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Dataset results
12 results for “cytoplasmic density”
In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density
<p>Cells control the properties of the cytoplasm to ensure proper functioning of biochemical processes. Recent studies showed that cytoplasmic density varies in both physiological and pathological states of cells undergoing growth, division, differentiation, apoptosis, senescence, and metabolic starvation. Little is known about how cellular processes cope with these cytoplasmic variations. Here, we study how a cell cycle oscillator comprising cyclin-dependent kinase (Cdk1) responds to changes in cytoplasmic density by systematically diluting or concentrating cycling <em>Xenopus</em> egg extracts in cell-like microfluidic droplets. We found that the cell cycle maintains robust oscillations over a wide range of deviations from the endogenous density: as low as 0.2× to more than 1.22× relative cytoplasmic density (RCD). A further dilution or concentration from these values arrested the system in a low or high steady state of Cdk1 activity, respectively. Interestingly, diluting an arrested cytoplasm of 1.22× RCD recovers oscillations at lower than 1× RCD. Thus, the cell cycle switches reversibly between oscillatory and stable steady states at distinct thresholds depending on the direction of tuning, forming a hysteresis loop. We propose a mathematical model which recapitulates these observations and predicts that the Cdk1/Wee1/Cdc25 positive feedback loops do not contribute to the observed robustness, supported by experiments. Our system can be applied to study how cytoplasmic density affects other cellular processes.</p>
In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density
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3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh outward facing state (OFS) conformation at apo condition, imaged from the cytoplasmic side
<p>3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh outward facing state (OFS) conformation at apo condition, imaged from the cytoplasmic side, in <code>.afm</code> format and in <code>.mrc</code> format.</p> <p>Note: The <code>.afm</code> file encodes details for constructing 3D-LAFM density maps and includes experimental conditions in its header. Using <code>.afm</code> files requires the additional installation of the AFM file encoder (available from <a href="https://github.com/rafaeljiang23/3D-LAFM/tree/main/ChimeraX-AfmFormat_v2">GitHub</a>). Once the relevant installation is complete, <code>.afm</code> files can be opened in ChimeraX via drag-and-drop. In contrast, <code>.mrc</code> files, which encode only the density values equivalent to <code>.afm</code> files, can be directly opened in ChimeraX without requiring additional software installation.</p> <p>The deposited <code>.afm</code> file follows the 'AFM1' (metacode) format standard.</p>
3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state closed (IFSclosed) conformation at apo condition, imaged from the cytoplasmic side
<p>3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state closed (IFSclosed) conformation at apo condition, imaged from the cytoplasmic side, in <code>.afm</code> format and in <code>.mrc</code> format.</p> <p>Note: The <code>.afm</code> file encodes details for constructing 3D-LAFM density maps and includes experimental conditions in its header. Using <code>.afm</code> files requires the additional installation of the AFM file encoder (available from <a href="https://github.com/rafaeljiang23/3D-LAFM/tree/main/ChimeraX-AfmFormat_v2">GitHub</a>). Once the relevant installation is complete, <code>.afm</code> files can be opened in ChimeraX via drag-and-drop. In contrast, <code>.mrc</code> files, which encode only the density values equivalent to <code>.afm</code> files, can be directly opened in ChimeraX without requiring additional software installation.</p> <p>The deposited <code>.afm</code> file follows the 'AFM1' (metacode) format standard.</p>
3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state open (IFSopen) conformation at apo condition, imaged from the cytoplasmic side
<p>3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state open (IFSopen) conformation at apo condition, imaged from the cytoplasmic side , in <code>.afm</code> format and in <code>.mrc</code> format.</p> <p>Note: The <code>.afm</code> file encodes details for constructing 3D-LAFM density maps and includes experimental conditions in its header. Using <code>.afm</code> files requires the additional installation of the AFM file encoder (available from <a href="https://github.com/rafaeljiang23/3D-LAFM/tree/main/ChimeraX-AfmFormat_v2">GitHub</a>). Once the relevant installation is complete, <code>.afm</code> files can be opened in ChimeraX via drag-and-drop. In contrast, <code>.mrc</code> files, which encode only the density values equivalent to <code>.afm</code> files, can be directly opened in ChimeraX without requiring additional software installation.</p> <p>The deposited <code>.afm</code> file follows the 'AFM1' (metacode) format standard.</p>
3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state open, kinetically locked, (IFSopen-1) conformation at apo condition, imaged from the cytoplasmic side
