midrib (BMR) and plant age impact fall armyworm (Spodoptera frugiperda) growth and development in sorghum-sudangrass (Sorghum x drummondii).

Vasquez A, Balakrishnan D, Ayala J, Loftin K, Louis J, Kariyat R. Sci Rep. 2024 Jun 2;14(1):12649. doi: 10.1038/s41598-024-63397-x.PMID: 38825611

The role of extracellular structures in Clostridioides difficile biofilm formation.

Ronish LA, Biswas B, Bauer RM, Jacob ME, Piepenbrink KH. Anaerobe. 2024 Jun 4:102873. doi: 10.1016/j.anaerobe.2024.102873. Online ahead of print. PMID: 38844261

Liver matrin-3 protects mice against hepatic steatosis and stress response via constitutive androstane receptor.

Cheng X, Baki VB, Moran M, Liu B, Yu J, Zhao M, Li Q, Riethoven JJ, Gurumurth CB, Harris EN, Sun X. Mol Metab. 2024 Jun 25:101977. doi: 10.1016/j.molmet.2024.101977. Online ahead of print. PMID: 38936659

Tissue- and time-dependent metabolite profiles during early grain development under normal and high night-time temperature conditions.

Abshire N, Hauck AL, Walia H, Obata T. BMC Plant Biol. 2024 Jun 18;24(1):568. doi: 10.1186/s12870-024-05190-6. PMID: 38886651

descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques.

Otomo K, Omura T, Nozawa Y, Edwards SJ, Sato Y, Saito Y, Yagishita S, Uchida H, Watakabe Y, Naitou K, Yanai R, Sahara N, Takagi S, Katayama R, Iwata Y, Shiokawa T, Hayakawa Y, Otsuka K, Watanabe-Takano H, Haneda Y, Fukuhara S, Fujiwara M, Nii T, Meno C, Takeshita N, Yashiro K, Rosales Rocabado JM, Kaku M, Yamada T, Oishi Y, Koike H, Cheng Y, Sekine K, Koga JI, Sugiyama K, Kimura K, Karube F, Kim H, Manabe I, Nemoto T, Tainaka K, Hamada A, Brismar H, Susaki EA. Nat Commun. 2024 Jun 12;15(1):4941. doi: 10.1038/s41467-024-49131-1. PMID: 38866781

WhiB-like proteins: Diversity of structure, function and mechanism.

Guiza Beltran D, Wan T, Zhang L. Biochim Biophys Acta Mol Cell Res. 2024 Jun 13;1871(7):119787. doi: 10.1016/j.bbamcr.2024.119787. Online ahead of print. PMID: 3887913

Perspectives on computational modeling of biological systems and the significance of the SysMod community.

Puniya BL, Verma M, Damiani C, Bakr S, Dräger A. Bioinform Adv. 2024 Jun 26;4(1):vbae090. doi: 10.1093/bioadv/vbae090. eCollection 2024. PMID: 38948011

May 2024

Glucosylceramides impact cellulose deposition and cellulose synthase complex motility in Arabidopsis.

Villalobos JA, Cahoon RE, Cahoon EB, Wallace IS. Glycobiology. 2024 May 1:cwae035. doi: 10.1093/glycob/cwae035. Online ahead of print. PMID: 38690785

Project ChemicalBlooms: Collaborating with citizen scientists to survey the chemical diversity and phylogenetic distribution of plant epicuticular wax blooms.

Nguyen LTD, Groth N, Mondloch K, Cahoon EB, Jones K, Busta L. Plant Direct. 2024 May 17;8(5):e588. doi: 10.1002/pld3.588. eCollection 2024 May. PMID: 38766509

Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution.

Huang Y, Kumar S, Lee J, Lü W, Du J.Nat Struct Mol Biol. 2024 May 21. doi: 10.1038/s41594-024-01316-4. Online ahead of print. PMID: 38773335

Rhythmic lipid and gene expression responses to chilling in panicoid grasses.

Kenchanmane Raju SK, Zhang Y, Mahboub S, Ngu DW, Qiu Y, Harmon FG, Schnable JC, Roston RL. J Exp Bot. 2024 May 29:erae247. doi: 10.1093/jxb/erae247. Online ahead of print. PMID: 38808657

Plant and Algal Lipids: In All Their States and On All Scales.

Li-Beisson Y, Roston RL. Plant Cell Physiol. 2024 May 29:pcae061. doi: 10.1093/pcp/pcae061. Online ahead of print. PMID: 38808362

April 2024

TSG-6 mediated extracellular matrix modifications regulate hypoxic-ischemic brain injury.

Srivastava T, Nguyen H, Haden G, Diba P, Sowa S, LaNguyen N, Reed-Dustin W, Zhu W, Gong X, Harris EN, Baltan S, Back SA. J Neurosci. 2024 Apr 3:e2215232024. doi: 10.1523/JNEUROSCI.2215-23.2024. Online ahead of print. PMID: 38569926

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5.

Smith LP, Bergmann FT, Garny A, Helikar T, Karr J, Nickerson D, Sauro H, Waltemath D, König M. J Integr Bioinform. 2024 Apr 15. doi: 10.1515/jib-2024-0008. Online ahead of print. PMID: 38613325

March 2024

Metabolic collaboration between cells in the tumor microenvironment has a negligible effect on tumor growth.

Gustafsson J, Roshanzamir F, Hagnestål A, Patel SM, Daudu OI, Becker DF, Robinson JL, Nielsen J. Innovation (Camb). 2024 Jan 30;5(2):100583. doi: 10.1016/j.xinn.2024.100583. eCollection 2024 Mar 4. PMID: 38445018

Non-photochemical quenching upregulation improves water use efficiency and reduces whole plant level water consumption under drought.

