# Cytoplasmic organization and systems-level function in Xenopus extracts

> **NIH NIH R35** · STANFORD UNIVERSITY · 2024 · $691,968

## Abstract

PROJECT SUMMARY—ABSTRACT
The combination of quantitative experimental studies and ordinary differential modeling has yielded great
insight into how biological switches and oscillators can and do function. Implicit in both the experimental and
theoretical approaches is the assumption that the systems in question are essentially homogeneous bags of
enzymes, which of course is incorrect. Here we propose studies aimed at understanding two intriguing aspects
of regulation in spatially organized cytoplasm. The first is the mechanism underpinning self-organization of the
cytoplasm, and the second is the propagation of activity states through the cytoplasm via trigger waves. The
main experimental system we will use is Xenopus egg extracts, which are more manipulable than intact cells,
but more complex and realistic than in vitro systems. The main modeling approaches will be partial differential
equations and agent based models that explicitly account for spatial dynamics. Over the next five years we
plan to focus on four basic aspects of cellular organization and dynamics:
1. Self-organization. Incredibly, it turns out that crude, heterogenous interphase Xenopus egg extracts self-
 organize into sheets of cell-like compartments. The mechanism underpinning this self-organization is not
 yet understood. We plan to use inhibitors and depletions in extracts, reconstitution in vitro, and
 mathematical modeling to gain insight into the basis of this biological self-organization.
2. Trade-offs, speed, and homeostasis. We will use self-organized extracts to determine how basic aspects
 of cell physiology are affected by the crowding of the cytoplasm, initially focusing on ATP production and
utilization.
3. Trigger waves. Trigger waves are self-regenerating fronts of chemical activity that can propagate without
 diminishing in amplitude or speed. Action potentials are trigger waves; so are calcium waves, mitotic
 waves, and apoptotic waves. We are examining the robustness of mitotic and apoptotic trigger waves in
 Xenopus egg extracts, and are testing hypotheses about the possible compartmentalization of trigger
 waves and bistable states.
4. Reconstitution of transcription. Under the right conditions, Xenopus egg extracts can carry out cell
 cycles for many hours, with DNA replication alternating with mitosis. Recently we have found that extracts
 appear to undergo the midblastula transition once 13-15 cell cycles have taken place. We plan to use the
 extract system to study the mechanism of the midblastula transition and to develop extracts as a new
 system for studying transcription.

## Key facts

- **NIH application ID:** 10840628
- **Project number:** 2R35GM131792-06
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** JAMES E. FERRELL
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $691,968
- **Award type:** 2
- **Project period:** 2019-05-01 → 2029-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10840628

## Citation

> US National Institutes of Health, RePORTER application 10840628, Cytoplasmic organization and systems-level function in Xenopus extracts (2R35GM131792-06). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10840628. Licensed CC0.

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