The Cul3–KLHL21 E3 ubiquitin ligase targets Aurora B to midzone microtubules in anaphase and is required for cytokinesis

Selective ubiquitination of Aurora B by different Cul3 adaptors targets it at the correct time to the correct place during mitosis

CellCognition : time-resolved phenotype annotation in high-throughput live cell imaging

Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Methods 7 (2010): 747-754, doi:10.1038/nmeth.1486.Fluorescence time-lapse imaging has become a powerful tool to investigate complex dynamic processes such as cell division or intracellular trafficking. Automated microscopes generate time-resolved imaging data at high throughput, yet tools for quantification of large-scale movie data are largely missing. Here, we present CellCognition, a computational framework to annotate complex cellular dynamics. We developed a machine learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states. The incorporation of time information into the annotation scheme was essential to suppress classification noise at state transitions, and confusion between different functional states with similar morphology. We demonstrate generic applicability in a set of different assays and perturbation conditions, including a candidate-based RNAi screen for mitotic exit regulators in human cells. CellCognition is published as open source software, enabling live imaging-based screening with assays that directly score cellular dynamics.Work in the Gerlich laboratory is supported by Swiss National Science Foundation (SNF) research grant 3100A0-114120, SNF ProDoc grant PDFMP3_124904, a European Young Investigator (EURYI) award of the European Science Foundation, an EMBO YIP fellowship, and a MBL Summer Research Fellowship to D.W.G., an ETH TH grant, a grant by the UBS foundation, a Roche Ph.D. fellowship to M.H.A.S, and a Mueller fellowship of the Molecular Life Sciences Ph.D. program Zurich to M.H. M.H. and M.H.A.S are fellows of the Zurich Ph.D. Program in Molecular Life Sciences. B.F. was supported by European Commission’s seventh framework program project Cancer Pathways. Work in the Ellenberg laboratory is supported by a European Commission grant within the Mitocheck consortium (LSHG-CT-2004-503464). Work in the Peter laboratory is supported by the ETHZ, Oncosuisse, SystemsX.ch (LiverX) and the SNF

Use of Thioredoxin as a Reporter To Identify a Subset of Escherichia coli Signal Sequences That Promote Signal Recognition Particle-Dependent Translocation

We have previously reported that the DsbA signal sequence promotes efficient, cotranslational translocation of the cytoplasmic protein thioredoxin-1 via the bacterial signal recognition particle (SRP) pathway. However, two commonly used signal sequences, those of PhoA and MalE, which promote export by a posttranslational mechanism, do not export thioredoxin. We proposed that this difference in efficiency of export was due to the rapid folding of thioredoxin in the cytoplasm; cotranslational export by the DsbA signal sequence avoids the problem of cytoplasmic folding (C. F. Schierle, M. Berkmen, D. Huber, C. Kumamoto, D. Boyd, and J. Beckwith, J. Bacteriol. 185:5706-5713, 2003). Here, we use thioredoxin as a reporter to distinguish SRP-dependent from non-SRP-dependent cleavable signal sequences. We screened signal sequences exhibiting a range of hydrophobicity values based on a method that estimates hydrophobicity. Successive iterations of screening and refining the method defined a threshold hydrophobicity required for SRP recognition. While all of the SRP-dependent signal sequences identified were above this threshold, there were also a few signal sequences above the threshold that did not utilize the SRP pathway. These results suggest that a simple measure of the hydrophobicity of a signal sequence is an important but not a sufficient indicator for SRP recognition. In addition, by fusing a number of both classes of signal sequences to DsbA, we found that DsbA utilizes an SRP-dependent signal sequence to achieve efficient export to the periplasm. Our results suggest that those proteins found to be exported by SRP-dependent signal sequences may require this mode of export because of their tendency to fold rapidly in the cytoplasm

RNAi-based screening identifies the Mms22L-Nfkbil2 complex as a novel regulator of DNA replication in human cells

A state-of-the-art microscopy-based RNAi screen for potential cell cycle roles of human DNA damage-binding 1–Cul4-associated factors, substrate adaptors associated with DDB1-cullin 4-based ubiquitin ligases, reveals a homologue of the yeast genome stability factor Mms22 to be required for DNA replication. Interestingly, human Mms22-like protein appears not to be a subunit, but rather a substrate, of the cullin 4 complex

Datawarehouse-enabled quality control of atrial fibrillation detection in the stroke unit setting

Objective: (1) To assess the accuracy of a standard operating procedure (SOP) regarding the utilization of atrial fibrillation (AF) alarms in everyday clinical practice, and (2) to evaluate the performance of automated continuous surveillance for atrial fibrillation (AF) in hospitalized acute stroke patients. Design: Retrospective cohort study. Setting: Two stroke units from two tertiary care hospitals in Berlin, Germany. Participants: We identified 635 patients with ischemic stroke diagnosis for the time period between 01. January and 30. September 2021 of which 176 patients had recorded AF alarms during monitoring. Of those, 115 patients were randomly selected for evaluation. After excluding 6 patients with hemorrhagic stroke in their records, 109 patients (mean age: 79.1 years, median NIHSS at admission: 6, 57% female) remained for analysis. Intervention: Using a clinical data warehouse for comprehensive data storage we retrospectively downloaded and visualized ECG data segments of 65 s duration around the automated AF alarms. We restricted the maximum number of ECG segments to ten per patient. Each ECG segment plot was uploaded into a REDCap database and categorized as either AF, non-AF or artifact by manual review. Atrial flutter was subsumed as AF. These classifications were then matched with 1) medical history and known diseases before stroke, 2) discharge diagnosis, and 3) recommended treatment plan in the medical history using electronic health records. Main outcome measures: The primary outcome was the proportion of previously unknown AF diagnoses correctly identified by the monitoring system but missed by the clinical team during hospitalization. Secondary outcomes included the proportion of patients in whom a diagnosis of AF would likely have led to anticoagulant therapy. We also evaluated the accuracy of the automated detection system in terms of its positive predictive value (PPV). Results: We evaluated a total of 717 ECG alarm segments from 109 patients. In 4 patients (3.7, 95% confidence interval [CI] 1.18–9.68%) physicians had missed AF despite at least one true positive alarm. All four patients did not receive long-term secondary prevention in form of anticoagulant therapy. 427 out of 717 alarms were rated true positives, resulting in a positive predictive value of 0.6 (CI 0.56–0.63) in this cohort. Conclusion: By connecting a data warehouse, electronic health records and a REDCap survey tool, we introduce a path to assess the monitoring quality of AF in acute stroke patients. We find that implemented standards of procedure to detect AF during stroke unit care are effective but leave room for improvement. Such data warehouse-based concepts may help to adjust internal processes or identify targets of further investigations