Project 4: Optical monitoring of post-translational modification of proteins in vivo (Thorn)(#27)We developed tools to study protein modification and interactions using fluorescence resonance energytransfer (FRET) microscopy. The main effort was to detect protein-protein interactions in wVo12 and use thesedata to predict the structure of large protein complexes. We developed methods to produce precise andreproducible FRET data from yeast, and used them to derive a low-resolution structure for the septin complex(which is required for cell division from yeast to mammals). With Michael Laub (project 7) we found interactionsbetween two-component signaling proteins, the predominant participants in post-translational regulation inbacteria, and collaborated with Daugherty and his colleagues to develop high throughput, quantitative, FRETbasedmethods to identify protein interactions13. Kurt Thorn, the PI, was a Bauer Fellow and is now Director ofthe Nikon Imaging Center at UCSF.New project 4: Tandem repeats in genes: hyper-variable modules for adaptation? (Verstrepen) (#28-30)We tested the hypothesis35 that in budding yeast, tandemly repeated sequences are hyper-variable geneticmodules, whose variability helps organisms adapt to changing environments. Most sequenced genomescontain tandem repeats; some of these occur in coding sequences, where recombination can alter the numberof peptide repeats in translated proteins. We have, 1) developed an algorithm36(http://hulsweb1.cgr.harvard.edu/SERV/) to find and annotate repeats, predict whether they vary in number,associate them with other information (expression level, overlap with transcription factor binding sites,nucleosome sites etc.), and deposit this data in a publicly accessible database(http://hulsweb1.cgr.harvard.edu/TandemRepeat/) that allows rapid and automated comparison to existingdatabases; 2) generated yeast strains with different numbers of repeats in the promoters and open readingframes of selected genes, and studied the phenotypic consequences of this variation (ongoing); 3) studiedtandem repeats in Arabidopsis thaliana and Oryza sativa (with C. Queitsch, new project 7). We have used twosequenced genomes to find all ORFs containing variable numbers of repeats, selected 150 genes,characterized their variation across twelve A. thaliana isolates from different locations, and found more than 70genes that show variation in repeat number between different isolates. Kevin Verstrepen became a BauerFellow in 2005 and joined the CMB in 2006.
| Westerman, Erica L; VanKuren, Nicholas W; Massardo, Darli et al. (2018) Aristaless Controls Butterfly Wing Color Variation Used in Mimicry and Mate Choice. Curr Biol 28:3469-3474.e4 |
| Bonham, Kevin S; Wolfe, Benjamin E; Dutton, Rachel J (2017) Extensive horizontal gene transfer in cheese-associated bacteria. Elife 6: |
| Hormoz, Sahand; Singer, Zakary S; Linton, James M et al. (2016) Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements. Cell Syst 3:419-433.e8 |
| Renn, Suzy C P; O'Rourke, Cynthia F; Aubin-Horth, Nadia et al. (2016) Dissecting the Transcriptional Patterns of Social Dominance across Teleosts. Integr Comp Biol 56:1250-1265 |
| Kastman, Erik K; Kamelamela, Noelani; Norville, Josh W et al. (2016) Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species. MBio 7: |
| Lavrentovich, Maxim O; Wahl, Mary E; Nelson, David R et al. (2016) Spatially Constrained Growth Enhances Conversional Meltdown. Biophys J 110:2800-2808 |
| Battle, Christopher; Broedersz, Chase P; Fakhri, Nikta et al. (2016) Broken detailed balance at mesoscopic scales in active biological systems. Science 352:604-7 |
| Tamari, Zvi; Yona, Avihu H; Pilpel, Yitzhak et al. (2016) Rapid evolutionary adaptation to growth on an 'unfamiliar' carbon source. BMC Genomics 17:674 |
| Kim, Wook; Levy, Stuart B; Foster, Kevin R (2016) Rapid radiation in bacteria leads to a division of labour. Nat Commun 7:10508 |
| Muller, Nicolas; Piel, Matthieu; Calvez, Vincent et al. (2016) A Predictive Model for Yeast Cell Polarization in Pheromone Gradients. PLoS Comput Biol 12:e1004795 |
Showing the most recent 10 out of 205 publications
