Budding yeast colony growth study based on circular granular cell

Aprianti, Devi; Khotimah, Siti Nurul; Viridi, Sparısoma

doi:10.1088/1742-6596/739/1/012026

Cited by 7 publications

(9 citation statements)

References 5 publications

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“…Developing a modeling framework for investigating prion disease dynamics within an entire yeast colony is challenging because it requires capturing the physical processes on an individual cell level that determine colony growth (i.e., budding and variable cell cycle length) as well as capturing the interplay of individual cell processes with protein aggregation dynamics (i.e., asymmetric protein distribution at the time of division, persistence of diseased phenotype/aggregate that was given to daughter while it grows to begin a new cell cycle, lineage-dependent protein propagation). Several models have already been developed to investigate physical mechanisms controlling patterns of yeast colony growth such as cell division polarity, mother-daughter size asymmetry, and cell-cell adhesion via budding of the new daughter cell [92,93,105]. Jönsson and Levchenko developed an offlattice, center-based model in which cells are modeled as elastic spheres of variable size [92].…”

Section: Discussionmentioning

confidence: 99%

“…Center-based models have been used to analyze multicellular processes in tumors [91,99,100], intestinal crypts and epithelial tissues [85,103], cell migration in extracellular matrix [85,100], and tissue regeneration, growth, and organization [91,99,100,103,104]. In addition, several center-based models have been developed for studying macroscopic properties of yeast colonies [92,93,105]. (See Section 4 for more details.)…”

Section: Application Of Center-based Models In Biologymentioning

confidence: 99%

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Multi-Scale Mathematical Modeling of Prion Aggregate Dynamics and Phenotypes in Yeast Colonies

Banwarth-Kuhn¹,

Sindi²

2020

Apolipoproteins, Triglycerides and Cholesterol

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Prion diseases are a multi-scale biological phenomenon that requires understanding intracellular processes as well as how cells interact with each other and their environment. In mammals, prion diseases are progressive, untreatable, and fatal. Yeast prion phenotypes are harmless and reversible, which suggests a deep understanding of the reversal of prion phenotypes in yeast may be informative to mammalian diseases. In yeast, the loss of some prion phenotypes appears to be stochastic and spatially dependent, suggesting a cell-based model of yeast prion dynamics would be a powerful tool for comparisons with experimental results and hypothesis generation. In this work, we consider the components necessary to develop such a model that depicts both the biochemical-, intracellular-, and colonylevel scales in yeast prion phenotypes. We first review the literature of mathematical models of the intracellular processes of prion disease. We then review common approaches to cell-based modeling of multicellular systems and how they have led to biological insights in other systems. This chapter ends with a discussion of future studies aimed at motivating how these two types of models can be coupled to produce multi-scale models of prion phenotypes.

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Section: Discussionmentioning

confidence: 99%

Section: Application Of Center-based Models In Biologymentioning

confidence: 99%

Multi-Scale Mathematical Modeling of Prion Aggregate Dynamics and Phenotypes in Yeast Colonies

Banwarth-Kuhn¹,

Sindi²

2020

Apolipoproteins, Triglycerides and Cholesterol

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“…Sistem granular merupakan sistem banyak partikel klasik yang bersifat disipatif yang berinteraksi umumnya melalui gaya normal dan juga gaya gesek [1]. Pada studi ini dikaji interaksi antar partikel pada perkembangbiakan koloni ragi yang telah disimulasikan sebelumnya menggunakan javascript.…”

