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Medley JC, Yim RN, DiPanni J, Sebou B, Shaffou B, Cramer E, Wu C, Kabara M, Song MH. Site-specific phosphorylation of ZYG-1 regulates ZYG-1 stability and centrosome number. iScience 2023; 26:108410. [PMID: 38034351 PMCID: PMC10687292 DOI: 10.1016/j.isci.2023.108410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/21/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023] Open
Abstract
Spindle bipolarity is critical for genomic integrity. As centrosome number often dictates bipolarity, tight control of centrosome assembly is vital for faithful cell division. The master centrosome regulator ZYG-1/Plk4 plays a pivotal role in this process. In C. elegans, casein kinase II (CK2) negatively regulates centrosome duplication by controlling centrosome-associated ZYG-1 levels. Here, we investigated CK2 as a regulator of ZYG-1 and its impact on centrosome assembly. We show that CK2 phosphorylates ZYG-1 in vitro and physically interacts with ZYG-1 in vivo. Depleting CK2 or blocking ZYG-1 phosphorylation at CK2 target sites leads to centrosome amplification. Non-phosphorylatable ZYG-1 mutants exhibit elevated ZYG-1 levels, leading to increased ZYG-1 and downstream factors at centrosomes, thus driving centrosome amplification. Moreover, inhibiting the 26S proteasome prevents degradation of the phospho-mimetic ZYG-1. Our findings suggest that CK2-dependent phosphorylation of ZYG-1 controls ZYG-1 levels via proteasomal degradation to limit centrosome number.
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Cramer E, Starcovic S, Avey R, Kaya A, Robart A. Structure of a 10-23 Deoxyribozyme Exhibiting a Homodimer Conformation. RESEARCH SQUARE 2023:rs.3.rs-2252941. [PMID: 37398199 PMCID: PMC10312968 DOI: 10.21203/rs.3.rs-2252941/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: 07/04/2023]
Abstract
Deoxyribozymes (DNAzymes) are in vitro evolved DNA sequences capable of catalyzing chemical reactions. The RNA cleaving 10-23 DNAzyme was the first DNAzyme to be evolved and possesses clinical and biotechnical applications as a biosensor and a knockdown agent. DNAzymes do not require the recruitment of other components to cleave RNA and can turnover, thus they have a distinct advantage over other knockdown methods (siRNA, CRISPR, morpholinos). Despite this, a lack of structural and mechanistic information has hindered the optimization and application of the 10-23 DNAzyme. Here, we report a 2.7 Å crystal structure of the RNA cleaving 10-23 DNAzyme in a homodimer conformation. Although proper coordination of the DNAzyme to substrate is observed along with intriguing patterns of bound magnesium ions, the dimer conformation likely does not capture the true catalytic form of the 10-23 DNAzyme.
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Medley JC, Yim N, DiPanni J, Sebou B, Shaffou B, Cramer E, Wu C, Kabara M, Song MH. Site-Specific Phosphorylation of ZYG-1 Regulates ZYG-1 Stability and Centrosome Number. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539463. [PMID: 37333374 PMCID: PMC10274923 DOI: 10.1101/2023.05.07.539463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Spindle bipolarity is critical for genomic integrity. Given that centrosome number often dictates mitotic bipolarity, tight control of centrosome assembly is vital for the fidelity of cell division. The kinase ZYG-1/Plk4 is a master centrosome factor that is integral for controlling centrosome number and is modulated by protein phosphorylation. While autophosphorylation of Plk4 has been extensively studied in other systems, the mechanism of ZYG-1 phosphorylation in C. elegans remains largely unexplored. In C. elegans, Casein Kinase II (CK2) negatively regulates centrosome duplication by controlling centrosome-associated ZYG-1 levels. In this study, we investigated ZYG-1 as a potential substrate of CK2 and the functional impact of ZYG-1 phosphorylation on centrosome assembly. First, we show that CK2 directly phosphorylates ZYG-1 in vitro and physically interacts with ZYG-1 in vivo. Intriguingly, depleting CK2 or blocking ZYG-1 phosphorylation at putative CK2 target sites leads to centrosome amplification. In the non-phosphorylatable (NP)-ZYG-1 mutant embryo, the overall levels of ZYG-1 are elevated, leading to an increase in centrosomal ZYG-1 and downstream factors, providing a possible mechanism of the NP-ZYG-1 mutation to drive centrosome amplification. Moreover, inhibiting the 26S proteasome blocks degradation of the phospho-mimetic (PM)-ZYG-1, while the NP-ZYG-1 mutant shows partial resistance to proteasomal degradation. Our findings suggest that site-specific phosphorylation of ZYG-1, partly mediated by CK2, controls ZYG-1 levels via proteasomal degradation, limiting centrosome number. We provide a mechanism linking CK2 kinase activity to centrosome duplication through direct phosphorylation of ZYG-1, which is critical for the integrity of centrosome number.
