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Gedeon T. Lattice structures that parameterize regulatory network dynamics. Math Biosci 2024; 374:109225. [PMID: 38866065 DOI: 10.1016/j.mbs.2024.109225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024]
Abstract
We consider two types of models of regulatory network dynamics: Boolean maps and systems of switching ordinary differential equations. Our goal is to construct all models in each category that are compatible with the directed signed graph that describe the network interactions. This leads to consideration of lattice of monotone Boolean functions (MBF), poset of non-degenerate MBFs, and a lattice of chains in these sets. We describe explicit inductive construction of these posets where the induction is on the number of inputs in MBF. Our results allow enumeration of potential dynamic behavior of the network for both model types, subject to practical limitation imposed by the size of the lattice of MBFs described by the Dedekind number.
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Affiliation(s)
- Tomáš Gedeon
- Montana State University, Bozeman, 59717, MT, USA.
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2
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Choudhary R, Mahadevan R. DyMMM-LEAPS: An ML-based framework for modulating evenness and stability in synthetic microbial communities. Biophys J 2024:S0006-3495(24)00320-5. [PMID: 38733081 DOI: 10.1016/j.bpj.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024] Open
Abstract
There have been a growing number of computational strategies to aid in the design of synthetic microbial consortia. A framework to identify regions in parametric space to maximize two essential properties, evenness and stability, is critical. In this study, we introduce DyMMM-LEAPS (dynamic multispecies metabolic modeling-locating evenness and stability in large parametric space), an extension of the DyMMM framework. Our method explores the large parametric space of genetic circuits in synthetic microbial communities to identify regions of evenness and stability. Due to the high computational costs of exhaustive sampling, we utilize adaptive sampling and surrogate modeling to reduce the number of simulations required to map the vast space. Our framework predicts engineering targets and computes their operating ranges to maximize the probability of the engineered community to have high evenness and stability. We demonstrate our approach by simulating five cocultures and one three-strain culture with different social interactions (cooperation, competition, and predation) employing quorum-sensing-based genetic circuits. In addition to guiding circuit tuning, our pipeline gives an opportunity for a detailed analysis of pockets of evenness and stability for the circuit under investigation, which can further help dissect the relationship between the two properties. DyMMM-LEAPS is easily customizable and can be expanded to a larger community with more complex interactions.
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Affiliation(s)
- Ruhi Choudhary
- University of Toronto, Department of Chemical Engineering and Applied Chemistry, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- University of Toronto, Department of Chemical Engineering and Applied Chemistry, Toronto, ON, Canada.
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Barr J, Diegmiller R, Colonnetta MM, Ke W, Imran Alsous J, Stern T, Shvartsman SY, Schedl P. To be or not to be: orb, the fusome and oocyte specification in Drosophila. Genetics 2024; 226:iyae020. [PMID: 38345426 PMCID: PMC10990432 DOI: 10.1093/genetics/iyae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/21/2024] [Indexed: 04/05/2024] Open
Abstract
In the fruit fly Drosophila melanogaster, two cells in a cyst of 16 interconnected cells have the potential to become the oocyte, but only one of these will assume an oocyte fate as the cysts transition through regions 2a and 2b of the germarium. The mechanism of specification depends on a polarized microtubule network, a dynein dependent Egl:BicD mRNA cargo complex, a special membranous structure called the fusome and its associated proteins, and the translational regulator orb. In this work, we have investigated the role of orb and the fusome in oocyte specification. We show here that specification is a stepwise process. Initially, orb mRNAs accumulate in the two pro-oocytes in close association with the fusome. This association is accompanied by the activation of the orb autoregulatory loop, generating high levels of Orb. Subsequently, orb mRNAs become enriched in only one of the pro-oocytes, the presumptive oocyte, and this is followed, with a delay, by Orb localization to the oocyte. We find that fusome association of orb mRNAs is essential for oocyte specification in the germarium, is mediated by the orb 3' UTR, and requires Orb protein. We also show that the microtubule minus end binding protein Patronin functions downstream of orb in oocyte specification. Finally, in contrast to a previously proposed model for oocyte selection, we find that the choice of which pro-oocyte becomes the oocyte does not seem to be predetermined by the amount of fusome material in these two cells, but instead depends upon a competition for orb gene products.
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Affiliation(s)
- Justinn Barr
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rocky Diegmiller
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Megan M Colonnetta
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Wenfan Ke
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jasmin Imran Alsous
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Tomer Stern
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Stanislav Y Shvartsman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Diegmiller R, Imran Alsous J, Li D, Yamashita YM, Shvartsman SY. Fusome topology and inheritance during insect gametogenesis. PLoS Comput Biol 2023; 19:e1010875. [PMID: 36821548 PMCID: PMC9949678 DOI: 10.1371/journal.pcbi.1010875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/16/2023] [Indexed: 02/24/2023] Open
Abstract
From insects to mammals, oocytes and sperm develop within germline cysts comprising cells connected by intercellular bridges (ICBs). In numerous insects, formation of the cyst is accompanied by growth of the fusome-a membranous organelle that permeates the cyst. Fusome composition and function are best understood in Drosophila melanogaster: during oogenesis, the fusome dictates cyst topology and size and facilitates oocyte selection, while during spermatogenesis, the fusome synchronizes the cyst's response to DNA damage. Despite its distinct and sex-specific roles during insect gametogenesis, elucidating fusome growth and inheritance in females and its structure and connectivity in males has remained challenging. Here, we take advantage of advances in three-dimensional (3D) confocal microscopy and computational image processing tools to reconstruct the topology, growth, and distribution of the fusome in both sexes. In females, our experimental findings inform a theoretical model for fusome assembly and inheritance and suggest that oocyte selection proceeds through an 'equivalency with a bias' mechanism. In males, we find that cell divisions can deviate from the maximally branched pattern observed in females, leading to greater topological variability. Our work consolidates existing disjointed experimental observations and contributes a readily generalizable computational approach for quantitative studies of gametogenesis within and across species.
