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Mathematical Modeling of Cell Polarity Establishment of budding yeast

Communications on Applied Mathematics and Computation 2024年第1期6卷 218-235页

作者： Yue Liu Jun Xie Hay-Oak Park Wing-Cheong Lo Department of Mathematics City University of Hong KongTat Chee AvenueKowloonHong KongChina Department of Molecular Genetics The Ohio State UniversityColumbusOHUSA

The budding yeast Saccharomyces cerevisiae is a powerful model system for studying the cell polarity establishment.The cell polarization process is regulated by signaling molecules,which are initially distributed in the cytoplasm and then recruited to a proper location on the cell membrane in response to spatial cues or spontaneously.Polarization of these signaling molecules involves complex regulation,so the mathematical models become a useful tool to investigate the mechanism behind the process.In this review,we discuss how mathematical modeling has shed light on different regulations in the cell polarization.We also propose future applications for the mathematical modeling of cell polarization and morphogenesis.

关键词： budding yeast Cdc42 Morphogenesis Septin Mathematical models

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Efficient de novo assembly and modification of large DNA fragments

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Science China(Life Sciences) 2022年第7期65卷 1445-1455页

作者： Shuangying Jiang Yuanwei Tang Liang Xiang Xinlu Zhu Zelin Cai Ling Li Yingxi Chen Peishuang Chen Yuge Feng Xin Lin Guoqiang Li Jafar Sharif Junbiao Dai CAS Key Laboratory of Quantitative Engineering Biology Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China RIKEN Center for Integrative Medical Sciences(IMS) Developmental Genetics LaboratoryYokohama 230-0045Japan

Synthetic genomics has provided new bottom-up platforms for the functional study of viral and microbial genomes.The construction of the large,gigabase(Gb)-sized genomes of higher organisms will deepen our understanding of genetic blueprints significantly.But for the synthesis and assembly of such large-scale genomes,the development of new or expanded methods is required.In this study,we develop an efficient pipeline for the construction of large DNA fragments sized 100 kilobases(kb)or above from scratches and describe an efficient method for“scar-free”engineering of the assembled sequences.Our method,therefore,should provide a standard framework for producing long DNA molecules,which are critical materials for synthetic genomics and metabolic engineering.

关键词： DNA assembly budding yeast large DNA fragments sequence modification DNA synthesis Synthetic Biology

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Saccharomyces cerevisiae in neuroscience:how unicellular organism helps to better understand prion protein?

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Neural Regeneration Research 2021年第3期16卷 489-495页

作者： Takao Ishikawa Department of Molecular Biology Institute of BiochemistryFaculty of BiologyUniversity of WarsawWarsawPoland

The baker's yeast Saccharomyces(S.)cerevisiae is a single-celled eukaryotic model organism widely used in research on life sciences.Being a unicellular organism,S.cerevisiae has some evident limitations in application to neuroscience.However,yeast prions are extensively studied and they are known to share some hallmarks with mammalian prion protein or other amyloidogenic proteins found in the pathogenesis of Alzheimer's,Parkinson's,or Huntington's diseases.Therefore,the yeast S.cerevisiae has been widely used for basic research on aggregation properties of proteins in cellulo and on their propagation.Recently,a yeast-based study revealed that some regions of mammalian prion protein and amyloidβ1–42 are capable of induction and propagation of yeast prions.It is one of the examples showing that evolutionarily distant organisms share common mechanisms underlying the structural conversion of prion proteins making yeast cells a useful system for studying mammalian prion protein.S.cerevisiae has also been used to design novel screening systems for anti-prion compounds from chemical libraries.yeastbased assays are cheap in maintenance and safe for the researcher,making them a very good choice to perform preliminary screening before further characterization in systems engaging mammalian cells infected with prions.In this review,not only classical red/white colony assay but also yeast-based screening assays developed during last year are discussed.Computational analysis and research carried out using yeast prions force us to expect that prions are widely present in nature.Indeed,the last few years brought us several examples indicating that the mammalian prion protein is no more peculiar protein–it seems that a better understanding of prion proteins nature-wide may aid us with the treatment of prion diseases and other amyloid-related medical conditions.

关键词： amyloid artificial prion baker's yeast budding yeast drug screening fusion protein neurodegenerative diseases prion protein yeast-based assay

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