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For: Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC, Conaway JW, Florens L, Washburn MP. Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci U S A 2006;103:18928-33. [PMID: 17138671 PMCID: PMC1672612 DOI: 10.1073/pnas.0606379103] [Citation(s) in RCA: 439] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Tareb R, Rezé S, Harb M, Dubreil L, Monnet V, Björkroth J, Passerini D, Leroi F, Pilet MF. A bacteriolysin of Lactococcus carnosus is potentially involved in mediating contact-dependent antagonism against Listeria monocytogenes. Sci Rep 2025;15:18595. [PMID: 40425677 PMCID: PMC12116727 DOI: 10.1038/s41598-025-03177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Accepted: 05/19/2025] [Indexed: 05/29/2025]  Open
2
Demeshkina NA, Ferré-D'Amaré AR. Large-scale purifications reveal yeast and human stress granule cores are heterogeneous particles with complex transcriptomes and proteomes. Cell Rep 2025;44:115738. [PMID: 40413746 DOI: 10.1016/j.celrep.2025.115738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 03/14/2025] [Accepted: 05/02/2025] [Indexed: 05/27/2025]  Open
3
Tuieng RJ, Disney C, Cartmell SH, Kirwan CC, Eckersley A, Newham E, Gupta HS, Hoyland JA, Lee PD, Sherratt MJ. Impact of therapeutic X-ray exposure on collagen I and associated proteins. Acta Biomater 2025;197:294-311. [PMID: 40058620 DOI: 10.1016/j.actbio.2025.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 02/11/2025] [Accepted: 03/03/2025] [Indexed: 03/23/2025]
4
Lama B, Park H, Saraf A, Hassebroek V, Keifenheim D, Saito-Fujita T, Saitoh N, Aksenova V, Arnaoutov A, Dasso M, Clarke DJ, Azuma Y. PICH impacts the spindle assembly checkpoint via its DNA translocase and SUMO-interaction activities. Life Sci Alliance 2025;8:e202403140. [PMID: 39919802 PMCID: PMC11806350 DOI: 10.26508/lsa.202403140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 01/30/2025] [Accepted: 01/31/2025] [Indexed: 02/09/2025]  Open
5
Dwyer K, Essak MA, Awada A, Dhoondia Z, Ansari A. Protein-interaction network analysis reveals a role of Prp19 splicing factor in transcription of both intron-containing and intron-lacking genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.31.646471. [PMID: 40236183 PMCID: PMC11996550 DOI: 10.1101/2025.03.31.646471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
6
Jain A, Heremans I, Rademaker G, Detomasi TC, Rohweder P, Anderson D, Zhang J, Hernandez GA, Gupta S, von Linde T, Lange M, Spacci M, Luo J, Citron YR, Olzmann JA, Dawson DW, Craik CS, Bommer G, Perera RM, Zoncu R. Leucine aminopeptidase LyLAP enables lysosomal degradation of membrane proteins. Science 2025;387:eadq8331. [PMID: 40146846 DOI: 10.1126/science.adq8331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 11/25/2024] [Accepted: 01/13/2025] [Indexed: 03/29/2025]
7
Zagorščak M, Abdelhakim L, Rodriguez-Granados NY, Široká J, Ghatak A, Bleker C, Blejec A, Zrimec J, Novák O, Pěnčík A, Baebler Š, Perez Borroto L, Schuy C, Županič A, Afjehi-Sadat L, Wurzinger B, Weckwerth W, Pompe Novak M, Knight MR, Strnad M, Bachem C, Chaturvedi P, Sonnewald S, Sasidharan R, Panzarová K, Gruden K, Teige M. Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato. PLANT PHYSIOLOGY 2025;197:kiaf126. [PMID: 40173380 PMCID: PMC12012603 DOI: 10.1093/plphys/kiaf126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Accepted: 02/21/2025] [Indexed: 04/04/2025]
8
Honda K, Tasaki M, Yamano T, Ueda M, Naiki H, Tanaka N, Morinaga Y, Miyagawa-Hayashino A. High frequency of occult transthyretin and apolipoprotein AI-type amyloid in aortic valves removed by valve replacement for aortic stenosis. Amyloid 2025;32:22-28. [PMID: 39526702 DOI: 10.1080/13506129.2024.2426508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 10/01/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024]