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Affiliation(s)
- Rocky Diegmiller
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Jasmin Imran Alsous
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
| | - Duojia Li
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Yukiko M. Yamashita
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
| | - Stanislav Y. Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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Discovering design principles for biological functionalities: Perspectives from systems biology. J Biosci 2022. [DOI: 10.1007/s12038-022-00293-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Singh J, Imran Alsous J, Garikipati K, Shvartsman SY. Mechanics of stabilized intercellular bridges. Biophys J 2022; 121:3162-3171. [PMID: 35778841 PMCID: PMC9463629 DOI: 10.1016/j.bpj.2022.06.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/04/2022] [Accepted: 06/27/2022] [Indexed: 11/02/2022] Open
Abstract
Numerous engineered and natural systems form through reinforcement and stabilization of a deformed configuration that was generated by a transient force. An important class of such structures arises during gametogenesis, when a dividing cell undergoes incomplete cytokinesis, giving rise to daughter cells that remain connected through a stabilized intercellular bridge (ICB). ICBs can form through arrest of the contractile cytokinetic furrow and its subsequent stabilization. Despite knowledge of the molecular components, the mechanics underlying robust ICB assembly and the interplay between ring contractility and stiffening are poorly understood. Here, we report joint experimental and theoretical work that explores the physics underlying robust ICB assembly. We develop a continuum mechanics model that reveals the minimal requirements for the formation of stable ICBs, and validate the model's equilibrium predictions through a tabletop experimental analog. With insight into the equilibrium states, we turn to the dynamics: we demonstrate that contractility and stiffening are in dynamic competition and that the time intervals of their action must overlap to ensure assembly of ICBs of biologically observed proportions. Our results highlight a mechanism in which deformation and remodeling are tightly coordinated-one that is applicable to several mechanics-based applications and is a common theme in biological systems spanning several length scales.
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Affiliation(s)
- Jaspreet Singh
- Center for Computational Biology, Flatiron Institute, New York, New York
| | | | - Krishna Garikipati
- Departments of Mechanical Engineering, and Mathematics, Michigan Institute for Computational Discovery & Engineering, University of Michigan, Ann Arbor, Michigan.
| | - Stanislav Y Shvartsman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey; The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey.
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Diegmiller R, Nunley H, Shvartsman SY, Imran Alsous J. Quantitative models for building and growing fated small cell networks. Interface Focus 2022; 12:20210082. [PMID: 35865502 PMCID: PMC9184967 DOI: 10.1098/rsfs.2021.0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Small cell clusters exhibit numerous phenomena typically associated with complex systems, such as division of labour and programmed cell death. A conserved class of such clusters occurs during oogenesis in the form of germline cysts that give rise to oocytes. Germline cysts form through cell divisions with incomplete cytokinesis, leaving cells intimately connected through intercellular bridges that facilitate cyst generation, cell fate determination and collective growth dynamics. Using the well-characterized Drosophila melanogaster female germline cyst as a foundation, we present mathematical models rooted in the dynamics of cell cycle proteins and their interactions to explain the generation of germline cell lineage trees (CLTs) and highlight the diversity of observed CLT sizes and topologies across species. We analyse competing models of symmetry breaking in CLTs to rationalize the observed dynamics and robustness of oocyte fate specification, and highlight remaining gaps in knowledge. We also explore how CLT topology affects cell cycle dynamics and synchronization and highlight mechanisms of intercellular coupling that underlie the observed collective growth patterns during oogenesis. Throughout, we point to similarities across organisms that warrant further investigation and comment on the extent to which experimental and theoretical findings made in model systems extend to other species.
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Affiliation(s)
- Rocky Diegmiller
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Hayden Nunley
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Stanislav Y. Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA,Department of Molecular Biology, Princeton University, Princeton, NJ, USA,Flatiron Institute, Simons Foundation, New York, NY, USA
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Diegmiller R, Doherty CA, Stern T, Imran Alsous J, Shvartsman SY. Size scaling in collective cell growth. Development 2021; 148:271938. [PMID: 34463760 DOI: 10.1242/dev.199663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/12/2021] [Indexed: 02/03/2023]
Abstract
Size is a fundamental feature of living entities and is intimately tied to their function. Scaling laws, which can be traced to D'Arcy Thompson and Julian Huxley, have emerged as a powerful tool for studying regulation of the growth dynamics of organisms and their constituent parts. Yet, throughout the 20th century, as scaling laws were established for single cells, quantitative studies of the coordinated growth of multicellular structures have lagged, largely owing to technical challenges associated with imaging and image processing. Here, we present a supervised learning approach for quantifying the growth dynamics of germline cysts during oogenesis. Our analysis uncovers growth patterns induced by the groupwise developmental dynamics among connected cells, and differential growth rates of their organelles. We also identify inter-organelle volumetric scaling laws, finding that nurse cell growth is linear over several orders of magnitude. Our approach leverages the ever-increasing quantity and quality of imaging data, and is readily amenable for studies of collective cell growth in other developmental contexts, including early mammalian embryogenesis and germline development.
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Affiliation(s)
- Rocky Diegmiller
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Caroline A Doherty
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Tomer Stern
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jasmin Imran Alsous
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.,Flatiron Institute, Simons Foundation, New York, NY 10010, USA
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