Section: Metodologi Penelitianunclassified

Analisis Network Dan Geometri Pada Sistem Granular Dua Dimensi

Meiriska¹,

Viridi²,

Dimas³

et al. 2018

Prosiding Seminar Nasional Fisika (E-Journal) Snf2018 Unj

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Pengaturan partikel dan gaya dalam material granular dan materi partikulat memiliki organisasi yang kompleks pada skala spasial. Organisasi seperti ini dapat mempengaruhi bagaimana material merespon atau mengkonfigurasi ulang ketika terkena gangguan atau pemuatan eksternal. Studi teoritis sifat-sifat partikel, force-chain dan domain memerlukan pengembangan dan penerapan kerangka kerja matematis, stastistik, fisika dan komputasi yang tepat. Secara tradisional bahan granular telah diselidiki menggunakan partikel atau model rangkaian yang masing-masing cederung secara implisit. Dewasa ini pengembangan ilmu jaringan (network science) telah muncul sebagai pendekatan yang kuat untuk menyelidiki dan mencirikan arsitektur heterogen dalam sistem yang kompleks dan beragam metode telah menghasilkan wawasan yang menarik kedalam material granular. Dalam studi ini akan meninjau pendekatan berbasis jaringan untuk mempelajari material granular dan mengeksplorasi potensi kerangka tersebut untuk memberikan deskripsi yang berguna dari material granular ini. Serta untuk meningkatkan pemahaman tentang fisis yang mendasarinya. Penelitian dilakukan dengan melakukan simulasi menggunakan program python 3.6. Dari hasil simulasi dan dilakukan analisis network pada material granular (perkembangbiakan koloni ragi) dapat disimpulkan pendekatan berbasis network ini mampu memberikan informasi yang tidak dapat diketahui sebelumnya, bahwa perkembangbiakan koloni ragi tidak dipengaruhi oleh umur dan diameter sel, serta kecenderungan sel anak yang sering berada pada jarak yang cukup dekat dengan sel induk.

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“…In each of these previous studies, results focused on the colony as a whole-size, shape and expansion-and not how the colony itself was organized. An additional set of studies used ABMs to investigate the impact of individual cell growth and reproduction times on colony expanse as well as study the relationship between cell generation and birth location in the colony [43][44][45][46][47]. However, likely for computational simplicity, these prior studies focused primarily on populations of a few hundred or few thousand cells.…”

Section: Introductionmentioning

confidence: 99%

Quantifying the Biophysical Impact of Budding Cell Division on the Spatial Organization of Growing Yeast Colonies

2020

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Spatial patterns in microbial colonies are the consequence of cell-division dynamics coupled with cell-cell interactions on a physical media. Agent-based models (ABMs) are a powerful tool for understanding the emergence of large scale structure from these individual cell processes. However, most ABMs have focused on fission, a process by which cells split symmetrically into two daughters. The yeast, Saccharomyces cerevisiae, is a model eukaryote which commonly undergoes an asymmetric division process called budding. The resulting mother and daughter cells have unequal sizes and the daughter cell does not inherit the replicative age of the mother. In this work, we develop and analyze an ABM to study the impact of budding cell division and nutrient limitation on yeast colony structure. We find that while budding division does not impact large-scale properties of the colony (such as shape and size), local spatial organization of cells with respect to spatial layout of mother-daughter cell pairs and connectivity of subcolonies is greatly impacted. In addition, we find that nutrient limitation further promotes local spatial organization of cells and changes global colony organization by driving variation in subcolony sizes. Moreover, resulting differences in spatial organization, coupled with differential growth rates from nutrient limitation, create distinct sectoring patterns within growing yeast colonies. Our findings offer novel insights into mechanisms driving experimentally observed sectored yeast colony phenotypes. Furthermore, our work illustrates the need to include relevant biophysical mechanisms when using ABMs to compare to experimental studies.

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Budding yeast colony growth study based on circular granular cell

Cited by 7 publications

References 5 publications

Multi-Scale Mathematical Modeling of Prion Aggregate Dynamics and Phenotypes in Yeast Colonies

Multi-Scale Mathematical Modeling of Prion Aggregate Dynamics and Phenotypes in Yeast Colonies

Analisis Network Dan Geometri Pada Sistem Granular Dua Dimensi

Quantifying the Biophysical Impact of Budding Cell Division on the Spatial Organization of Growing Yeast Colonies

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