9
Goubran H, Ahmed S, Ragab G, Seghatchian J, Burnouf T. Platelet proteomics: Clinical implications - Decoding the black box! Transfus Apher Sci 2025;64:104060. [PMID: 39719751 DOI: 10.1016/j.transci.2024.104060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2024]
10
Routray D, Ghatak A, Chaturvedi P, Petijová L, Weckwerth W, Ručová D, Bačkor M, Lang I, Goga M. Comparative analysis of geotypic variations in the proteome of Nostoc commune. PLANT SIGNALING & BEHAVIOR 2024;19:2370719. [PMID: 38913942 PMCID: PMC11197914 DOI: 10.1080/15592324.2024.2370719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/02/2024] [Indexed: 06/26/2024]
11
Powell T, Widdowson P, Nägeli A, Ebner M, Creese A. GingisREX: A Complementary Enzyme for the Detection of Bacterial Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024;35:2790-2794. [PMID: 39392299 PMCID: PMC11622235 DOI: 10.1021/jasms.4c00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/30/2024] [Accepted: 10/09/2024] [Indexed: 10/12/2024]
12
Bedi M, Das S, Das J, Mukherjee S, Basu A, Saha S, Ghosh A. Mitochondrial proteome analysis reveals that an augmented cytochrome c oxidase assembly and activity potentiates respiratory capacity in sarcoma. Biochem Biophys Res Commun 2024;736:150501. [PMID: 39116681 DOI: 10.1016/j.bbrc.2024.150501] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
13
Plouhinec L, Bonnin E, Kielbasa M, Armengaud J, Neugnot V, Berrin JG, Lafond M. A time-course analysis of Aspergillus terreus secretomes reveals the importance of pectin-degrading enzymes to increase the digestibility of soybean meal. Appl Environ Microbiol 2024;90:e0215323. [PMID: 39162561 PMCID: PMC11409638 DOI: 10.1128/aem.02153-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 07/29/2024] [Indexed: 08/21/2024]  Open
14
Jalan M, Sharma A, Pei X, Weinhold N, Buechelmaier ES, Zhu Y, Ahmed-Seghir S, Ratnakumar A, Di Bona M, McDermott N, Gomez-Aguilar J, Anderson KS, Ng CKY, Selenica P, Bakhoum SF, Reis-Filho JS, Riaz N, Powell SN. RAD52 resolves transcription-replication conflicts to mitigate R-loop induced genome instability. Nat Commun 2024;15:7776. [PMID: 39237529 PMCID: PMC11377823 DOI: 10.1038/s41467-024-51784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 08/15/2024] [Indexed: 09/07/2024]  Open
15
Bhola M, Abe K, Orozco P, Rahnamoun H, Avila-Lopez P, Taylor E, Muhammad N, Liu B, Patel P, Marko JF, Starner AC, He C, Van Nostrand EL, Mondragón A, Lauberth SM. RNA interacts with topoisomerase I to adjust DNA topology. Mol Cell 2024;84:3192-3208.e11. [PMID: 39173639 PMCID: PMC11380577 DOI: 10.1016/j.molcel.2024.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 07/07/2023] [Accepted: 07/31/2024] [Indexed: 08/24/2024]
16
O’Brien MJ, Schrader JM, Ansari A. TFIIB-Termination Factor Interaction Affects Termination of Transcription on Genome-Wide Scale. Int J Mol Sci 2024;25:8643. [PMID: 39201330 PMCID: PMC11354755 DOI: 10.3390/ijms25168643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024]  Open
17
Chang G, Aroge FA, Venkateshappa R, Claydon TW, Sun B. Development of an Absolute Quantification Method for hERG Using PRM with Single Isotopologue in-Sample Calibration. ACS OMEGA 2024;9:33972-33982. [PMID: 39130540 PMCID: PMC11308013 DOI: 10.1021/acsomega.4c04541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 08/13/2024]
18
Fernandes DC, Eto SF, Baldassi AC, Balbuena TS, Charlie-Silva I, de Andrade Belo MA, Pizauro JM. Meningitis caused by Aeromonas hydrophila in Oreochromis niloticus: Proteomics and druggability of virulence factors. FISH & SHELLFISH IMMUNOLOGY 2024;151:109687. [PMID: 38866348 DOI: 10.1016/j.fsi.2024.109687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 06/14/2024]
