Publications

Preparation of Uniformly Oriented Inverted Inner (Cytoplasmic) Membrane Vesicles from Gram-Negative Bacterial Cells. Bogdanov M. Methods Mol Biol. 2024;2715:159-180. doi: 10.1007/978-1-0716-3445-5_10.PMID: 37930527

Exploring Uniform, Dual, and Dynamic Topologies of Membrane Proteins by Substituted Cysteine Accessibility Method (SCAM™). Bogdanov M. Methods Mol Biol. 2024;2715:121-157. doi: 10.1007/978-1-0716-3445-5_9.PMID: 37930526

CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames. Zheng C, Wei Y, Zhang P, Lin K, He D, Teng H, Manyam G, Zhang Z, Liu W, Lee HRL, Tang X, He W, Islam N, Jain A, Chiu Y, Cao S, Diao Y, Meyer-Gauen S, Höök M, Malovannaya A, Li W, Hu M, Wang W, Xu H, Kopetz S, Chen Y.  Nat Struct Mol Biol. 2023 Nov 6;. doi: 10.1038/s41594-023-01117-1. [Epub ahead of print] PubMed PMID: 37932451.

Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Calandrelli R, Wen X, Charles Richard JL, Luo Z, Nguyen TC, Chen CJ, Qi Z, Xue S, Chen W, Yan Z, Wu W, Zaleta-Rivera K, Hu R, Yu M, Wang Y, Li W, Ma J, Ren B, Zhong S.  Nat Commun. 2023 Oct 16;14(1):6519. doi: 10.1038/s41467-023-42274-7. PubMed PMID: 37845234; PubMed Central PMCID: PMC10579264.

Channel Gating in Kalium Channelrhodopsin Slow Mutants.  Sineshchekov OA, Govorunova EG, Li H, Wang Y, Spudich JL. J Mol Biol. 2023 Oct 5:168298. doi: 10.1016/j.jmb.2023.168298. Online ahead of print. PMID: 37802216

Tissue Transglutaminase: A Multifunctional and Multisite Regulator in Health and Disease.  Yao Z, Fan Y, Lin L, Kellems RE, Xia Y. Physiol Rev. 2023 Sep 15. doi: 10.1152/physrev.00003.2023. Online ahead of print. PMID: 37712623 Review.

The Circadian Nobiletin-ROR Axis Suppresses Adipogenic Differentiation and IκBα/NF-κB Signaling in Adipocytes.Kim E, Mawatari K, Yoo SH, Chen Z. Nutrients. 2023 Sep 9;15(18):3919. doi: 10.3390/nu15183919. PMID: 37764703 Free PMC article.

Isospectral intermediates in the photochemical reaction cycle of anion channelrhodopsin GtACR1.  Schleissner P, Szundi I, Chen E, Li H, Spudich JL, Kliger DS. Biophys J. 2023 Oct 17;122(20):4091-4103. doi: 10.1016/j.bpj.2023.09.009. Epub 2023 Sep 25.PMID: 37749886

Differentiation of gram-negative intermembrane phospholipid transporter function by intrinsic substrate preference. Rai AK, Sawasato K, Kozlova A, Sparagna GC, Bogdanov M, Mitchell AM. bioRxiv. 2023 Sep 14:2023.06.21.545913. doi: 10.1101/2023.06.21.545913. Preprint. PMID: 37745482 Free PMC article.

Regulation of store-operated calcium entry. Kodakandla G, Akimzhanov AM, Boehning D. ArXiv. 2023 Sep 26:arXiv:2309.06907v2. Preprint. PMID: 37744466 Free PMC article.

Animal models in systemic sclerosis: an update. Bi X, Mills T, Wu M.  Curr Opin Rheumatol. 2023 Nov 1;35(6):364-370. doi: 10.1097/BOR.0000000000000967. Epub 2023 Aug 21. Review. PubMed PMID: 37605874; PubMed Central PMCID: PMC10553484.

Erythrocyte ENT1-AMPD3 Axis is an Essential Purinergic Hypoxia Sensor and Energy Regulator Combating CKD in a Mouse Model.Chen C, Xie T, Zhang Y, Wang Y, Yu F, Lin L, Zhang W, Brown BC, Zhang X, Kellems RE, D’Alessandro A, Xia Y. J Am Soc Nephrol. 2023 Oct 1;34(10):1647-1671. doi: 10.1681/ASN.0000000000000195. Epub 2023 Aug 7. PMID: 37725437

 Partial agonism in heteromeric GLUK2/GLUK5 kainate receptor. Paudyal N, Das A, Carrillo E, Berka V, Jayaraman V.  Proteins. 2023 Aug 1;. doi: 10.1002/prot.26565. [Epub ahead of print] PubMed PMID: 37526035; NIHMSID:NIHMS1919771.

Snakes and Ladders: A Potential Therapy of Hepatocyte Growth Factor and Pigment Epithelium-derived Factor in Pulmonary Hypertension. Zambelas JM, Karmouty-Quintana H. Am J Respir Cell Mol Biol. 2023 Jul;69(1):10-12. doi: 10.1165/rcmb.2023-0118ED. PubMed PMID: 37167541; PubMed Central PMCID: PMC10324039.

