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Genetics Nov 2015Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with...
Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with them a century ago. Work with Drosophila has enabled dramatic advances in cell and developmental biology, neurobiology and behavior, molecular biology, evolutionary and population genetics, and other fields. With more tissue types and observable behaviors than in other short-generation model organisms, and with vast genome data available for many species within the genus, the fly's tractable complexity will continue to enable exciting opportunities to explore mechanisms of complex developmental programs, behaviors, and broader evolutionary questions. This primer describes the organism's natural history, the features of sequenced genomes within the genus, the wide range of available genetic tools and online resources, the types of biological questions Drosophila can help address, and historical milestones.
Topics: Animals; Drosophila; Models, Biological; Models, Genetic
PubMed: 26564900
DOI: 10.1534/genetics.115.183392 -
Bulletin of Mathematical Biology Sep 2022In evolutionary studies, it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or...
In evolutionary studies, it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has occurred in the past, a tree may not provide a complete picture of their history. In such cases, tree-based phylogenetic networks can provide a useful, more refined representation of the species' evolution. Such a network is essentially a phylogenetic tree with some arcs added between the tree's edges so as to represent reticulate events such as gene transfer, hybridization and recombination. Even so, this model does not permit the direct representation of evolutionary scenarios where reticulate events have taken place between different subfamilies or lineages of species. To represent such scenarios, in this paper we introduce the notion of a forest-based network, that is, a collection of leaf-disjoint phylogenetic trees on a set of species with arcs added between the edges of distinct trees within the collection. Forest-based networks include the recently introduced class of overlaid species forests which can be used to model introgression. As we shall see, even though the definition of forest-based networks is closely related to that of tree-based networks, they lead to new mathematical theory which complements that of tree-based networks. As well as studying the relationship of forest-based networks with other classes of phylogenetic networks, such as tree-child networks and universal tree-based networks, we present some characterizations of some special classes of forest-based networks. We expect that our results will be useful for developing new models and algorithms to understand reticulate evolution, such as introgression and gene transfer between species.
Topics: Humans; Forests; Mathematical Concepts; Models, Biological; Models, Genetic; Phylogeny
PubMed: 36107279
DOI: 10.1007/s11538-022-01081-9 -
Acta Biochimica Et Biophysica Sinica Aug 2022A whole-cell model represents certain aspects of the cell structure and/or function. Due to the high complexity of the cell, an integrative modeling approach is often... (Review)
Review
A whole-cell model represents certain aspects of the cell structure and/or function. Due to the high complexity of the cell, an integrative modeling approach is often taken to utilize all available information including experimental data, prior knowledge and prior models. In this review, we summarize an emerging workflow of whole-cell modeling into five steps: (i) gather information; (ii) represent the modeled system into modules; (iii) translate input information into scoring function; (iv) sample the whole-cell model; (v) validate and interpret the model. In particular, we propose the integrative modeling of the cell by combining available (whole-cell) models to maximize the accuracy, precision, and completeness. In addition, we list quantitative predictions of various aspects of cell biology from existing whole-cell models. Moreover, we discuss the remaining challenges and future directions, and highlight the opportunity to establish an integrative spatiotemporal multi-scale whole-cell model based on a community approach.
Topics: Models, Biological
PubMed: 36017893
DOI: 10.3724/abbs.2022115 -
Cell Proliferation Sep 2022Planarian has attracted increasing attentions in the regeneration field for its usefulness as an important biological model organism attributing to its strong... (Review)
Review
BACKGROUND
Planarian has attracted increasing attentions in the regeneration field for its usefulness as an important biological model organism attributing to its strong regeneration ability. Both the complexity of multiple regulatory networks and their coordinate functions contribute to the maintenance of normal cellular homeostasis and the process of regeneration in planarian. The polarity, size, location and number of regeneration tissues are regulated by diverse mechanisms. In this review we summarize the recent advances about the importance genetic and molecular mechanisms for regeneration control on various tissues in planarian.
