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Imaging methodologies for systems biology

Sarah E Smith, Brian D Slaughter, Jay R Unruh
2014 Cell Adhesion & Migration  
C r/ ¡ I.t; r/ ð Þ 2 i t;r h I i 2 t;r D G.t/exp ¡ r 2 w 2 0 C MSD.t/ (13) Here r and t are spatial (radial) and temporal shifts.  ...  the depletion of the spatial correlation over time. 43, 45 STICS is simply the spatial correlation of each image of a movie with images taken at a time shift, t, later: 43,46-48 G.r; t/ D h I.t C t; r  ... 
doi:10.4161/cam.29152 pmid:25482526 pmcid:PMC4594334 fatcat:bllglpu5zjfexcdb4agx6g3cbm

A distinct inner nuclear membrane proteome in Saccharomyces cerevisiae gametes [article]

Shary N Shelton, Sarah E. Smith, Jay R. Unruh, Sue L. Jaspersen
2021 bioRxiv   pre-print
The inner nuclear membrane (INM) proteome regulates gene expression, chromatin organization, and nuclear transport, however, it is poorly understood how changes in INM protein composition contribute to developmentally regulated processes, such as gametogenesis. Using a split-GFP complementation system, we compared the distribution of all C-terminally tagged transmembrane proteins in Saccharomyces cerevisiae in gametes to that of mitotic cells. Gametes contain a distinct INM proteome needed to
more » ... mplete gamete formation, including expression of genes linked to cell wall biosynthesis, lipid biosynthetic and metabolic pathways, protein degradation and unknown functions. Based on the inheritance pattern, INM components are made de novo in the gametes. Whereas mitotic cells show a strong preference for proteins with small extraluminal domains, gametes do not exhibit this size preference likely due to the changes in the nuclear permeability barrier during gametogenesis.
doi:10.1101/2021.08.02.454801 fatcat:zh3usg26obfnpmyrduaoosq5hq

Quality Control: Putting Protein Aggregates in a Bind

Jay R. Unruh, Brian D. Slaughter, Rong Li
2013 Current Biology  
Jay R. Unruh 1 , Brian D.  ... 
doi:10.1016/j.cub.2012.12.005 pmid:23347944 fatcat:af5vhwamyzcihiuuhxpkoko5wq

Synaptonemal complex architecture facilitates the chromosome-specific regulation of recombination in Drosophila [article]

Cori Cahoon, G. Matthew Heenan, Zulin Yu, Jay R Unruh, Sean McKinney, R. Scott Hawley
2018 bioRxiv   pre-print
MATERIALS AND METHODS Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, R. Scott Hawley (  ...  X and 4 th chromosome nondisjunction was assayed by crossing virgin y w; c(3)G ccΔ1 ; sv spa-pol and y w; c(3)G ccΔ1 /+; sv spa-pol females to attached-XY, y + v f B; C(4)RM, ci ey R males, as described  ... 
doi:10.1101/277764 fatcat:ph6ggqoz6bakfhzk5yivdkcwui

Distribution of γ-tubulin ring complex at the Schizosaccharomyces pombe spindle pole

Sajjita Saha, Jay R Unruh, Sue L Jaspersen
2021 microPublication Biology  
f ( ) ] + * [ 1 + E r f ( ) ] A 1 2 − x P P C 8 9 x c 1 2 - √ σ 1 A 2 2 − x P P C 8 9 x c 2 2 - √ σ 2 R i g h t i n t e  ...  n s i t y = * [ 1 − E r f ( ) ] + * [ 1 − E r f ( ) ] A 1 2 − x P P C 8 9 x c 1 2 - √ σ 1 A 2 2 − x P P C 8 9 x c 2 2 -  ... 
doi:10.17912/micropub.biology.000464 pmid:35622906 pmcid:PMC9015813 fatcat:bvt5j6qavvgydoo3r4kpnpdbpq

Redistribution of centrosomal proteins by centromeres and Polo kinase controls nuclear envelope breakdown [article]

