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Cytoplasmic organization and systems-level function in Xenopus extracts

Award Number: R35GM131792
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 05/01/2019
PERIOD OF PERFORMANCE END DATE: 01/31/2029

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Cytoplasmic organization and systems-level function in Xenopus extracts - 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.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $622,741 )
2026	2026	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	000	8	1/28/2026	NON-COMPETING CONTINUATION	$622,741
														Subtotal = $622,741

Issue Date FY: 2025 ( Subtotal = $691,934 )
2025	2025	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	002	7	1/17/2025	NON-COMPETING CONTINUATION	$622,741
2025	2025	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	003	7	8/8/2025	NON-COMPETING CONTINUATION	$69,193
2025	2024	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	000	6	11/14/2024	COMPETING CONTINUATION	$0
2025	2023	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	001	5	1/16/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $691,934

Issue Date FY: 2024 ( Subtotal = $691,968 )
2024	2024	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	000	6	3/6/2024	COMPETING CONTINUATION	$691,968
														Subtotal = $691,968

Issue Date FY: 2023 ( Subtotal = $685,868 )
2023	2023	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	000	5	2/3/2023	NON-COMPETING CONTINUATION	$617,284
2023	2023	THE LELAND STANFORD JUNIOR UNIVERSITY	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	001	5	3/24/2023	NON-COMPETING CONTINUATION	$68,584
														Subtotal = $685,868

Issue Date FY: 2022 ( Subtotal = $685,868 )
2022	2022	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	000	4	2/17/2022	NON-COMPETING CONTINUATION	$617,275
2022	2022	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	001	4	7/22/2022	NON-COMPETING CONTINUATION	$68,593
														Subtotal = $685,868

Issue Date FY: 2021 ( Subtotal = $815,496 )
2021	2021	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	000	3	3/1/2021	NON-COMPETING CONTINUATION	$685,868
2021	2021	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	001	3	8/19/2021	SUPPLEMENT FOR EXPANSION	$129,628
														Subtotal = $815,496

Issue Date FY: 2020 ( Subtotal = $685,868 )
2020	2020	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 JANE STANFORD WAY	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	000	2	2/28/2020	NON-COMPETING CONTINUATION	$685,868
														Subtotal = $685,868

Issue Date FY: 2019 ( Subtotal = $685,868 )
2019	2019	LELAND STANFORD JUNIOR UNIVERSITY, THE	450 SERRA MALL	STANFORD	CA	94305	SANTA CLARA	USA	Biomedical Research and Research Training	000	1	4/12/2019	NEW	$685,868
														Subtotal = $685,868

Grand Total All Awards = $5,565,611

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Cytoplasmic organization and systems-level function in Xenopus extracts

Award Number: R35GM131792

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 05/01/2019

PERIOD OF PERFORMANCE END DATE: 01/31/2029

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