19
Zhao H, Li J, Xiang Y, Malik S, Vartak SV, Veronezi GMB, Young N, Riney M, Kalchschmidt J, Conte A, Jung SK, Ramachandran S, Roeder RG, Shi Y, Casellas R, Asturias FJ. An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II. Mol Cell 2024;84:2648-2664.e10. [PMID: 38955181 PMCID: PMC11283359 DOI: 10.1016/j.molcel.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 02/29/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
20
O’Brien MJ, Schrader J, Ansari A. Genome-wide analysis of TFIIB's role in termination of transcription. RESEARCH SQUARE 2024:rs.3.rs-4619136. [PMID: 39070618 PMCID: PMC11276024 DOI: 10.21203/rs.3.rs-4619136/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
21
Goto S, Hosojima M, Kabasawa H, Arai K, Takemoto K, Aoki H, Komochi K, Kobayashi R, Sugita N, Endo T, Kaseda R, Yoshida Y, Narita I, Hirayama Y, Saito A. Megalin-related mechanism of hemolysis-induced acute kidney injury and the therapeutic strategy. J Pathol 2024;263:315-327. [PMID: 38721910 DOI: 10.1002/path.6284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/08/2024] [Accepted: 03/15/2024] [Indexed: 06/12/2024]
22
Chen L, Shao F, Chen K, Wu N, Sun B, Ge D, Wang G, Wang H, Yang Q. Organized assembly of chitosan into mechanically strong bio-composite by introducing a recombinant insect structural protein OfCPH-1. Carbohydr Polym 2024;334:122044. [PMID: 38553240 DOI: 10.1016/j.carbpol.2024.122044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/06/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
23
O'Brien MJ, Schrader J, Ansari A. Genome-wide analysis of TFIIB's role in termination of transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.22.581640. [PMID: 38915573 PMCID: PMC11195087 DOI: 10.1101/2024.02.22.581640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
24
Goto S, Tsutsumi A, Lee Y, Hosojima M, Kabasawa H, Komochi K, Nagatoishi S, Takemoto K, Tsumoto K, Nishizawa T, Kikkawa M, Saito A. Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc Natl Acad Sci U S A 2024;121:e2318859121. [PMID: 38771880 PMCID: PMC11145282 DOI: 10.1073/pnas.2318859121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/19/2024] [Indexed: 05/23/2024]  Open
25
Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024:10.1002/mas.21887. [PMID: 38742660 PMCID: PMC11561166 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
26
kammoun I, Miotello G, Ben Slama K, Armengaud J, Ghodhbane-Gtari F, Gtari M. The impact of Elaeagnus angustifolia root exudates on Parafrankia soli NRRL B-16219 exoproteome. J Genomics 2024;12:58-70. [PMID: 38751381 PMCID: PMC11093716 DOI: 10.7150/jgen.93243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/21/2024] [Indexed: 05/18/2024]  Open
27
Skurat AV, Segvich DM, Contreras CJ, Hu YC, Hurley TD, DePaoli-Roach AA, Roach PJ. Impaired malin expression and interaction with partner proteins in Lafora disease. J Biol Chem 2024;300:107271. [PMID: 38588813 PMCID: PMC11063907 DOI: 10.1016/j.jbc.2024.107271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024]  Open
28
Molinelli L, Drula E, Gaillard JC, Navarro D, Armengaud J, Berrin JG, Tron T, Tarrago L. Methionine oxidation of carbohydrate-active enzymes during white-rot wood decay. Appl Environ Microbiol 2024;90:e0193123. [PMID: 38376171 PMCID: PMC10952391 DOI: 10.1128/aem.01931-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024]  Open
29
Kudapa H, Ghatak A, Barmukh R, Chaturvedi P, Khan A, Kale S, Fragner L, Chitikineni A, Weckwerth W, Varshney RK. Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.). THE PLANT GENOME 2024;17:e20337. [PMID: 37165696 DOI: 10.1002/tpg2.20337] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 05/12/2023]