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Mol Cell. 2023 Aug 3;83(15):2624-2640. doi: 10.1016/j.molcel.2023.06.018. Epub 2023 Jul 6. Review. PubMed PMID: 37419111; PubMed Central PMCID: PMC10528254.

Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K⁺ and Na⁺ selectivities. Morizumi T, Kim K, Li H, Govorunova EG, Sineshchekov OA, Wang Y, Zheng L, Bertalan É, Bondar AN, Askari A, Brown LS, Spudich JL, Ernst OP. Nat Commun. 2023 Jul 20;14(1):4365. doi: 10.1038/s41467-023-40041-2.PMID: 37474513 Free PMC article.

When a calorie is not just a calorie: Diet quality and timing as mediators of metabolism and healthy aging.  Mihaylova MM, Chaix A, Delibegovic M, Ramsey JJ, Bass J, Melkani G, Singh R, Chen Z, Ja WW, Shirasu-Hiza M, Latimer MN, Mattison JA, Thalacker-Mercer AE, Dixit VD, Panda S, Lamming DW. Cell Metab. 2023 Jul 11;35(7):1114-1131. doi: 10.1016/j.cmet.2023.06.008. Epub 2023 Jun 30. PMID: 37392742 Review.

Understanding IP₃R channels: From structural underpinnings to ligand-dependent conformational landscape. Baker MR, Fan G, Arige V, Yule DI, Serysheva II. Cell Calcium. 2023 Sep;114:102770. doi: 10.1016/j.ceca.2023.102770. Epub 2023 Jun 22. PMID: 37393815 Review.

Targeting myocardial equilibrative nucleoside transporter ENT1 provides cardioprotection by enhancing myeloid Adora2b signaling. Ruan W, Li J, Choi S, Ma X, Liang Y, Nair R, Yuan X, Mills TW, Eltzschig HK.  JCI Insight. 2023 Jun 8;8(11). doi: 0.1172/jci.insight.166011. PubMed PMID: 37288658; PubMed Central PMCID: PMC10393224.

Ca(2+) efflux facilitated by co-transport of inorganic phosphate anion in the H(+)/Ca(2+) antiporter YfkE. Niu W, Zhou W, Lu S, Vu T, Jayaraman V, Faraldo-Gómez JD, Zheng L.  Commun Biol. 2023 May 29;6(1):573. doi: 10.1038/s42003-023-04944-6. PubMed PMID: 37248347; PubMed Central PMCID: PMC10227063.

Structural insights into cardiolipin replacement by phosphatidylglycerol in a cardiolipin-lacking yeast respiratory supercomplex. Hryc CF, Mallampalli VKPS, Bovshik EI, Azinas S, Fan G, Serysheva II, Sparagna GC, Baker ML, Mileykovskaya E, Dowhan W. Nat Commun. 2023 May 15;14(1):2783. doi: 10.1038/s41467-023-38441-5.PMID: 37188665 Free PMC article.

Sequential absorption of two photons creates a bistable form of RubyACR responsible for its strong desensitization.Sineshchekov OA, Govorunova EG, Li H, Wang Y, Spudich JL. Proc Natl Acad Sci U S A. 2023 May 23;120(21):e2301521120. doi: 10.1073/pnas.2301521120. Epub 2023 May 15. PMID: 37186849 Free PMC article.

Ca²⁺ efflux facilitated by co-transport of inorganic phosphate anion in the H⁺/Ca²⁺ antiporter YfkE. Niu W, Zhou W, Lu S, Vu T, Jayaraman V, Faraldo-Gómez JD, Zheng L. Commun Biol. 2023 May 29;6(1):573. doi: 10.1038/s42003-023-04944-6.PMID: 37248347 Free PMC article.

Probiotic-Derived Ecto-5′-Nucleotidase Produces Anti-Inflammatory Adenosine Metabolites in Treg-Deficient Scurfy Mice. Liu Y, Armbrister SA, Okeugo B, Mills TW, Daniel RC, Oh JH, van Pijkeren JP, Park ES, Saleh ZM, Lahiri S, Roos S, Rhoads J.  Probiotics Antimicrob Proteins. 2023 Aug;15(4):1001-1013. doi: 10.1007/s12602-023-10089-z. Epub 2023 May 13. PubMed PMID: 37178405.

High-resolution transcriptomic and epigenetic profiling identifies novel regulators of COPD. Schwartz U, Llamazares Prada M, Pohl ST, Richter M, Tamas R, Schuler M, Keller C, Mijosek V, Muley T, Schneider MA, Quast K, Hey J, Heußel CP, Warth A, Winter H, Serçin Ö, Karmouty-Quintana H, Jyothula SS, Patel MK, Herth F, Koch I, Petrosino G, Titimeaua A, Mardin BR, Weichenhan D, Jurkowski TP, Imbusch CD, Brors B, Benes V, Jung B, Wyatt D, Stahl HF, Plass C, Jurkowska RZ. EMBO J. 2023 Jun 15;42(12):e111272. doi: 10.15252/embj.2022111272. Epub 2023 May 5. PubMed PMID: 37143403; PubMed Central PMCID: PMC10267701.