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Cramer E, Enste P. Auswirkungen regionaler, sozio-ökonomisch-gesundheitlicher
Unterschiede im Ruhrgebiet im Zwei-Jahres-Verlauf der Covid-19
Pandemie. DAS GESUNDHEITSWESEN 2022. [DOI: 10.1055/s-0042-1753724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Taylor A, Hathaway Q, Robart A, Cook C, Kunovac A, Durr A, Rizwan S, Cramer E, Starcovic S, Hollander J. LncRNAs imported into mitochondria possess distinct features stratified by machine learning that promote interaction with the mitochondrial import protein PNPase. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r1986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Hermanns M, Cramer E, Ng HKT. EM algorithms for ordered and censored system lifetime data under a proportional hazard rate model. J STAT COMPUT SIM 2020. [DOI: 10.1080/00949655.2020.1800706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Cramer E, Ziadni M, Scherrer K, Mackey S. The somatic distribution of chronic pain and emotional distress utilizing the collaborative health outcomes information registry (CHOIR) bodymap. THE JOURNAL OF PAIN 2018. [DOI: 10.1016/j.jpain.2017.12.128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Bomsel M, Real F, Capron C, Cramer E, Rouveix E. Platelets from HIV-infected cART-treated patients carry infectious viruses and predict poor immunological recovery. J Virus Erad 2017. [DOI: 10.1016/s2055-6640(20)30546-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Tanaka-Sahker M, Braun P, Yuki K, Hing B, Chronis T, Gaul L, Coon N, Cramer E, Heinzman J, Sparr N, Robles J, Shinozaki G, Stein K. Psychiatric Symptoms Following Glucocorticid Administration in Oral Surgery. J Oral Maxillofac Surg 2017. [DOI: 10.1016/j.joms.2017.07.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Seger H, Cramer E. Merkmale zur Beurteilung von Kalksteinen, Dolomit und ähnlichen Carbonatgesteinen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.19230367604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Hermanns M, Cramer E. Likelihood inference for the component lifetime distribution based on progressively censored parallel systems data. J STAT COMPUT SIM 2016. [DOI: 10.1080/00949655.2016.1222392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Leisinger C, Markle M, Paccamonti D, Cramer E, Pinto C. Production of equine embryos in vitro using conventional intracytoplasmic sperm injection and a complete human embryo culture system. J Equine Vet Sci 2016. [DOI: 10.1016/j.jevs.2016.04.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Cramer E, Burkschat M, Górny J. On the exact distribution of the MLEs based on Type-II progressively hybrid censored data from exponential distributions. J STAT COMPUT SIM 2015. [DOI: 10.1080/00949655.2015.1099657] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Volterman W, Cramer E, Davies KF, Balakrishnan N. Further Results on Order Statistics Generated by Two Simulation Methods. COMMUN STAT-SIMUL C 2014. [DOI: 10.1080/03610918.2013.769596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Beutner E, Cramer E. Using linear interpolation to reduce the order of the coverage error of nonparametric prediction intervals based on right-censored data. J MULTIVARIATE ANAL 2014. [DOI: 10.1016/j.jmva.2014.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Balakrishnan N, Cramer E, Iliopoulos G. On the method of pivoting the CDF for exact confidence intervals with illustration for exponential mean under life-test with time constraints. Stat Probab Lett 2014. [DOI: 10.1016/j.spl.2014.02.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Heller S, Amin W, Hansen L, Winkel S, Stripling J, Awwad N, Lehmann C, Cramer E, Rieß FC. Complete arterial coronary revascularization using skeletonized bilateral mammary arteries in T-graft technique performed in on-pump or off-pump approach: Clinical results up to 13 years in 3513 patients consecutive. Thorac Cardiovasc Surg 2014. [DOI: 10.1055/s-0034-1367083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Heller L, Hansen L, Winkel S, Stripling J, Awwad N, Lehmann C, Cramer E, Rieß FC. The Medtronic Mosaic prothesis in aortic and mitral position: Clinical perfomance in 1540 patients up to 13 years. Thorac Cardiovasc Surg 2014. [DOI: 10.1055/s-0034-1367097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Cramer E, Wahl G, Kremer P, Rieß FC. The Medtronic Mosaic Prosthesis: Clinical performance up to 18 years. Thorac Cardiovasc Surg 2014. [DOI: 10.1055/s-0034-1367237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Dahmen K, Burkschat M, Cramer E. A- and D-optimal progressive Type-II censoring designs based on Fisher information. J STAT COMPUT SIM 2012. [DOI: 10.1080/00949655.2011.560118] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Balakrishnan N, Cramer E, Dembińska A. Characterizations of geometric distribution through progressively Type-II right-censored order statistics. STATISTICS-ABINGDON 2011. [DOI: 10.1080/02331880903573146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Tamm M, Cramer E, Kennes LN, Heussen N. Influence of selection bias on the test decision. A simulation study. Methods Inf Med 2011; 51:138-43. [PMID: 22101391 DOI: 10.3414/me11-01-0043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 09/09/2011] [Indexed: 11/09/2022]
Abstract
BACKGROUND Selection bias arises in clinical trials by reason of selective assignment of patients to treatment groups. Even in randomized clinical trials with allocation concealment this phenomenon can occur if future assignments can be predicted due to knowledge of former allocations. OBJECTIVES Considering unmasked randomized clinical trials with allocation concealment the impact of selection bias on type I error rate under permuted block randomization is investigated. We aimed to extend the existing research into this topic by including practical assumptions concerning misclassification of patient characteristics to get an estimate of type I error close to clinical routine. To establish an upper bound for the type I error rate different biasing strategies of the investigator are compared first. In addition, the aspect of patient availability is considered. METHODS To evaluate the influence of selection bias on type I error rate under several practical situations, different block sizes, selection effects, biasing strategies and success rates of patient classification were simulated using SAS. RESULTS Type I error rate exceeds 5 percent significance level; it reaches values up to 21 percent. More cautious biasing strategies and misclassification of patient characteristics may diminish but cannot eliminate selection bias. The number of screened patients is about three times larger than the needed number for the trial. CONCLUSIONS Even in unmasked randomized clinical trials using permuted block randomization with allocation concealment the influence of selection bias must not be disregarded evaluating the test decision. It should be incorporated when designing and reporting a clinical trial.
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Schenk N, Burkschat M, Cramer E, Kamps U. Bayesian estimation and prediction with multiply Type-II censored samples of sequential order statistics from one- and two-parameter exponential distributions. J Stat Plan Inference 2011. [DOI: 10.1016/j.jspi.2010.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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