METHODS
A comprehensive literature search of original articles published in recent years was performed in regards to the molecular mechanism of each cell types during the planarian regeneration, including neoblast, nerve system, eye spot, excretory system and epidermal.
RESULTS
Available molecular mechanisms gave us an overview of regeneration process in every tissue. The sense of injuries and initiation of regeneration is regulated by diverse genes like follistatin and ERK signaling. The Neoblasts differentiate into tissue progenitors under the regulation of genes such as egfr-3. The regeneration polarity is controlled by Wnt pathway, BMP pathway and bioelectric signals. The neoblast within the blastema differentiate into desired cell types and regenerate the missing tissues. Those tissue specific genes regulate the tissue progenitor cells to differentiate into desired cell types to complete the regeneration process.
CONCLUSION
All tissue types in planarian participate in the regeneration process regulated by distinct molecular factors and cellular signaling pathways. The neoblasts play vital roles in tissue regeneration and morphology maintenance. These studies provide new insights into the molecular mechanisms for regulating planarian regeneration.
Topics: Animals; Homeostasis; Models, Biological; Planarians; Signal Transduction; Stem Cells
PubMed: 35811385
DOI: 10.1111/cpr.13276 -
Philosophical Transactions of the Royal... May 2011A metacommunity can be defined as a set of communities that are linked by migration, and extinction and recolonization. In metacommunities, evolution can occur not only... (Review)
Review
A metacommunity can be defined as a set of communities that are linked by migration, and extinction and recolonization. In metacommunities, evolution can occur not only by processes that occur within communities such as drift and individual selection, but also by among-community processes, such as divergent selection owing to random differences among communities in species composition, and group and community-level selection. The effect of these among-community-level processes depends on the pattern of migration among communities. Migrating units may be individuals (migrant pool model), groups of individuals (single-species propagule pool model) or multi-species associations (multi-species propagule pool model). The most interesting case is the multi-species propagule pool model. Although this pattern of migration may a priori seem rare, it becomes more plausible in small well-defined 'communities' such as symbiotic associations between two or a few species. Theoretical models and experimental studies show that community selection is potentially an effective evolutionary force. Such evolution can occur either through genetic changes within species or through changes in the species composition of the communities. Although laboratory studies show that community selection can be important, little is known about how important it is in natural populations.
Topics: Biological Evolution; Ecosystem; Models, Biological
PubMed: 21444314
DOI: 10.1098/rstb.2010.0290 -
Advanced Biosystems May 2019Studying and understanding of tissue and disease mechanisms largely depend on the availability of suitable and representative biological model systems. These model... (Review)
Review
Studying and understanding of tissue and disease mechanisms largely depend on the availability of suitable and representative biological model systems. These model systems should be carefully engineered and faithfully reproduce the biological system of interest to understand physiological effects, pharmacokinetics, and toxicity to better identify new drug compounds. By relying on microfluidics, microphysiological systems (MPSs) enable the precise control of culturing conditions and connections of advanced in vitro 3D organ models that better reproduce in vivo environments. This review focuses on transferable in vitro organ models and integrated MPSs that host these transferable biological units and enable interactions between different tissue types. Interchangeable and transferrable in vitro organ models allow for independent quality control of the biological model before system assembly and building MPS assays on demand. Due to the complexity and different maturation times of individual in vitro tissues, off-chip production and quality control entail improved stability and reproducibility of the systems and results, which is important for large-scale adoption of the technology. Lastly, the technical and biological challenges and open issues for realizing and implementing integrated MPSs with transferable in vitro organ models are discussed.
Topics: Humans; Lab-On-A-Chip Devices; Microchip Analytical Procedures; Models, Biological; Tissue Engineering
PubMed: 32627410
DOI: 10.1002/adbi.201900018 -
Bulletin of Mathematical Biology Oct 2023Coordination of cell behaviour is key to a myriad of biological processes including tissue morphogenesis, wound healing, and tumour growth. As such, individual-based...