Cloning a profibrotic stem cell variant in idiopathic pulmonary fibrosis. Wang S, Rao W, Hoffman A, Lin J, Li J, Lin T, Liew AA, Vincent M, Mertens TCJ, Karmouty-Quintana H, Crum CP, Metersky ML, Schwartz DA, Davies PJA, Stephan C, Jyothula SSK, Sheshadri A, Suarez EE, Huang HJ, Engelhardt JF, Dickey BF, Parekh KR, McKeon FD, Xian W.  Sci Transl Med. 2023 Apr 26;15(693):eabp9528. doi: 10.1126/scitranslmed.abp9528. Epub 2023 Apr 26. PubMed PMID: 37099633.

The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization. Zhang Q, Gao Y, Baker ML, Liu S, Jia X, Xu H, He J, Kaelber JT, Weng S, Jiang W. PLoS Pathog. 2023 Apr 21;19(4):e1011341. doi: 10.1371/journal.ppat.1011341. eCollection 2023 Apr. PMID: 37083840 Free PMC article.

Probiotic-derived ecto-5′-nucleotidase produces anti-inflammatory adenosine metabolites in Treg-deficient scurfy mice. Liu Y, Armbrister SA, Okeugo B, Mills TW, Daniel RC, Oh JH, Pijkeren JP, Park ES, Saleh ZM, Lahiri S, Roos S, Rhoads JM.  Res Sq. 2023 Apr 7;. doi: 10.21203/rs.3.rs-2781715/v1. PubMed PMID: 37066419; PubMed Central PMCID: PMC10104250.

CD73-Dependent Adenosine Signaling through Adora2b Drives Immunosuppression in Ductal Pancreatic Cancer. Faraoni EY, Singh K, Chandra V, Le Roux O, Dai Y, Sahin I, O’Brien BJ, Strickland LN, Li L, Vucic E, Warner AN, Pruski M, Clark T, Van Buren G, Thosani NC, Bynon JS, Wray CJ, Bar-Sagi D, Poulsen KL, Vornik LA, Savage MI, Sei S, Mohammed A, Zhao Z, Brown PH, Mills T, Eltzschig HK, McAllister F, Bailey-Lundberg JM.  Cancer Res. 2023 Apr 4;83(7):1111-1127. doi: 10.1158/0008-5472.CAN-22-2553. PubMed PMID: 36720042; PubMed Central PMCID: PMC10071819.

Renovating a double fence with or without notifying the next door and across the street neighbors: why the biogenic cytoplasmic membrane of Gram-negative bacteria display asymmetry? Bogdanov M. Emerg Top Life Sci. 2023 Mar 31;7(1):137-150. doi: 10.1042/ETLS20230042.PMID: 36960750

The Polymethoxyflavone Sudachitin Modulates the Circadian Clock and Improves Liver Physiology. Mawatari K, Koike N, Nohara K, Wirianto M, Uebanso T, Shimohata T, Shikishima Y, Miura H, Nii Y, Burish MJ, Yagita K, Takahashi A, Yoo SH, Chen Z. Mol Nutr Food Res. 2023 May;67(9):e2200270. doi: 10.1002/mnfr.202200270. Epub 2023 Mar 17. PMID: 36829302

Linoleic acid improves PIEZO2 dysfunction in a mouse model of Angelman Syndrome. Romero LO, Caires R, Kaitlyn Victor A, Ramirez J, Sierra-Valdez FJ, Walsh P, Truong V, Lee J, Mayor U, Reiter LT, Vásquez V, Cordero-Morales JF.  Nat Commun. 2023 Mar 1;14(1):1167. doi: 10.1038/s41467-023-36818-0. PubMed PMID: 36859399; PubMed Central PMCID: PMC9977963.

Circadian Features of Cluster Headache and Migraine: A Systematic Review, Meta-analysis, and Genetic Analysis.Benkli B, Kim SY, Koike N, Han C, Tran CK, Silva E, Yan Y, Yagita K, Chen Z, Yoo SH, Burish MJ. Neurology. 2023 May 30;100(22):e2224-e2236. doi: 10.1212/WNL.0000000000207240. Epub 2023 Mar 29. PMID: 36990725

The power and challenge of lipid (a)symmetry across the membrane and cell.  Bogdanov M. Emerg Top Life Sci. 2023 Mar 31;7(1):1-6. doi: 10.1042/ETLS20220088.PMID: 36988943

Disruption of GCN2 Pathway Aggravates Vascular and Parenchymal Remodeling during Pulmonary Fibrosis. Santos-Ribeiro D, Lecocq M, de Beukelaer M, Verleden S, Bouzin C, Ambroise J, Dorfmuller P, Yakoub Y, Huaux F, Quarck R, Karmouty-Quintana H, Ghigna MR, Bignard J, Nadaud S, Soubrier F, Horman S, Perros F, Godinas L, Pilette C. Am J Respir Cell Mol Biol. 2023 Mar;68(3):326-338. doi: 10.1165/rcmb.2021-0541OC. PubMed PMID: 36476191.

SARS-CoV-2 restructures host chromatin architecture. Wang R, Lee JH, Kim J, Xiong F, Hasani LA, Shi Y, Simpson EN, Zhu X, Chen YT, Shivshankar P, Krakowiak J, Wang Y, Gilbert DM, Yuan X, Eltzschig HK, Li W.  Nat Microbiol. 2023 Apr;8(4):679-694. doi: 10.1038/s41564-023-01344-8. Epub 2023 Mar 23. PubMed PMID: 36959507; PubMed Central PMCID: PMC10116496.