Turc B, Sahay S, Haupt J, de Oliveira Santos T, Bai G, Glowacka K. J Exp Bot. 2024 Mar 12:erae113. doi: 10.1093/jxb/erae113. Online ahead of print. PMID: 38470077

Addressing the climate crisis through engineering biology.

Aurand, E.R., Moon, T.S., Buan, N.R. et al. NPJ Clim. Action 3, 9 2024 Feb. 21.

Toward mechanistic medical digital twins: some use cases in immunology.

Laubenbacher R, Adler F, An G, Castiglione F, Eubank S, Fonseca LL, Glazier J, Helikar T, Jett-Tilton M, Kirschner D, Macklin P, Mehrad B, Moore B, Pasour V, Shmulevich I, Smith A, Voigt I, Yankeelov TE, Ziemssen T. Front Digit Health. 2024 Mar 7;6:1349595. doi: 10.3389/fdgth.2024.1349595. eCollection 2024. PMID: 38515550

Beyond Bites: Differential Role of Fall Armyworm Oral Secretions and Saliva in Modulating Sorghum Defenses.

Shinde S, Kundu P, Louis J. Mol Plant Microbe Interact. 2024 Mar;37(3):232-238. doi: 10.1094/MPMI-12-23-0213-FI. Epub 2024 Mar 28. PMID: 38240672

Multifaceted roles of Meg3 in cellular senescence and atherosclerosis.

Cheng X, Shihabudeen Haider Ali MS, Baki VB, Moran M, Su H, Sun X. Atherosclerosis. 2024 Mar 8;392:117506. doi: 10.1016/j.atherosclerosis.2024.117506. Online ahead of print. PMID: 38518516

Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography.

Smith N, Dasgupta M, Wych DC, Dolamore C, Sierra RG, Lisova S, Marchany-Rivera D, Cohen AE, Boutet S, Hunter MS, Kupitz C, Poitevin F, Moss FR 3rd, Mittan-Moreau DW, Brewster AS, Sauter NK, Young ID, Wolff AM, Tiwari VK, Kumar N, Berkowitz DB, Hadt RG, Thompson MC, Follmer AH, Wall ME, Wilson MA. Sci Adv. 2024 Mar 29;10(13):eadk7201. doi: 10.1126/sciadv.adk7201. Epub 2024 Mar 27. PMID: 38536910

Endurance training increases mitochondrial myoglobin and enhances its interaction with complex IV in rat plantaris muscle.

Koma R, Shibaguchi T, Yamada T, Nonaka Y, Jue T, Yamazaki A, Masuda K. Acta Physiol (Oxf). 2024 Mar 21:e14139. doi: 10.1111/apha.14139. Online ahead of print. PMID: 38509816

February 2024

Emerging Roles of Cullin-RING Ubiquitin Ligases in Cardiac Development.

Zambrano-Carrasco J, Zou J, Wang W, Sun X, Li J, Su H. Cells. 2024 Jan 26;13(3):235. doi: 10.3390/cells13030235. PMID: 38334627

Maize terpene synthase 1 impacts insect behavior via the production of monoterpene volatiles β-myrcene and linalool.

Yactayo-Chang JP, Broadhead GT, Housler RJ, Resende MFR Jr, Verma K, Louis J, Basset GJ, Beck JJ, Block AK. Phytochemistry. 2024 Feb;218:113957. doi: 10.1016/j.phytochem.2023.113957. Epub 2023 Dec 27. PMID: 38154731

Vitamin E biofortification: enhancement of seed tocopherol concentrations by altered chlorophyll metabolism.

Qin P, Chen P, Zhou Y, Zhang W, Zhang Y, Xu J, Gan L, Liu Y, Romer J, Dörmann P, Cahoon EB, Zhang C. Front Plant Sci. 2024 Feb 26;15:1344095. doi: 10.3389/fpls.2024.1344095. eCollection 2024. PMID: 38469330

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.

Niarakis A, Ostaszewski M, Mazein A, … Puniya BL, Naldi A, Helikar T, … COVID-19 Disease Map Community. Front Immunol. 2024 Feb 13;14:1282859. doi: 10.3389/fimmu.2023.1282859. eCollection 2023. PMID: 38414974

Forum on immune digital twins: a meeting report.

Laubenbacher R, Adler F, An G, Castiglione F, Eubank S, Fonseca LL, Glazier J, Helikar T, Jett-Tilton M, Kirschner D, Macklin P, Mehrad B, Moore B, Pasour V, Shmulevich I, Smith A, Voigt I, Yankeelov TE, Ziemssen T. NPJ Syst Biol Appl. 2024 Feb 16;10(1):19. doi: 10.1038/s41540-024-00345-5. PMID: 38365857

Recurrent evolutionary switches of mitochondrial cytochrome c maturation systems in Archaeplastida.

Li H, Akella S, Engstler C, Omini JJ, Rodriguez M, Obata T, Carrie C, Cerutti H, Mower JP. Nat Commun. 2024 Feb 20;15(1):1548. doi: 10.1038/s41467-024-45813-y.PMID: 38378784

All Members of the Arabidopsis DGAT and PDAT Acyltransferase Families Operate During High and Low Temperatures.

Shomo ZD, Mahboub S, Vanviratikul H, McCormick M, Tulyananda T, Roston RL, Warakanont J. Plant Physiol. 2024 Feb 22:kiae074. doi: 10.1093/plphys/kiae074. Online ahead of print. PMID: 38386316