<p>3D localization AFM (3D-LAFM) density map of glutamate transporter GltPh inward facing state open, kinetically locked, (IFSopen-1) conformation at apo condition, imaged from the cytoplasmic side , in <code>.afm</code> format and in <code>.mrc</code> format.</p> <p>Note: The <code>.afm</code> file encodes details for constructing 3D-LAFM density maps and includes experimental conditions in its header. Using <code>.afm</code> files requires the additional installation of the AFM file encoder (available from <a href="https://github.com/rafaeljiang23/3D-LAFM/tree/main/ChimeraX-AfmFormat_v2">GitHub</a>). Once the relevant installation is complete, <code>.afm</code> files can be opened in ChimeraX via drag-and-drop. In contrast, <code>.mrc</code> files, which encode only the density values equivalent to <code>.afm</code> files, can be directly opened in ChimeraX without requiring additional software installation.</p> <p>The deposited <code>.afm</code> file follows the 'AFM1' (metacode) format standard.</p>
The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis
<p>All cells must increase their volumes in response to biomass growth to maintain intracellular mass density within physiologically permissive bounds. Here, we investigate the regulation of volume growth in the Gram-positive bacterium <em>Bacillus subtilis</em>. To increase volume, bacteria enzymatically expand their cell envelopes and insert new envelope material. First, we demonstrate that cell-volume growth is determined indirectly, by expanding their envelopes in proportion to mass growth, similarly to the Gram-negative <em>Escherichia coli</em>, despite their fundamentally different envelope structures. Next, we studied, which pathways might be responsible for robust surface-to-mass coupling: We found that both peptidoglycan synthesis and membrane synthesis are required for proper surface-to-mass coupling. However, surprisingly, neither pathway is solely rate-limiting, contrary to wide-spread belief, since envelope growth continues at a reduced rate upon complete inhibition of either process. To arrest cell-envelope growth completely, the simultaneous inhibition of both envelope-synthesis processes is required. Thus, we suggest that multiple envelope-synthesis pathways collectively confer an important aspect of volume regulation, the coordination between surface growth and biomass growth.</p>
The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis
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Data from: Exposure to opposing temperature extremes causes comparable effects on Cardinium density but contrasting effects on Cardinium-induced cytoplasmic incompatibility
Terrestrial arthropods, including insects, commonly harbor maternally inherited intracellular symbionts that confer benefits to the host or manipulate host reproduction to favor infected female progeny. These symbionts may be especially vulnerable to thermal stress, potentially leading to destabilization of the symbiosis and imposing costs to the host. For example, increased temperatures can reduce the density of a common reproductive manipulator, Wolbachia, and the strength of its crossing incompatibility (cytoplasmic incompatibility, or CI) phenotype. Another manipulative symbiont, Cardinium hertigii, infects ~ 6-10% of Arthropods, and also can induce CI, but there is little homology between the molecular mechanisms of CI induced by Cardinium and Wolbachia. Here we investigated whether temperature disrupts the CI phenotype of Cardinium in a parasitic wasp host, Encarsia suzannae. We examined the effects of both warm (32°C day/ 29°C night) and cool (20°C day/ 17°C night) temperatures on Cardinium CI and found that both types of temperature stress modified aspects of this symbiosis. Warm temperatures reduced symbiont density, pupal developmental time, vertical transmission rate, and the strength of both CI modification and rescue. Cool temperatures also reduced symbiont density, however this resulted in stronger CI, likely due to cool temperatures prolonging the host pupal stage. The opposing effects of cool and warm-mediated reductions in symbiont density on the resulting CI phenotype indicates that CI strength may be independent of density in this system. Temperature stress also modified the CI phenotype only if it occurred during the pupal stage, highlighting the likely importance of this stage for CI induction in this symbiosis.
Data from: Exposure to opposing temperature extremes causes comparable effects on Cardinium density but contrasting effects on Cardinium-induced cytoplasmic incompatibility
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The relative importance of DNA methylation and Dnmt2-mediated epigenetic regulation on Wolbachia densities and cytoplasmic incompatibility
GEO Series GSE63795. Drosophila melanogaster. 2 samples. Type: Methylation profiling by high throughput sequencing.
Cytoplasmic translocation of tumor suppressor HINT1 and its impact on cell shape during density transition
GEO Series GSE270956. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
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