3,197 research outputs found
In vivo characterisation of fluorescent proteins in budding yeast
No full textFluorescent proteins (FPs) are widely used in many organisms, but are commonly characterised in vitro. However, the in vitro properties may poorly reflect in vivo performance. Therefore, we characterised 27 FPs in vivo using Saccharomyces cerevisiae as model organism. We linked the FPs via a T2A peptide to a control FP, producing equimolar expression of the 2 FPs from 1 plasmid. Using this strategy, we characterised the FPs for brightness, photostability, photochromicity and pH-sensitivity, achieving a comprehensive in vivo characterisation. Many FPs showed different in vivo properties compared to existing in vitro data. Additionally, various FPs were photochromic, which affects readouts due to complex bleaching kinetics. Finally, we codon optimized the best performing FPs for optimal expression in yeast, and found that codon-optimization alters FP characteristics. These FPs improve experimental signal readout, opening new experimental possibilities. Our results may guide future studies in yeast that employ fluorescent proteins
An integrated model quantitatively describing metabolism, growth and cell cycle in budding yeast
Full text linkComputational models are expected to increase understanding of how complex biological functions arise from the interactions of large numbers of gene products and biologically active low molecular weight molecules. Recent studies underline the need to develop quantitative models of the whole cell in order to tackle this challenge and to accelerate biological discoveries. In this work we describe three major functions of a yeast cell: Metabolism, Growth and Cycle, through two coarse grain models, MeGro (Metabolism + Growth) and GroCy (Growth + Cycle). GroCy effectively recapitulates major phenotypic properties of cells grown in glucose and ethanol supplement media. MeGro can act as a parameter generator for GroCy. The resulting iMeGroCy integrated model can be used as a scaffold for molecularly detailed models of yeast functions.</p
Systems Biology of lactic acid bacteria: a critical review.
Full text linkUnderstanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute.There has been a tendency in the Systems Biology community to think that the collection and integration of data should continue ad infinitum, or that we will otherwise not be able to understand the systems that we study in their details. However, it may sometimes be useful to take a step back and consider whether the knowledge that we already have may not explain the system behaviour that we find so intriguing. Reasoning about systems can be difficult, and may require the application of mathematical techniques. The reward is sometimes the realization of unexpected conclusions, or in the worst case, that we still do not know enough details of the parts, or of the interactions between them.We will discuss a number of cases, with a focus on LAB-related work, where a typical systems approach has brought new knowledge or perspective, often counterintuitive, and clashing with conclusions from simpler approaches. Also novel types of testable hypotheses may be generated by the systems approach, which we will illustrate. Finally we will give an outlook on the fields of research where the systems approach may point the way for the near future. © 2011 Teusink et al; licensee BioMed Central Ltd
Bas-Relief Modeling from Normal Layers
No full textBas-relief is characterized by its unique presentation of intrinsic shape properties and/or detailed appearance using materials raised up in different degrees above a background. However, many bas-relief modeling methods could not manipulate scene details well. We propose a simple and effective solution for two kinds of bas-relief modeling (i.e., structure-preserving and detail-preserving), which is different from the prior tone mapping alike methods. Our idea originates from an observation on typical 3D models which are decomposed into a piecewise smooth base layer and a detail layer in normal field. Proper manipulation of the two layers contributes to both structure-preserving and detail-preserving bas-relief modeling. We solve the modeling problem in a discrete geometry processing setup that uses normal-based mesh processing as a theoretical foundation. Specifically, using the two-step mesh smoothing mechanism as a bridge, we transfer the bas-relief modeling problem into a discrete space, and solve it in a least-squares manner. Experiments and comparisons to other methods show that (i) geometry details are better preserved in the scenario with high compression ratios, and (ii) structures are clearly preserved without shape distortion and interference from details.Accepted author manuscriptMaterials and Manufacturin
Faculty Opinions recommendation of Sugar Influx Sensing by the Phosphotransferase System of Escherichia coli.
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Faculty Opinions recommendation of Phosphoinositide 3-Kinase Regulates Glycolysis through Mobilization of Aldolase from the Actin Cytoskeleton.
No full textFaculty Opinions recommendation of Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli.
No full textFaculty Opinions recommendation of Expression noise facilitates the evolution of gene regulation.
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