shapiro lab stanford
We have developed a technique, termed superresolution by power-dependent active intermittency and points accumulation for imaging in nanoscale topography (SPRAIPAINT) that combines imaging of intracellular enhanced YFP (eYFP) fusions (SPRAI) with stochastic localization of the cell surface (PAINT) to image two different fluorophores sequentially with only one laser. We are interested in the ion currents and signaling pathways regulating excitability of dopaminergic neurons in midbrain, so as to understand the pathophysiology of drug addiction, as well as ion channels in lymphocytes critical to lymphomas. SURF scholar, 2022- Postdoc. The E1076Q point mutation in the SMC ATPase domain caused a dominant-negative phenotype in which DNA replication was able to proceed, but duplicated parS centromeres, normally found at opposite cell poles, remained at one pole. John Vaughen in Tom Clandinin lab successfully defended his thesis titled Sphingolipid Control of Neural Circuits by Glial Catabolism. Dye, N. A., Pincus, Z., Theriot, J. PleA is also required for the assembly of substructures of the flagellar basal body hook complex that are located in or traverse the peptidoglycan layer. One of the simplest organisms to divide asymmetrically is the bacterium Caulobacter crescentus. Thus, CpdR function is regulated by a feedback loop that incorporates its differential phosphorylation, the transient polar localization and activity of the ClpXP protease, and the clearance of the CpdR by polar ClpXP that, in turn, releases ClpXP from the pole relieving the degradation of CtrA. Caulobacter crescentus is motile by virtue of a polar flagellum assembled during the predivisional stage of the cell cycle. View details for Web of Science ID A1997WE44000004, View details for PubMedCentralID PMC178736. However, many of the mechanistic details underlying these functions are unknown. View details for Web of Science ID A1991EW29800007. Biomedical Engineering, University of Toronto The effect of cyclic GMP derivatives was shown to be the repression of synthesis of specific structural proteins. In an effort to understand this developmental control of replication, we employed pulsed-field gel electrophoresis to localize and to isolate the chromosomal origin of replication. View details for Web of Science ID A1997XV69900030, View details for PubMedCentralID PMC179479. View details for DOI 10.1371/journal.pbio.1001979, View details for Web of Science ID 000344461700017, View details for PubMedCentralID PMC4211667. A third gene, flgJ, is also temporally regulated. & Gerardot, C. J. McGrath, P. T., Lee, H., Zhang, L., Iniesta, A. Shapiro, Andersen, and Tanter then received an NIH BRAIN Initiative grant to pursue the research. An additional level of control was revealed when it was found that an interruption of DNA replication caused the inhibition of flaS transcription. Zhou, X., Wang, J., Herrmann, J., Moerner, W. E., Shapiro, L. Protein Self-Assembly Drives Surface Layer Biogenesis and Maintenance in C. crescentus. View details for Web of Science ID A1978FP55600049. Research Technician, 2019-2021 The crystal structure of TadZ from Eubacterium rectale (ErTadZ), in complex with ATP and Mg(2+) , was determined to 2.1 resolution. M.Eng. New research on bacterial cells has demonstrated that they have a dynamic and complex subcellular organization. We show that the PopZ oligomeric network forms polar ribosome exclusion zones that change function during cell cycle progression. B.S. SciP is cell cycle-controlled and co-conserved with the global cell cycle regulator CtrA in the -proteobacteria. View details for Web of Science ID 000250043300002. Four transcripts, A, B, C, and D, which ranged in size from 2.9 X 10(6) to 0.53 X 10(6) daltons, were synthesized in vitro by the holoenzyme. The addition of dibutyryl cyclic AMP to the blocked cultures brought about the resumption of cell differentiation, growth, and the appearance of beta-galactosidase activity within 1 hr. We are interested in how Arctic species and populations responded to environmental and habitat change throughout the Pleistocene, and what role ecology, natural history, climate and community-level dynamics played in the The International Conference on Learning Representations (ICLR) 2023 is being hosted in Kigali, Rwanda from May 1st - May 5th. The Caulobacter cell cycle is driven by a cascade of transient regulators, starting with the expression of DnaA in G(1) and ending with the expression of the essential CcrM DNA methyltransferase at the completion of DNA replication. Surprisingly, many signal transduction proteins are dynamically localized to specific subcellular addresses during the cell division cycle and sporulation, and proper localization is essential for their function. Analysis of this organism is complicated by a limited selection of tools for genetic manipulation and inducible gene expression. M.D. The use of sigma 54 promoters, known to require cognate binding proteins, could allow the fine-tuning that provides the temporal ordering of flagellar gene transcription. Saurabh, S., Perez, A., Comerci, C., Shapiro, L., Moerner, W. A Localized Complex of Two Protein Oligomers Controls the Orientation of Cell Polarity. A C. crescentus mutant deficient in glycerol 3-phosphate dehydrogenase activity (gpsA) blocks phospholipid synthesis, ceases DNA replication, and loses viability in the absence of a glycerol phosphate supplement. Predictions from Brownian dynamics simulations of the packing of supercoiled DNA polymers in an elongated cell-like confinement are also consistent with a branched DNA structure, and simulated interloci distance distributions predict that confinement leads to "freezing" of the supercoiled configuration. Several fla- mutants were also