Coordination of cell behaviour is key to a myriad of biological processes including tissue morphogenesis, wound healing, and tumour growth. As such, individual-based computational models, which explicitly describe inter-cellular interactions, are commonly used to model collective cell dynamics. However, when using individual-based models, it is unclear how descriptions of cell boundaries affect overall population dynamics. In order to investigate this we define three cell boundary descriptions of varying complexities for each of three widely used off-lattice individual-based models: overlapping spheres, Voronoi tessellation, and vertex models. We apply our models to multiple biological scenarios to investigate how cell boundary description can influence tissue-scale behaviour. We find that the Voronoi tessellation model is most sensitive to changes in the cell boundary description with basic models being inappropriate in many cases. The timescale of tissue evolution when using an overlapping spheres model is coupled to the boundary description. The vertex model is demonstrated to be the most stable to changes in boundary description, though still exhibits timescale sensitivity. When using individual-based computational models one should carefully consider how cell boundaries are defined. To inform future work, we provide an exploration of common individual-based models and cell boundary descriptions in frequently studied biological scenarios and discuss their benefits and disadvantages.
Topics: Mathematical Concepts; Models, Biological; Software; Cell Communication; Morphogenesis
PubMed: 37805982
DOI: 10.1007/s11538-023-01214-8 -
Journal of Bacteriology Apr 2024
Topics: Soil Microbiology; Models, Biological
PubMed: 38529952
DOI: 10.1128/jb.00073-24 -
BMC Bioinformatics Sep 2019Mathematics and Phy sics-based simulation models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form....
BACKGROUND
Mathematics and Phy sics-based simulation models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form. Similarly, comprehensive descriptions of such models help to ensure that such models are accessible, discoverable, and reusable. To this end, researchers have developed tools and standards to encode mathematical models of biological systems enabling reproducibility and reuse, tools and guidelines to facilitate semantic description of mathematical models, and repositories in which to archive, share, and discover models. Scientists can leverage these resources to investigate specific questions and hypotheses in a more efficient manner.
RESULTS
We have comprehensively annotated a cohort of models with biological semantics. These annotated models are freely available in the Physiome Model Repository (PMR). To demonstrate the benefits of this approach, we have developed a web-based tool which enables users to discover models relevant to their work, with a particular focus on epithelial transport. Based on a semantic query, this tool will help users discover relevant models, suggesting similar or alternative models that the user may wish to explore or use.
CONCLUSION
The semantic annotation and the web tool we have developed is a new contribution enabling scientists to discover relevant models in the PMR as candidates for reuse in their own scientific endeavours. This approach demonstrates how semantic web technologies and methodologies can contribute to biomedical and clinical research. The source code and links to the web tool are available at https://github.com/dewancse/model-discovery-tool.
Topics: Humans; Models, Biological; Patient-Specific Modeling; Reproducibility of Results; Semantics; Software
PubMed: 31492098
DOI: 10.1186/s12859-019-2987-y -
Briefings in Bioinformatics Jan 2022Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models...
Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have many unknown and nonmeasurable parameters, which have to be determined by fitting the model to experimental data. In order to perform this task, known as parameter estimation or model calibration, the modeller faces challenges such as poor parameter identifiability, lack of sufficiently informative experimental data and the existence of local minima in the objective function landscape. These issues tend to worsen with larger model sizes, increasing the computational complexity and the number of unknown parameters. An incorrectly calibrated model is problematic because it may result in inaccurate predictions and misleading conclusions. For nonexpert users, there are a large number of potential pitfalls. Here, we provide a protocol that guides the user through all the steps involved in the calibration of dynamic models. We illustrate the methodology with two models and provide all the code required to reproduce the results and perform the same analysis on new models. Our protocol provides practitioners and researchers in biological modelling with a one-stop guide that is at the same time compact and sufficiently comprehensive to cover all aspects of the problem.
Topics: Calibration; Models, Biological; Systems Biology
PubMed: 34619769
DOI: 10.1093/bib/bbab387