James E. Ferrell
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View article: Geometrical compartmentalization of trigger waves
Geometrical compartmentalization of trigger waves Open
Trigger waves, self-regenerating fronts of biochemical activity that spread without losing speed or amplitude, are widespread in cell signaling. Apoptosis is one example of a process that propagates through the cytoplasm via trigger waves.…
View article: Mechanistic origins of temperature scaling in the early embryonic cell cycle
Mechanistic origins of temperature scaling in the early embryonic cell cycle Open
Temperature profoundly impacts organismal physiology and ecological dynamics, particularly affecting ectothermic species and making them especially vulnerable to climate changes. Although complex physiological processes usually involve doz…
View article: Long-range regulation of transcription scales with genomic distance in a gene-specific manner
Long-range regulation of transcription scales with genomic distance in a gene-specific manner Open
Although critical for tuning the timing and level of transcription, enhancer communication with distal promoters is not well understood. Here, we bypass the need for sequence-specific transcription factors (TFs) and recruit activators dire…
View article: Long range regulation of transcription scales with genomic distance in a gene specific manner
Long range regulation of transcription scales with genomic distance in a gene specific manner Open
Summary While critical for tuning the timing and level of transcription, enhancer communication with distal promoters is not well understood. Here we bypass the need for sequence-specific transcription factors and recruit activators direct…
View article: Viscosity-dependent control of protein synthesis and degradation
Viscosity-dependent control of protein synthesis and degradation Open
It has been proposed that the concentration of proteins in the cytoplasm maximizes the speed of important biochemical reactions. Here we have used Xenopus egg extracts, which can be diluted or concentrated to yield a range of cytoplasmic p…
View article: Membrane localization accelerates association under conditions relevant to cellular signaling
Membrane localization accelerates association under conditions relevant to cellular signaling Open
Translocation of cytoplasmic molecules to the plasma membrane is commonplace in cell signaling. Membrane localization has been hypothesized to increase intermolecular association rates; however, it has also been argued that association sho…
View article: Robust trigger wave speed in<i>Xenopus</i>cytoplasmic extracts
Robust trigger wave speed in<i>Xenopus</i>cytoplasmic extracts Open
Self-regenerating trigger waves can spread rapidly through the crowded cytoplasm without diminishing in amplitude or speed, providing consistent, reliable, long-range communication. The macromolecular concentration of the cytoplasm varies …
View article: Protein homeostasis from diffusion-dependent control of protein synthesis and degradation
Protein homeostasis from diffusion-dependent control of protein synthesis and degradation Open
Summary It has been proposed that the concentration of proteins in the cytoplasm maximizes the speed of important biochemical reactions. Here we have used the Xenopus extract system, which can be diluted or concentrated to yield a range of…
View article: Data from Systems Biologists Seek Fuller Integration of Systems Biology Approaches in New Cancer Research Programs
Data from Systems Biologists Seek Fuller Integration of Systems Biology Approaches in New Cancer Research Programs Open
Systems biology takes an interdisciplinary approach to the systematic study of complex interactions in biological systems. This approach seeks to decipher the emergent behaviors of complex systems rather than focusing only on their constit…
View article: Ultrafast and long-range coordination of wound responses is essential for whole-body regeneration
Ultrafast and long-range coordination of wound responses is essential for whole-body regeneration Open
Summary Injury induces systemic, global responses whose functions remain elusive. In addition, mechanisms that rapidly synchronize wound responses through long distances across the organismal scale are mostly unknown. Using planarians, whi…
View article: Membrane localization accelerates association under conditions relevant to cellular signaling
Membrane localization accelerates association under conditions relevant to cellular signaling Open
Translocation of cytoplasmic molecules to the plasma membrane is commonplace in cell signaling. Membrane localization has been hypothesized to increase intermolecular association rates; however, it has also been argued that association sho…
View article: Cytoplasmic organization promotes protein diffusion in Xenopus extracts
