scholarly journals JaponicusDB: Rapid deployment of a model organism database for an emerging model species

Genetics ◽  
2021 ◽  
Author(s):  
Kim M Rutherford ◽  
Midori A Harris ◽  
Snezhana Oliferenko ◽  
Valerie Wood
Keyword(s):  
Fission Yeast ◽  
Model Organism ◽  
Full Potential ◽  
Model Species ◽  
Model Organism Database ◽  
Cellular Processes ◽  
Growing Body ◽  
Central Resource ◽  
Ready Access ◽  
Rapid Deployment

Abstract The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realise the full potential of studying a newly emerging model species, and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.

scholarly journals JaponicusDB: Rapid deployment of a model organism database for an emerging model species

2021 ◽  
Author(s):  
Kim M. Rutherford ◽  
Midori A. Harris ◽  
Snezhana Oliferenko ◽  
Valerie Wood
Keyword(s):  
Fission Yeast ◽  
Model Organism ◽  
Full Potential ◽  
Model Species ◽  
Model Organism Database ◽  
Cellular Processes ◽  
Growing Body ◽  
Central Resource ◽  
Ready Access ◽  
Rapid Deployment

AbstractThe fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realise the full potential of studying a newly emerging model species, and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.

scholarly journals Fission stories: Using PomBase to understand Schizosaccharomyces pombe biology

Genetics ◽  
2021 ◽  
Author(s):  
Midori A Harris ◽  
Kim M Rutherford ◽  
Jacqueline Hayles ◽  
Antonia Lock ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism ◽  
Biological Knowledge ◽  
Model Organism Database ◽  
Comprehensive Data ◽  
Data Collections ◽  
Data Summaries

Abstract PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualisation, PomBase also drives innovation in the MOD community.

scholarly journals Fission stories: Using PomBase to understand Schizosaccharomyces pombe biology

2021 ◽  
Author(s):  
Midori A. Harris ◽  
Kim M. Rutherford ◽  
Jacqueline Hayles ◽  
Antonia Lock ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism ◽  
Biological Knowledge ◽  
Model Organism Database ◽  
Link Type ◽  
Comprehensive Data ◽  
Data Collections ◽  
Data Summaries

AbstractPomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualisation, PomBase also drives innovation in the MOD community.

scholarly journals The Multiple Functions of Rho GTPases in Fission Yeasts

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1422
Author(s):  
Jero Vicente-Soler ◽  
Teresa Soto ◽  
Alejandro Franco ◽  
José Cansado ◽  
Marisa Madrid
Keyword(s):  
Fission Yeast ◽  
Rho Gtpases ◽  
Current Knowledge ◽  
Model Organism ◽  
Nucleotide Exchange ◽  
Guanine Nucleotide Exchange ◽  
Nucleotide Exchange Factors ◽  
Physiological Processes ◽  
Evolutionary Changes ◽  
Rho Family

The Rho family of GTPases represents highly conserved molecular switches involved in a plethora of physiological processes. Fission yeast Schizosaccharomyces pombe has become a fundamental model organism to study the functions of Rho GTPases over the past few decades. In recent years, another fission yeast species, Schizosaccharomyces japonicus, has come into focus offering insight into evolutionary changes within the genus. Both fission yeasts contain only six Rho-type GTPases that are spatiotemporally controlled by multiple guanine–nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs), and whose intricate regulation in response to external cues is starting to be uncovered. In the present review, we will outline and discuss the current knowledge and recent advances on how the fission yeasts Rho family GTPases regulate essential physiological processes such as morphogenesis and polarity, cellular integrity, cytokinesis and cellular differentiation.

scholarly journals Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joris J. B. Messelink ◽  
Muriel C. F. van Teeseling ◽  
Jacqueline Janssen ◽  
Martin Thanbichler ◽  
Chase P. Broedersz
Keyword(s):  
Single Cell ◽  
Caulobacter Crescentus ◽  
Model Organism ◽  
Super Resolution ◽  
Chromosome Organization ◽  
General Strategy ◽  
Cell Axis ◽  
Cellular Processes ◽  
Emergent Order ◽  
Genomic Clusters

AbstractThe order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, we develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi–C experiments on the model organism Caulobacter crescentus. The predictive power of our model is validated by independent experiments. We find that on large genomic scales, organizational features are predominantly present along the long cell axis: chromosomal loci exhibit striking long-ranged two-point axial correlations, indicating emergent order. This organization is associated with large genomic clusters we term Super Domains (SuDs), whose existence we support with super-resolution microscopy. On smaller genomic scales, our model reveals chromosome extensions that correlate with transcriptional and loop extrusion activity. Finally, we quantify the information contained in chromosome organization that may guide cellular processes. Our approach can be extended to other species, providing a general strategy to resolve variability in single-cell chromosomal organization.

scholarly journals MaizeGDB update: new tools, data and interface for the maize model organism database