Andrew J Bestul, Zulin Yu, Jay R Unruh, Sue L Jaspersen
2020 bioRxiv   pre-print
Proper mitotic progression in Schizosaccharomyces pombe requires partial nuclear envelope breakdown (NEBD) and insertion of the spindle pole body (SPB; yeast centrosome) to build the mitotic spindle. Linkage of the centromere to the SPB is vital to this process, but why that linkage is important is not well understood. Utilizing high-resolution structured illumination microscopy (SIM), we show that the conserved SUN-protein Sad1 and other SPB proteins redistribute during mitosis to form a ring
more » ... omplex around SPBs, which is a precursor for NEBD and spindle formation. Although the Polo kinase Plo1 is not necessary for Sad1 redistribution, it localizes to the SPB region connected to the centromere, and its activity is vital for SPB ring protein redistribution and for complete NEBD to allow for SPB insertion. Our results lead to a model in which centromere linkage to the SPB drives redistribution of Sad1 and Plo1 activation that in turn facilitate NEBD and spindle formation through building of an SPB ring structure.
doi:10.1101/2020.12.01.406553 fatcat:pfl4t7mcm5dzdgddgf4623c3ja

Asi1 regulates the distribution of proteins at the inner nuclear membrane in Saccharomyces cerevisiae [article]

Christine J. Smoyer, Sarah E. Smith, Scott McCroskey, Jay R. Unruh, Sue L. Jaspersen
2018 bioRxiv   pre-print
AbstractInner nuclear membrane (INM) protein composition regulates nuclear function, affecting processes such as gene expression, chromosome organization, nuclear shape and stability. Mechanisms that drive changes in the INM proteome are poorly understood in part because it is difficult to definitively assay INM composition rigorously and systematically. Using a split-GFP complementation system to detect INM access, we examined the distribution of all C-terminally tagged Saccharomyces
more » ... membrane proteins in wild-type cells and in mutants affecting protein quality control pathways, such as INM-associated degradation (INMAD), ER-associated degradation (ERAD) and vacuolar proteolysis. Deletion of the E3 ligase Asi1 had the most pronounced effect on the INM compared to mutants in vacuolar or ER-associated degradation pathways, consistent with a role for Asi1 in the INMAD pathway. Our data suggests that Asi1 not only removes mis-targeted proteins at the INM, but it also controls the levels and distribution of native INM components, such as the membrane nucleoporin Pom33. Interestingly, loss of Asi1 does not affect Pom33 protein levels but instead alters Pom33 distribution in the NE through Pom33 ubiquitination, which drives INM redistribution. Taken together, our data demonstrate that the Asi1 E3 ligase has a novel function in INM protein regulation in addition to protein turnover.
doi:10.1101/442970 fatcat:mw77aefg6zewvmp5pgafqqg3om

Cell-Cycle-Coupled Structural Oscillation of Centromeric Nucleosomes in Yeast

Manjunatha Shivaraju, Jay R. Unruh, Brian D. Slaughter, Mark Mattingly, Judith Berman, Jennifer L. Gerton
2012 Cell  
Chloroquine intercalation caused topoisomers induced by Nap1 with Cse4 octamers to move slower than initially relaxed (R) circular plasmid.  ... 
doi:10.1016/j.cell.2012.05.034 pmid:22817893 pmcid:PMC3404468 fatcat:zno5lrlserd6hl3rocrvcynca4

Actin Depolymerization Drives Actomyosin Ring Contraction during Budding Yeast Cytokinesis

Inês Mendes Pinto, Boris Rubinstein, Andrei Kucharavy, Jay R. Unruh, Rong Li
2012 Developmental Cell  
Actin filaments and myosin II are evolutionarily conserved force-generating components of the contractile ring during cytokinesis. Here we show that in budding yeast, actin filament depolymerization plays a major role in actomyosin ring constriction. Cofilin mutation or chemically stabilizing actin filaments attenuate actomyosin ring constriction. Deletion of myosin II motor domain or the myosin regulatory light chain reduced the contraction rate and also the rate of actin depolymerization in
more » ... e ring. We constructed a quantitative microscopic model of actomyosin ring constriction via filament sliding driven by both actin depolymerization and myosin II motor activity. Model simulations based on experimental measurements support the notion that actin depolymerization is the predominant mechanism for ring constriction. The model predicts invariability of total contraction time regardless of the initial ring size, as originally reported for C. elegans embryonic cells. This prediction was validated in yeast cells of different sizes due to different ploidies.
doi:10.1016/j.devcel.2012.04.015 pmid:22698284 pmcid:PMC3376349 fatcat:z6uxynvwsfazpmgw6vvpeokku4