STAT6 suppression prevents bleomycin-induced dermal fibrosis. Huang J, Puente H, Wareing NE, Wu M, Mayes MD, Karmouty-Quintana H, Assassi S, Mills TW.  FASEB J. 2023 Feb;37(2):e22761. doi: 10.1096/fj.202200994R. PubMed PMID: 36629780; PubMed Central PMCID: PMC10226134.

Hyaluronan in the pathogenesis of acute and post-acute COVID-19 infection. Barnes HW, Demirdjian S, Haddock NL, Kaber G, Martinez HA, Nagy N, Karmouty-Quintana H, Bollyky PL.  Matrix Biol. 2023 Feb;116:49-66. doi: 10.1016/j.matbio.2023.02.001. Epub 2023 Feb 5. Review. PubMed PMID: 36750167; PubMed Central PMCID: PMC9899355.

Disrupted Ca²⁺ homeostasis and immunodeficiency in patients with functional IP₃ receptor subtype 3 defects.Neumann J, Van Nieuwenhove E, Terry LE, Staels F, Knebel TR, Welkenhuyzen K, Ahmadzadeh K, Baker MR, Gerbaux M, Willemsen M, Barber JS, Serysheva II, De Waele L, Vermeulen F, Schlenner S, Meyts I, Yule DI, Bultynck G, Schrijvers R, Humblet-Baron S, Liston A. Cell Mol Immunol. 2023 Jan;20(1):11-25. doi: 10.1038/s41423-022-00928-4. Epub 2022 Oct 27. PMID: 36302985 Free PMC article.

Lipid nanoparticle-mediated mRNA delivery in lung fibrosis. Massaro M, Wu S, Baudo G, Liu H, Collum S, Lee H, Stigliano C, Segura-Ibarra V, Karmouty-Quintana H, Blanco E.  Eur J Pharm Sci. 2023 Apr 1;183:106370. doi: 10.1016/j.ejps.2023.106370. Epub 2023 Jan 13. PubMed PMID: 36642345.

Characterization of pulmonary vascular remodeling and MicroRNA-126-targets in COPD-pulmonary hypertension. Goel K, Egersdorf N, Gill A, Cao D, Collum SD, Jyothula SS, Huang HJ, Sauler M, Lee PJ, Majka S, Karmouty-Quintana H, Petrache I.  Respir Res. 2022 Dec 15;23(1):349. doi: 10.1186/s12931-022-02267-4. PubMed PMID: 36522710; PubMed Central PMCID: PMC9756782.

The circadian E3 ligase FBXL21 regulates myoblast differentiation and sarcomere architecture via MYOZ1 ubiquitination and NFAT signaling. Lim JY, Kim E, Douglas CM, Wirianto M, Han C, Ono K, Kim SY, Ji JH, Tran CK, Chen Z, Esser KA, Yoo SH. PLoS Genet. 2022 Dec 27;18(12):e1010574. doi: 10.1371/journal.pgen.1010574. eCollection 2022 Dec. PMID: 36574402 Free PMC article.

Conformational motions and ligand-binding underlying gating and regulation in IP₃R channel. Fan G, Baker MR, Terry LE, Arige V, Chen M, Seryshev AB, Baker ML, Ludtke SJ, Yule DI, Serysheva II. Nat Commun. 2022 Nov 14;13(1):6942. doi: 10.1038/s41467-022-34574-1.PMID: 36376291 Free PMC article.

Structural Foundations of Potassium Selectivity in Channelrhodopsins. Govorunova EG, Sineshchekov OA, Brown LS, Bondar AN, Spudich JL. mBio. 2022 Dec 20;13(6):e0303922. doi: 10.1128/mbio.03039-22. Epub 2022 Nov 22. PMID: 36413022 Free PMC article.

Mucins MUC5AC and MUC5B Are Variably Packaged in the Same and in Separate Secretory Granules. Hoang ON, Ermund A, Jaramillo AM, Fakih D, French CB, Flores JR, Karmouty-Quintana H, Magnusson JM, Fois G, Fauler M, Frick M, Braubach P, Hales JB, Kurten RC, Panettieri R, Vergara L, Ehre C, Adachi R, Tuvim MJ, Hansson GC, Dickey BF.  Am J Respir Crit Care Med. 2022 Nov 1;206(9):1081-1095. doi: 10.1164/rccm.202202-0309OC. PubMed PMID: 35776514; PubMed Central PMCID: PMC9704839.

Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization. Zhu X, Qi C, Wang R, Lee JH, Shao J, Bei L, Xiong F, Nguyen PT, Li G, Krakowiak J, Koh SP, Simon LM, Han L, Moore TI, Li W.  Cell Rep. 2022 Nov 1;41(5):111576. doi: 10.1016/j.celrep.2022.111576. PubMed PMID: 36323253; PubMed Central PMCID: PMC9744245.