isolated by Tn5-VB32 mutagenesis and shown to confer kanamycin resistance. Agricultural Biotechnology, Seoul National University Ph.D. Student, Medical Engineering, Defended 2020 We found that in the absence of active Topo IV, replication initiation can occur but a significant percent of replication origins are either no longer moved to or maintained at the cell poles. We have isolated a group of temperature-sensitive mutants that are unable to complete this process at the restrictive temperature. Caulobacter crescentus is a model organism for the integrated circuitry that runs a bacterial cell cycle. View details for Web of Science ID A1996TQ17000011, View details for Web of Science ID A1996BG26T00006. Daniel E. Ho is the William Benjamin Scott and Luna M. Scott Professor of Law at Stanford Law School, Professor of Political Science, Senior Fellow at the Stanford Institute for Economic Policy Research, Associate Director of the Stanford Institute for Human-Centered Artificial Intelligence, and Director of the Regulation, Evaluation, and Governance Caulobacter crescentus cell division is asymmetric and yields distinct swarmer cell and stalked cell progeny. One hundred micromolar exogenously added xylose was required for maximal induction of P(xylX) in a strain that is unable to metabolize xylose. Caulobacter crescentus wild-type strain CB13 is unable to utilize galactose as the sole carbon source unless derivatives of cyclic AMP are present. We show here that genes differentially expressed in a ctrA temperature-sensitive (ts) mutant are similarly affected in a cckA ts mutant, that the phosphorylation of CckA coincides temporally with CtrA phosphorylation during the cell cycle, and that CckA is essential for viability because it is required for CtrA phosphorylation. Hodgson, D., Shaw, P., Letts, V., Henry, S., Shapiro, L. ISOLATION AND GENETIC-ANALYSIS OF CAULOBACTER MUTANTS DEFECTIVE IN CELL-SHAPE AND MEMBRANE LIPID-SYNTHESIS, GENERATION OF A TN5 PROMOTER PROBE AND ITS USE IN THE STUDY OF GENE-EXPRESSION IN CAULOBACTER-CRESCENTUS. This protein, CtrA, is homologous to response regulator transcription factors and controls transcription from a group of cell cycle-regulated promoters critical for DNA replication, DNA methylation, and flagellar biogenesis. In mammals, genes from the same organism are similar only in the second parameter, because GC content varies widely among isochores. The sequential changes in the chromosomal methylation state serve to couple the progression of DNA replication to cell-cycle events regulated by the master transcriptional regulatory cascade, thus providing a ratchet mechanism for robust cell-cycle control. View details for Web of Science ID A1992JM38600007. WebSafety First is designed to be implemented in high school classrooms by health teachers. How do you make a protein that self-assembles, fills with air, excludes water and withstands several atmospheres of pressure? The outcome of these experiences, together with the extraordinary scientists I came to know along the way, was and is an abiding passion to fully understand a simple cell in all its complexity and beauty. Immunoprecipitation of a DnaA'-beta-lactamase fusion protein showed that although expression occurs throughout the cell cycle, there is a doubling in the rate of expression just prior to the initiation of replication. Nature Communications13, 493 (2022). PopZ recruitment of ParA stimulates ParA to assemble on the nucleoid near the PopZ-proximal cell pole. The A transcript initiated primarily with GTP although a portion was also labeled with ATP. We propose that these genes are preferentially transcribed from the chromosome in the incipient swarmer cell pole of the predivisional cell. View details for Web of Science ID A1987G456800009. B., Shen, X., Shapiro, L., McAdams, H. H. Initiating bacterial mitosis Understanding the mechanism of ParA-mediated chromosome segregation, The Caulobacter Tol-Pal Complex Is Essential for Outer Membrane Integrity and the Positioning of a Polar Localization Factor. Single-molecule imaging enables biophysical measurements devoid of ensemble averaging, gives enhanced spatial resolution beyond the optical diffraction limit, and enables superresolution reconstruction of structures beyond the diffraction limit. The purification scheme minus the heating step also permitted the copurification of crotonase and 3-hydroxyacyl-CoA dehydrogenase. View details for Web of Science ID A1993LX92900005, View details for Web of Science ID A1993LF06100004, View details for Web of Science ID A1993LF06100002, View details for Web of Science ID A1993KX96501075, View details for Web of Science ID A1993KX96501060. SURF Scholar 2022- Homology modelling of the N-terminal atypical receiver domain of CpaE indicates that it has a conserved protein-protein binding surface similar to that of the polar localization module of the social mobility protein FrzS, suggesting a similar function. We have isolated DNA from this region of the chromosome by using a nonmotile mutant with a Tn5 insertion into flaE. The C. crescentus enzyme appeared similar to the Pseudomonas aeruginosa enzyme and unlike the Escherichia coli enzyme with respect to subunit molecular weights and failure to separate into core and sigma components upon phosphocellulose chromatography. In particular, little is known about the replication of multipartite genomes in bacteria. 2023 SLAC National Accelerator Laboratory is operated by Stanford University for the U.S. Department of Energy Office of Science. View details for DOI 10.1016/j.tim.2005.03.006, View details for Web of Science ID 000229467100008. These new reporter genes provide much greater sensitivity, nonlinear ultrasound contrast, and ease-of-use for expression in a variety of cell types.