30
Zhang S, Ghatak A, Mohammadi Bazargani M, Kramml H, Zang F, Gao S, Ramšak Ž, Gruden K, Varshney RK, Jiang D, Chaturvedi P, Weckwerth W. Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endosperm. PLANT BIOTECHNOLOGY JOURNAL 2024;22:555-571. [PMID: 38050335 PMCID: PMC12047074 DOI: 10.1111/pbi.14203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/21/2023] [Accepted: 10/03/2023] [Indexed: 12/06/2023]
31
Hollin T, Abel S, Banks C, Hristov B, Prudhomme J, Hales K, Florens L, Stafford Noble W, Le Roch KG. Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes. Nat Commun 2024;15:1365. [PMID: 38355719 PMCID: PMC10866993 DOI: 10.1038/s41467-024-45519-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024]  Open
32
Yamaguchi A, Tasaki M, Ueda M, Ando Y, Naiki H. Epidemiological study of the subtype frequency of systemic amyloidosis listed in the Annual of the Pathological Autopsy Cases in Japan. Pathol Int 2024;74:68-76. [PMID: 38088470 PMCID: PMC11551829 DOI: 10.1111/pin.13395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 02/03/2024]
33
O'Brien MJ, Ansari A. Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024;1872:140968. [PMID: 37863410 PMCID: PMC10872477 DOI: 10.1016/j.bbapap.2023.140968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
34
Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E. Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. RNA Biol 2024;21:1-15. [PMID: 38156797 PMCID: PMC10761087 DOI: 10.1080/15476286.2023.2298532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]  Open
35
Xu H, Akinyemi IA, Haley J, McIntosh MT, Bhaduri-McIntosh S. ATM, KAP1 and the Epstein-Barr virus polymerase processivity factor direct traffic at the intersection of transcription and replication. Nucleic Acids Res 2023;51:11104-11122. [PMID: 37852757 PMCID: PMC10639065 DOI: 10.1093/nar/gkad823] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/09/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023]  Open
36
Seregin AA, Smirnova LP, Dmitrieva EM, Zavialova MG, Simutkin GG, Ivanova SA. Differential Expression of Proteins Associated with Bipolar Disorder as Identified Using the PeptideShaker Software. Int J Mol Sci 2023;24:15250. [PMID: 37894929 PMCID: PMC10607299 DOI: 10.3390/ijms242015250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023]  Open
37
Wang H, Dai C, Pfeuffer J, Sachsenberg T, Sanchez A, Bai M, Perez-Riverol Y. Tissue-based absolute quantification using large-scale TMT and LFQ experiments. Proteomics 2023;23:e2300188. [PMID: 37488995 DOI: 10.1002/pmic.202300188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
38
Packard JE, Williams MR, Fromuth DP, Dembowski JA. Proliferating cell nuclear antigen inhibitors block distinct stages of herpes simplex virus infection. PLoS Pathog 2023;19:e1011539. [PMID: 37486931 PMCID: PMC10399828 DOI: 10.1371/journal.ppat.1011539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/03/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]  Open
39
Cheng A, Zhang Y, Sun J, Huang D, Sulaiman JE, Huang X, Wu L, Ye W, Wu C, Lam H, Shi Y, Qian PY. Pterosin sesquiterpenoids from Pteris laeta Wall. ex Ettingsh. protect cells from glutamate excitotoxicity by modulating mitochondrial signals. JOURNAL OF ETHNOPHARMACOLOGY 2023;308:116308. [PMID: 36822346 DOI: 10.1016/j.jep.2023.116308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/09/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
40
Stout AJ, Rittenberg ML, Shub M, Saad MK, Mirliani AB, Dolgin J, Kaplan DL. A Beefy-R culture medium: Replacing albumin with rapeseed protein isolates. Biomaterials 2023;296:122092. [PMID: 36965281 PMCID: PMC10111969 DOI: 10.1016/j.biomaterials.2023.122092] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/03/2023] [Accepted: 03/12/2023] [Indexed: 03/27/2023]