Fulminant lung fibrosis in non-resolvable COVID-19 requiring transplantation. Jyothula SSK, Peters A, Liang Y, Bi W, Shivshankar P, Yau S, Garcha PS, Yuan X, Akkanti B, Collum S, Wareing N, Thandavarayan RA, Poli de Frias F, Rosas IO, Zhao B, Buja LM, Eltzschig HK, Huang HJ, Karmouty-Quintana H.  EBioMedicine. 2022 Dec;86:104351. doi: 10.1016/j.ebiom.2022.104351. Epub 2022 Nov 11. PubMed PMID: 36375315; PubMed Central PMCID: PMC9667270.

Gating intermediates reveal inhibitory role of the voltage sensor in a cyclic nucleotide-modulated ion channel. Gao X, Schmidpeter PAM, Berka V, Durham RJ, Fan C, Jayaraman V, Nimigean CM. Nat Commun. 2022 Nov 14;13(1):6919. doi: 10.1038/s41467-022-34673-z. PubMed PMID: 36376326; PubMed Central PMCID: PMC9663499.

Regulation of T cell function by protein S-acylation. West SJ, Boehning D, Akimzhanov AM. Front Physiol. 2022 Nov 16;13:1040968. doi: 10.3389/fphys.2022.1040968. eCollection 2022.PMID: 36467682 Free PMC article. Review.

Circadian stabilization loop: the regulatory hub and therapeutic target promoting circadian resilience and physiological health. Kim E, Yoo SH, Chen Z. F1000Res. 2022 Oct 31;11:1236. doi: 10.12688/f1000research.126364.2. eCollection 2022.PMID: 36415204 Free PMC article. Review.

Radiofrequency ablation in combination with CD73 inhibitor AB680 reduces tumor growth and enhances anti-tumor immunity in a syngeneic model of pancreatic ductal adenocarcinoma. Faraoni EY, Strickland LN, O’Brien BJ, Barraza JF, Thosani NC, Wray CJ, Mills TW, Bailey-Lundberg JM.  Front Oncol. 2022;12:995027. doi: 10.3389/fonc.2022.995027. eCollection 2022. PubMed PMID: 36147911; PubMed Central PMCID: PMC9486545.

Functional determination of calcium-binding sites required for the activation of inositol 1,4,5-trisphosphate receptors.Arige V, Terry LE, Wagner LE 2nd, Malik S, Baker MR, Fan G, Joseph SK, Serysheva II, Yule DI. Proc Natl Acad Sci U S A. 2022 Sep 27;119(39):e2209267119. doi: 10.1073/pnas.2209267119. Epub 2022 Sep 19. PMID: 36122240 Free PMC article.

The emerging role of NOTCH3 receptor signalling in human lung diseases. Bodas M, Subramaniyan B, Karmouty-Quintana H, Vitiello PF, Walters MS.  Expert Rev Mol Med. 2022 Sep 2;24:e33. doi: 10.1017/erm.2022.27. Review. PubMed PMID: 36052538; PubMed Central PMCID: PMC9884775.

Genetic- and diet-induced ω-3 fatty acid enrichment enhances TRPV4-mediated vasodilation in mice. Caires R, Garrud TAC, Romero LO, Fernández-Peña C, Vásquez V, Jaggar JH, Cordero-Morales JF.  Cell Rep. 2022 Sep 6;40(10):111306. doi: 10.1016/j.celrep.2022.111306. PubMed PMID: 36070688; PubMed Central PMCID: PMC9498980.

Hepatic circadian and differentiation factors control liver susceptibility for fatty liver disease and tumorigenesis. Fekry B, Ribas-Latre A, Drunen RV, Santos RB, Shivshankar S, Dai Y, Zhao Z, Yoo SH, Chen Z, Sun K, Sladek FM, Younes M, Eckel-Mahan K. FASEB J. 2022 Sep;36(9):e22482. doi: 10.1096/fj.202101398R.PMID: 35947136 Free PMC article.

The Hypoxia-Adenosine Link during Myocardial Ischemia-Reperfusion Injury. Ruan W, Ma X, Bang IH, Liang Y, Muehlschlegel JD, Tsai KL, Mills TW, Yuan X, Eltzschig HK.  Biomedicines. 2022 Aug 10;10(8). doi: 10.3390/biomedicines10081939. Review. PubMed PMID: 36009485; PubMed Central PMCID: PMC9405579.

Dynamic S-acylation of the ER-resident protein stromal interaction molecule 1 (STIM1) is required for store-operated Ca²⁺ entry. Kodakandla G, West SJ, Wang Q, Tewari R, Zhu MX, Akimzhanov AM, Boehning D. J Biol Chem. 2022 Sep;298(9):102303. doi: 10.1016/j.jbc.2022.102303. Epub 2022 Aug 4. PMID: 35934052 Free PMC article.

Alternative adenosine Receptor activation: The netrin-Adora2b link. Yuan X, Mills T, Doursout MF, Evans SE, Vidal Melo MF, Eltzschig HK.  Front Pharmacol. 2022;13:944994. doi: 10.3389/fphar.2022.944994. eCollection 2022. Review. PubMed PMID: 35910389; PubMed Central PMCID: PMC9334855.