2015 ◽  
Vol 44 (D1) ◽  
pp. D1195-D1201 ◽  
Author(s):  
Carson M. Andorf ◽  
Ethalinda K. Cannon ◽  
John L. Portwood ◽  
Jack M. Gardiner ◽  
Lisa C. Harper ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database

scholarly journals ZFIN, The zebrafish model organism database: Updates and new directions

genesis ◽  
2015 ◽  
Vol 53 (8) ◽  
pp. 498-509 ◽  
Author(s):  
Leyla Ruzicka ◽  
Yvonne M. Bradford ◽  
Ken Frazer ◽  
Douglas G. Howe ◽  
Holly Paddock ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database ◽  
Zebrafish Model ◽  
Database Updates ◽  
New Directions

Visual detection of binary, ternary, and quaternary protein interactions in fission yeast by Pil1 co-tethering assay

2021 ◽  
Author(s):  
Zhong-Qiu Yu ◽  
Xiao-Man Liu ◽  
Dan Zhao ◽  
Dan-Dan Xu ◽  
Li-Lin Du
Keyword(s):  
Fission Yeast ◽  
Protein Interactions ◽  
Visual Detection ◽  
Protein Protein Interactions ◽  
Phosphatidylinositol 3 Kinase ◽  
Basic Form ◽  
Bait Protein ◽  
Cellular Processes ◽  
Prey Protein ◽  
Versatile Tool

Protein-protein interactions are vital for executing nearly all cellular processes. To facilitate the detection of protein-protein interactions in living cells of the fission yeast Schizosaccharomyces pombe, here we present an efficient and convenient method termed the Pil1 co-tethering assay. In its basic form, we tether a bait protein to mCherry-tagged Pil1, which forms cortical filamentary structures, and examine whether a GFP-tagged prey protein colocalizes with the bait. We demonstrate that this assay is capable of detecting pairwise protein-protein interactions of cytosolic proteins and nuclear proteins. Furthermore, we show that this assay can be used for detecting not only binary protein-protein interactions, but also ternary and quaternary protein-protein interactions. Using this assay, we systematically characterized the protein-protein interactions in the Atg1 complex and in the phosphatidylinositol 3-kinase (PtdIns3K) complexes and found that Atg38 is incorporated into the PtdIns3K complex I via an Atg38-Vps34 interaction. Our data show that this assay is a useful and versatile tool and should be added to the routine toolbox of fission yeast researchers.

scholarly journals A toolbox of Stable Integration Vectors (SIV) in the fission yeast Schizosaccharomyces pombe

2019 ◽  
Author(s):  
Aleksandar Vještica ◽  
Magdalena Marek ◽  
Pedro N’kosi ◽  
Laura Merlini ◽  
Gaowen Liu ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism ◽  
Experimental System ◽  
Single Copy ◽  
Cell Physiology ◽  
Large Set ◽  
Stable Integration ◽  
Wide Range ◽  
Fluorescent Tags

AbstractSchizosaccharomyces pombe is a widely used model organism that resembles higher eukaryotes in many aspects of cell physiology. Its popularity as an experimental system partially stems from the ease of genetic manipulations, where the innate homology-targeted repair is exploited to precisely edit the genome. While vectors to incorporate exogenous sequences into the chromosomes are available, most are poorly characterized. Here we show that commonly used fission yeast vectors, which upon integration produce repetitive genomic regions, yield unstable genomic loci. We overcome this problem by designing a new series of Stable Integration Vectors (SIV) that target four different prototrophy genes. SIV produce non-repetitive, stable genomic loci and integrate predominantly as single copy. Additionally, we develop a set of complementary auxotrophic alleles that preclude false-positive integration events. We expand the vector series to include antibiotic resistance markers, promoters, fluorescent tags and terminators, and build a highly modular toolbox to introduce heterologous sequences. Finally, as proof of concept, we generate a large set of ready-to-use, fluorescent probes to mark organelles and cellular processes with a wide range of applications in fission yeast research.

scholarly journals MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research

2008 ◽  
Vol 2008 ◽  
pp. 1-10 ◽  
Author(s):  
Carolyn J. Lawrence ◽  
Lisa C. Harper ◽  
Mary L. Schaeffer ◽  
Taner Z. Sen ◽  
Trent E. Seigfried ◽  
...  
Keyword(s):  
Model Organism ◽  
Basic Research ◽  
Model Organism Database ◽  
High Productivity ◽  
Group Activities ◽  
Food And Agriculture ◽  
Food And Agriculture Organization ◽  
Genetics And Genomics ◽  
Excellent Source ◽  
By Products

In 2001 maize became the number one production crop in the world with the Food and Agriculture Organization of the United Nations reporting over 614 million tonnes produced. Its success is due to the high productivity per acre in tandem with a wide variety of commercial uses. Not only is maize an excellent source of food, feed, and fuel, but also its by-products are used in the production of various commercial products. Maize's unparalleled success in agriculture stems from basic research, the outcomes of which drive breeding and product development. In order for basic, translational, and applied researchers to benefit from others' investigations, newly generated data must be made freely and easily accessible. MaizeGDB is the maize research community's central repository for genetics and genomics information. The overall goals of MaizeGDB are to facilitate access to the outcomes of maize research by integrating new maize data into the database and to support the maize research community by coordinating group activities.

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