Cytoplasmic organization promotes protein diffusion in Xenopus extracts Open
The cytoplasm is highly organized. However, the extent to which this organization influences the dynamics of cytoplasmic proteins is not well understood. Here, we use Xenopus laevis egg extracts as a model system to study diffusion dynamic…
View article: Mouse lemur transcriptomic atlas informs primate genes, mutations, physiology, and disease
Mouse lemur transcriptomic atlas informs primate genes, mutations, physiology, and disease Open
Mouse lemurs ( Microcebus spp.) are an emerging primate model organism. However, little is known about their genetics or cellular and molecular biology. In the accompanying paper, we used large-scale single cell RNA-sequencing of 27 organs…
View article: An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome
An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome Open
Hormones mediate long-range cell communication in multicellular organisms and play vital roles in normal physiology, metabolism, and health. Using the newly-completed organism-wide single cell transcriptional atlas of a non-human primate, …
View article: Stepwise oxidations play key roles in the structural and functional regulations of DJ-1
Stepwise oxidations play key roles in the structural and functional regulations of DJ-1 Open
DJ-1 is known to play neuroprotective roles by eliminating reactive oxygen species (ROS) as an antioxidant protein. However, the molecular mechanism of DJ-1 function has not been well elucidated. This study explored the structural and func…
View article: Cytoplasmic organization promotes protein diffusion
Cytoplasmic organization promotes protein diffusion Open
The cytoplasm is highly organized. However, the extent to which this organization influences the dynamics of cytoplasmic proteins is not well understood. Here, we used Xenopus laevis egg extracts as a model system to study diffusion dynami…
View article: <em>Xenopus laevis</em> Egg Extract Preparation and Live Imaging Methods for Visualizing Dynamic Cytoplasmic Organization
<em>Xenopus laevis</em> Egg Extract Preparation and Live Imaging Methods for Visualizing Dynamic Cytoplasmic Organization Open
Traditionally used for bulk biochemical assays, Xenopus laevis egg extracts have emerged as a powerful imaging-based tool for studying cytoplasmic phenomena, such as cytokinesis, mitotic spindle formation and assembly of the nucleus. Build…
View article: Stepwise Oxidations Play Key Roles in the Structural and Functional Regulations of DJ-1
Stepwise Oxidations Play Key Roles in the Structural and Functional Regulations of DJ-1 Open
DJ-1 is known to play neuroprotective roles by eliminating reactive oxygen species (ROS) as an antioxidant protein. However, the molecular mechanism of DJ-1 function has not been well elucidated. This study explored the structural and func…
View article: The nucleus serves as the pacemaker for the cell cycle
The nucleus serves as the pacemaker for the cell cycle Open
Mitosis is a dramatic process that affects all parts of the cell. It is driven by an oscillator whose various components are localized in the nucleus, centrosome, and cytoplasm. In principle, the cellular location with the fastest intrinsi…
View article: Bistable, biphasic regulation of PP2A-B55 accounts for the dynamics of mitotic substrate phosphorylation
Bistable, biphasic regulation of PP2A-B55 accounts for the dynamics of mitotic substrate phosphorylation Open
Summary The phosphorylation of mitotic proteins is bistable, which contributes to the decisiveness of the transitions into and out of M phase. The bistability in substrate phosphorylation has been attributed to bistability in the activatio…
View article: C. elegans colony formation as a phase separation phenomenon
C. elegans colony formation as a phase separation phenomenon Open
Phase separation at the molecular scale affects many biological processes. The theoretical requirements for phase separation are fairly minimal, and analogous phenomena may occur at other scales in biology. Here we have examined colony for…
View article: The Apparent Requirement for Protein Synthesis during G2 Phase Is due to Checkpoint Activation
The Apparent Requirement for Protein Synthesis during G2 Phase Is due to Checkpoint Activation Open
Protein synthesis inhibitors (e.g., cycloheximide) block mitotic entry, suggesting that cell cycle progression requires protein synthesis until right before mitosis. However, cycloheximide is also known to activate p38 mitogen-activated pr…
View article: The nucleus serves as the pacemaker for the cell cycle
The nucleus serves as the pacemaker for the cell cycle Open
Mitosis is a dramatic cellular process that affects all parts of the cell. In Xenopus embryos and extracts it is driven by the activation of a bistable trigger circuit, whose various components are localized in the nucleus, centrosome, and…