Biophysical characterization of light-gated ion channels using planar automated patch clamp. Govorunova EG, Sineshchekov OA, Brown LS, Spudich JL. Front Mol Neurosci. 2022 Aug 9;15:976910. doi: 10.3389/fnmol.2022.976910. eCollection 2022.PMID: 36017077 Free PMC article.

Toward a Topology-Based Therapeutic Design of Membrane Proteins: Validation of NaPi2b Topology in Live Ovarian Cancer Cells. Bulatova L, Savenkova D, Nurgalieva A, Reshetnikova D, Timonina A, Skripova V, Bogdanov M, Kiyamova R. Front Mol Biosci. 2022 Jul 15;9:895911. doi: 10.3389/fmolb.2022.895911. eCollection 2022.PMID: 35911971 Free PMC article.

Biochemical, biophysical, and immunological characterization of respiratory secretions in severe SARS-CoV-2 infections. Kratochvil MJ, Kaber G, Demirdjian S, Cai PC, Burgener EB, Nagy N, Barlow GL, Popescu M, Nicolls MR, Ozawa MG, Regula DP, Pacheco-Navarro AE, Yang S, de Jesus Perez VA, Karmouty-Quintana H, Peters AM, Zhao B, Buja ML, Johnson PY, Vernon RB, Wight TN, Milla CE, Rogers AJ, Spakowitz AJ, Heilshorn SC, Bollyky PL.  JCI Insight. 2022 Jun 22;7(12). doi: 10.1172/jci.insight.152629. PubMed PMID: 35730564; PubMed Central PMCID: PMC9309048.

TRPV6 channel mediates alcohol-induced gut barrier dysfunction and systemic response. Meena AS, Shukla PK, Bell B, Giorgianni F, Caires R, Fernández-Peña C, Beranova S, Aihara E, Montrose MH, Chaib M, Makowski L, Neeli I, Radic MZ, Vásquez V, Jaggar JH, Cordero-Morales JF, Rao R.  Cell Rep. 2022 Jun 14;39(11):110937. doi: 10.1016/j.celrep.2022.110937. PubMed PMID: 35705057; PubMed Central PMCID: PMC9250449.

3’UTR shortening of HAS2 promotes hyaluronan hyper-synthesis and bioenergetic dysfunction in pulmonary hypertension. Tseng V, Collum SD, Allawzi A, Crotty K, Yeligar S, Trammell A, Ryan Smith M, Kang BY, Sutliff RL, Ingram JL, Jyothula SSSK, Thandavarayan RA, Huang HJ, Nozik ES, Wagner EJ, Michael Hart C, Karmouty-Quintana H.  Matrix Biol. 2022 Aug;111:53-75. doi: 10.1016/j.matbio.2022.06.001. Epub 2022 Jun 4. PubMed PMID: 35671866; PubMed Central PMCID: PMC9676077.

Kalium channelrhodopsins are natural light-gated potassium channels that mediate optogenetic inhibition. Govorunova EG, Gou Y, Sineshchekov OA, Li H, Lu X, Wang Y, Brown LS, St-Pierre F, Xue M, Spudich JL. Nat Neurosci. 2022 Jul;25(7):967-974. doi: 10.1038/s41593-022-01094-6. Epub 2022 Jun 20. PMID: 35726059 Free PMC article.

Beyond the Backbone: The Next Generation of Pathwalking Utilities for Model Building in CryoEM Density Maps.Hryc CF, Baker ML. Biomolecules. 2022 Jun 2;12(6):773. doi: 10.3390/biom12060773. PMID: 35740898 Free PMC article.

Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis. Wilson C, Mertens TC, Shivshankar P, Bi W, Collum SD, Wareing N, Ko J, Weng T, Naikawadi RP, Wolters PJ, Maire P, Jyothula SS, Thandavarayan RA, Ren D, Elrod ND, Wagner EJ, Huang HJ, Dickey BF, Ford HL, Karmouty-Quintana H.  JCI Insight. 2022 May 23;7(10). doi: 10.1172/jci.insight.142984. PubMed PMID: 35420997; PubMed Central PMCID: PMC9220956.

Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis. Wilson C, Mertens TC, Shivshankar P, Bi W, Collum SD, Wareing N, Ko J, Weng T, Naikawadi RP, Wolters PJ, Maire P, Jyothula SS, Thandavarayan RA, Ren D, Elrod ND, Wagner EJ, Huang HJ, Dickey BF, Ford HL, Karmouty-Quintana H.  JCI Insight. 2022 May 23;7(10). doi: 10.1172/jci.insight.142984. PubMed PMID: 35420997; PubMed Central PMCID: PMC9220956.

AlphaFold2 and CryoEM: Revisiting CryoEM modeling in near-atomic resolution density maps.  Hryc CF, Baker ML. iScience. 2022 May 30;25(7):104496. doi: 10.1016/j.isci.2022.104496. eCollection 2022 Jul 15. PMID: 35733789 Free PMC article.