Dopamine receptor antagonists as potential therapeutic agents for ADPKD

Parama Paul, Sreekumar Ramachandran, Sheng Xia, Jay R. Unruh, Juliana Conkright-Fincham, Rong Li, Maria Fragiadaki
2019 PLoS ONE  
Next the images were spectrally unmixed (three spectral channels: r, g, and b) using Ki67 positive and negative nuclei as reference.  ... 
doi:10.1371/journal.pone.0216220 pmid:31059522 pmcid:PMC6502331 fatcat:6hboy3yjhbhehdizeuyhwqrqea

Molecular Imaging Reveals a Novel Yeast Centromere Structural Transition in Anaphase

Jay R. Unruh, Brian D. Slaughter, Manjunatha Shivaraju, Jennifer L. Gerton
2013 Biophysical Journal  
R.  ...  Unruh, Brian D. Slaughter, Manjunatha Shivaraju, Jennifer L. Gerton. Stowers Institute for Medical Research, Kansas City, KS, USA.  ... 
doi:10.1016/j.bpj.2012.11.3705 fatcat:lvrk7bd6dnblxdmmxsqslqg7ke

Evaluation of High-Content Screening Fluorescence Correlation Spectroscopic (HCS-FCS) Data

Will A. Marshall, Qingfeng E. Yu, Jeffrey J. Lange, Brian R. Slaughter, Jay R. Unruh, Christopher J. Wood, Winfried Wiegraebe
2012 Biophysical Journal  
Lange, Brian R. Slaughter, Jay R. Unruh, Christopher J. Wood, Winfried Wiegraebe. Stowers Institute, Kansas City, MO, USA.  ... 
doi:10.1016/j.bpj.2011.11.1129 fatcat:mpm635davbhl5fdajo375w2ivy

Motility and Segregation of Hsp104-Associated Protein Aggregates in Budding Yeast

Chuankai Zhou, Brian D. Slaughter, Jay R. Unruh, Amr Eldakak, Boris Rubinstein, Rong Li
2011 Cell  
The MSD was calculated using the equation MSD(t) = hjr(t + t) À r(t)j 2 i, in Mathematica (Wolfram Research, Champaign, IL).  ... 
doi:10.1016/j.cell.2011.11.002 pmid:22118470 pmcid:PMC3237388 fatcat:lbarfny6drcm7kkvmzvaazvhsy

Two-photon microscopy with wavelength switchable fiber laser excitation

Jay R. Unruh, E. S. Price, Roque G. Molla, Lisa Stehno-Bittel, Carey K. Johnson, Rongqing Hui
2006 Optics Express  
Two-photon scanning fluorescence microscopy has become a powerful tool for imaging living cells and tissues. Most applications of two-photon microscopy employ a Ti:sapphire laser excitation source, which is not readily portable or rapidly tunable. This work explores the use of two-photon fiber laser excitation (TP-FLEX) as an excitation source for scanning two-photon microscopy. We have further demonstrated the use of a photonic crystal fiber (PCF) for facile tuning of the excitation wavelength
more » ... over the range from 810 nm to 1100 nm. We generated two-photon fluorescence images at excitation wavelengths from 850 nm to 1100 nm detected on a scanning-stage microscope. By PCF wavelength tuning the dye BODIPY fl was selectively excited at 1000 nm whereas MitoTracker red was excited preferentially at 1100 nm. We discuss the potential for fiber laser sources coupled with PCF wavelength tuning as an attractive tunable excitation source for two-photon scanning fluorescence microscopy.
doi:10.1364/oe.14.009825 pmid:19529374 fatcat:s7lal57einc5pg4c2sfq52q5ki

Structural plasticity of the living kinetochore

Karthik Dhatchinamoorthy, Manjunatha Shivaraju, Jeffrey J. Lange, Boris Rubinstein, Jay R. Unruh, Brian D. Slaughter, Jennifer L. Gerton
2017 Journal of Cell Biology  
The reverse transition from N − 1 to N corresponding with inward movement is caused by the sleeve motion only and its rate, Using them, we found k out = κ * s * r M − N / f + β * s and k in = κ * r M −  ...  Now, we introduce the quantities s = e [ W ____ k×T ] < 1 and r = e [ ( −B ) ____ k×T ] < 1.  ... 
doi:10.1083/jcb.201703152 pmid:28939613 pmcid:PMC5674893 fatcat:brcnmqsi4jgedhjcjpbleaxihu
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