41
Suzuki H, Furugori K, Abe R, Ogawa S, Ito S, Akiyama T, Horiuchi K, Takahashi H. MED26-containing Mediator may orchestrate multiple transcription processes through organization of nuclear bodies. Bioessays 2023;45:e2200178. [PMID: 36852638 DOI: 10.1002/bies.202200178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 03/01/2023]
42
Bhattacharyya A, Sadhasivam S, Sinha M, Gupta S, Saini S, Singh H, Khurana A, Sachdeva S, Sardana K, Ghosh S. Treatment of recalcitrant cases of tinea corporis/cruris caused by T. mentagrophytes - interdigitale complex with mutations in ERG11 ERG 3, ERG4, MDR1 MFS genes & SQLE and their potential implications. Int J Dermatol 2023;62:637-648. [PMID: 36929499 DOI: 10.1111/ijd.16622] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 01/10/2023] [Accepted: 02/07/2023] [Indexed: 03/18/2023]
43
Wong TY, Yan N, Kwan KKL, Pan Y, Liu J, Xiao Y, Wu L, Lam H. Comparative proteomic analysis reveals the different hepatotoxic mechanisms of human hepatocytes exposed to silver nanoparticles. JOURNAL OF HAZARDOUS MATERIALS 2023;445:130599. [PMID: 37055998 DOI: 10.1016/j.jhazmat.2022.130599] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 06/19/2023]
44
Misumi Y, Tabata Y, Tasaki M, Obayashi K, Yamakawa S, Nomura T, Ueda M. Binding of serum-derived amyloid-associated proteins to amyloid fibrils. Amyloid 2023;30:67-73. [PMID: 36094798 DOI: 10.1080/13506129.2022.2120800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
45
Shen S, Wang X, Zhu X, Rasam S, Ma M, Huo S, Qian S, Zhang M, Qu M, Hu C, Jin L, Tian Y, Sethi S, Poulsen D, Wang J, Tu C, Qu J. High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation. Nat Protoc 2023;18:700-731. [PMID: 36494494 PMCID: PMC10673696 DOI: 10.1038/s41596-022-00780-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
46
Hadjeras L, Bartel J, Maier LK, Maaß S, Vogel V, Svensson SL, Eggenhofer F, Gelhausen R, Müller T, Alkhnbashi OS, Backofen R, Becher D, Sharma CM, Marchfelder A. Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry. MICROLIFE 2023;4:uqad001. [PMID: 37223747 PMCID: PMC10117724 DOI: 10.1093/femsml/uqad001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/29/2022] [Accepted: 01/13/2023] [Indexed: 05/25/2023]
47
Kumar R, Ghatak A, Goyal I, Sarkar NK, Weckwerth W, Grover A, Chaturvedi P. Heat-induced proteomic changes in anthers of contrasting rice genotypes under variable stress regimes. FRONTIERS IN PLANT SCIENCE 2023;13:1083971. [PMID: 36756226 PMCID: PMC9901367 DOI: 10.3389/fpls.2022.1083971] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/02/2022] [Indexed: 06/18/2023]
48
Preston SEJ, Richard VR, Del Rincón SV, Borchers CH, Zahedi RP. Proteomic Assessment of the Murine Mammary Gland Extracellular Matrix. Methods Mol Biol 2023;2614:261-271. [PMID: 36587130 DOI: 10.1007/978-1-0716-2914-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
49
Pible O, Petit P, Steinmetz G, Rivasseau C, Armengaud J. Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool. Front Microbiol 2023;14:1148976. [PMID: 37125163 PMCID: PMC10133526 DOI: 10.3389/fmicb.2023.1148976] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023]  Open
50
Zhang X, Jiang Q, Li J, Zhang S, Cao Y, Xia X, Cai D, Tan J, Chen J, Han JDJ. KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA-DNA triplexes and HP1 binding. Nat Cell Biol 2022;24:1617-1629. [PMID: 36266489 DOI: 10.1038/s41556-022-01008-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 09/07/2022] [Indexed: 01/18/2023]
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