Neonatal rodent ventilation and clinical correlation in congenital diaphragmatic hernia. Gupta VS, Wilson C, Popp EC, Zhaorigetu S, Collum S, Jin D, Khan AM, Karmouty-Quintana H, Lally KP, Harting MT.  Pediatr Pulmonol. 2022 Jul;57(7):1600-1607. doi: 10.1002/ppul.25911. Epub 2022 May 5. PubMed PMID: 35355453.

p97 dysfunction underlies a loss of quality control of damaged membrane proteins and promotes oxidative stress and sickling in sickle cell disease. Song A, Wen AQ, Wen YE, Dzieciatkowska M, Kellems RE, Juneja HS, D’Alessandro A, Xia Y. FASEB J. 2022 May;36(5):e22246. doi: 10.1096/fj.202101500RR.PMID: 35405035

NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency. Choi KJ, Quan MD, Qi C, Lee JH, Tsoi PS, Zahabiyon M, Bajic A, Hu L, Prasad BVV, Liao SJ, Li W, Ferreon ACM, Ferreon JC.  Nat Cell Biol. 2022 May;24(5):737-747. doi: 10.1038/s41556-022-00896-x. Epub 2022 Apr 28. PubMed PMID: 35484250; PubMed Central PMCID: PMC9106587.

Hereditary retinoblastoma iPSC model reveals aberrant spliceosome function driving bone malignancies. Tu J, Huo Z, Yu Y, Zhu D, Xu A, Huang MF, Hu R, Wang R, Gingold JA, Chen YH, Tsai KL, Forcioli-Conti NR, Huang SXL, Webb TR, Su J, Bazer DA, Jia P, Yustein JT, Wang LL, Hung MC, Zhao Z, Huff CD, Shen J, Zhao R, Lee DF. Proc Natl Acad Sci U S A. 2022 Apr 19;119(16):e2117857119. doi: 10.1073/pnas.2117857119. Epub 2022 Apr 11. PMID: 35412907 Free PMC article.

ROR activation by Nobiletin enhances antitumor efficacy via suppression of IκB/NF-κB signaling in triple-negative breast cancer. Kim E, Kim YJ, Ji Z, Kang JM, Wirianto M, Paudel KR, Smith JA, Ono K, Kim JA, Eckel-Mahan K, Zhou X, Lee HK, Yoo JY, Yoo SH, Chen Z. Cell Death Dis. 2022 Apr 19;13(4):374. doi: 10.1038/s41419-022-04826-5.PMID: 35440077 Free PMC article.

SARS-CoV-2 Infection: Host Response, Immunity, and Therapeutic Targets. Shivshankar P, Karmouty-Quintana H, Mills T, Doursout MF, Wang Y, Czopik AK, Evans SE, Eltzschig HK, Yuan X.  Inflammation. 2022 Aug;45(4):1430-1449. doi: 10.1007/s10753-022-01656-7. Epub 2022 Mar 23. Review. PubMed PMID: 35320469; PubMed Central PMCID: PMC8940980.

Lung Regeneration by Transplantation of Allogeneic Lung Progenitors Using a Safer Conditioning Regimen and Clinical-grade Reagents. Milman Krentsis I, Orgad R, Zheng Y, Bachar Lustig E, Rosen C, Shezen E, Yadav S, Nathansohn Levi B, Assayag M, Berkman N, Karmouty Quintana H, Shoshan E, Blagdon C, Reisner Y.  Stem Cells Transl Med. 2022 Mar 17;11(2):178-188. doi: 10.1093/stcltm/szab016. PubMed PMID: 35298657; PubMed Central PMCID: PMC8929438.

The clock modulator Nobiletin mitigates astrogliosis-associated neuroinflammation and disease hallmarks in an Alzheimer’s disease model. Wirianto M, Wang CY, Kim E, Koike N, Gomez-Gutierrez R, Nohara K, Escobedo G Jr, Choi JM, Han C, Yagita K, Jung SY, Soto C, Lee HK, Morales R, Yoo SH, Chen Z. FASEB J. 2022 Mar;36(3):e22186. doi: 10.1096/fj.202101633R.PMID: 35120261 Free PMC article.

SARS-CoV-2 Infection: Host Response, Immunity, and Therapeutic Targets. Shivshankar P, Karmouty-Quintana H, Mills T, Doursout MF, Wang Y, Czopik AK, Evans SE, Eltzschig HK, Yuan X. Inflammation. 2022 Aug;45(4):1430-1449. doi: 10.1007/s10753-022-01656-7. Epub 2022 Mar 23. Review. PubMed PMID: 35320469; PubMed Central PMCID: PMC8940980.

Glutamine synthetase licenses APC/C-mediated mitotic progression to drive cell growth. Zhao JS, Shi S, Qu HY, Keckesova Z, Cao ZJ, Yang LX, Yu X, Feng L, Shi Z, Krakowiak J, Mao RY, Shen YT, Fan YM, Fu TM, Ye C, Xu D, Gao X, You J, Li W, Liang T, Lu Z, Feng YX.  Nat Metab. 2022 Feb;4(2):239-253. doi: 10.1038/s42255-021-00524-2. Epub 2022 Feb 10. PubMed PMID: 35145325.

ADAM8 signaling drives neutrophil migration and ARDS severity. Conrad C, Yildiz D, Cleary SJ, Margraf A, Cook L, Schlomann U, Panaretou B, Bowser JL, Karmouty-Quintana H, Li J, Berg NK, Martin SC, Aljohmani A, Moussavi-Harami SF, Wang KM, Tian JJ, Magnen M, Valet C, Qiu L, Singer JP, Eltzschig HK, Bertrams W, Herold S, Suttorp N, Schmeck B, Ball ZT, Zarbock A, Looney MR, Bartsch JW.  JCI Insight. 2022 Feb 8;7(3). doi: 10.1172/jci.insight.149870. PubMed PMID: 35132956; PubMed Central PMCID: PMC8855804.

Erythrocyte transglutaminase-2 combats hypoxia and chronic kidney disease by promoting oxygen delivery and carnitine homeostasis.  Xu P, Chen C, Zhang Y, Dzieciatkowska M, Brown BC, Zhang W, Xie T, Abdulmalik O, Song A, Tong C, Qi H, Roach R, Kellems RE, D’Alessandro A, Xia Y. Cell Metab. 2022 Feb 1;34(2):299-316.e6. doi: 10.1016/j.cmet.2021.12.019. PMID: 35108516 Free PMC article.

Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis. Hanmandlu A, Zhu L, Mertens TCJ, Collum S, Bi W, Xiong F, Wang R, Amirthalingam RT, Ren D, Han L, Jyothula SSSK, Li W, Zheng WJ, Karmouty-Quintana H.  Am J Respir Cell Mol Biol. 2022 Jan;66(1):53-63. doi: 10.1165/rcmb.2020-0437OC. PubMed PMID: 34370624; PubMed Central PMCID: PMC8803355.

Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis. Hanmandlu A, Zhu L, Mertens TCJ, Collum S, Bi W, Xiong F, Wang R, Amirthalingam RT, Ren D, Han L, Jyothula SSSK, Li W, Zheng WJ, Karmouty-Quintana H.  Am J Respir Cell Mol Biol. 2022 Jan;66(1):53-63. doi: 10.1165/rcmb.2020-0437OC. PubMed PMID: 34370624; PubMed Central PMCID: PMC8803355.

Cleavage stimulating factor 64 depletion mitigates cardiac fibrosis through alternative polyadenylation. Neupane R, Youker K, Yalamanchili HK, Cieslik KA, Karmouty-Quintana H, Guha A, Thandavarayan RA.  Biochem Biophys Res Commun. 2022 Mar 15;597:109-114. doi: 10.1016/j.bbrc.2022.01.093. Epub 2022 Jan 29. PubMed PMID: 35134608; PubMed Central PMCID: PMC9334457.

Emerging Diversity of Channelrhodopsins and Their Structure-Function Relationships.  Govorunova EG, Sineshchekov OA, Spudich JL. Front Cell Neurosci. 2022 Jan 24;15:800313. doi: 10.3389/fncel.2021.800313. eCollection 2021. PMID: 35140589 Free PMC article. Review.

Structure of a type IV secretion system core complex encoded by multi-drug resistance F plasmids. Liu X, Khara P, Baker ML, Christie PJ, Hu B. Nat Commun. 2022 Jan 19;13(1):379. doi: 10.1038/s41467-022-28058-5. PMID: 35046412 Free PMC article.

In situ structure of the AcrAB-TolC efflux pump at subnanometer resolution.

Chen M, Shi X, Yu Z, Fan G, Serysheva II, Baker ML, Luisi BF, Ludtke SJ, Wang Z. Structure. 2022 Jan 6;30(1):107-113.e3. doi: 10.1016/j.str.2021.08.008. Epub 2021 Sep 9. PMID: 34506732 Free PMC article.

Circadian regulation of cardiac muscle function and protein degradation. Yoo SH. Chronobiol Int. 2023 Jan;40(1):4-12. doi: 10.1080/07420528.2021.1957911. Epub 2021 Sep 14. PMID: 34521283

In situ structure of the AcrAB-TolC efflux pump at subnanometer resolution.  Chen M, Shi X, Yu Z, Fan G, Serysheva II, Baker ML, Luisi BF, Ludtke SJ, Wang Z. Structure. 2022 Jan 6;30(1):107-113.e3. doi: 10.1016/j.str.2021.08.008. Epub 2021 Sep 9. PMID: 34506732 Free PMC article.

Emerging roles of alternative cleavage and polyadenylation (APA) in human disease. Dharmalingam P, Mahalingam R, Yalamanchili HK, Weng T, Karmouty-Quintana H, Guha A, A Thandavarayan RJ. Cell Physiol. 2022 Jan;237(1):149-160. doi: 10.1002/jcp.30549. Epub 2021 Aug 11. Review. PubMed PMID: 34378793.

Ca2+-dependent protein acyltransferase DHHC21 controls activation of CD4+ T cells.  Bieerkehazhi S, Fan Y, West SJ, Tewari R, Ko J, Mills T, Boehning D, Akimzhanov AM. J Cell Sci. 2022 Mar 1;135(5):jcs258186. doi: 10.1242/jcs.258186. Epub 2021 Jun 3.PMID: 34080635 Free PMC article.

S-acylation of Orai1 regulates store-operated Ca2+ entry.  West SJ, Kodakandla G, Wang Q, Tewari R, Zhu MX, Boehning D, Akimzhanov AM. J Cell Sci. 2022 Mar 1;135(5):jcs258579. doi: 10.1242/jcs.258579. Epub 2021 Jun 22.PMID: 34156466 Free PMC article.