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Only accessible information is useful: insights from gradient-mediated patterning.

ABSTRACT: Information theory is gaining popularity as a tool to characterize performance of biological systems. However, information is commonly quantified without reference to whether or how a system could extract and use it; as a result, information-theoretic quantities are easily misinterpreted. Here, we take the example of pattern-forming developmental systems which are commonly structured as cascades of sequential gene expression steps. Such a multi-tiered structure appears to constitute sub-optimal use of the positional information provided by the input morphogen because noise is added at each tier. However, one must distinguish between the total information in a morphogen and information that can be usefully extracted and interpreted by downstream elements. We demonstrate that quantifying the information that is accessible to the system naturally explains the prevalence of multi-tiered network architectures as a consequence of the noise inherent to the control of gene expression. We support our argument with empirical observations from patterning along the major body axis of the fruit fly embryo. We use this example to highlight the limitations of the standard information-theoretic characterization of biological signalling, which are frequently de-emphasized, and illustrate how they can be resolved.

SUBMITTER: Tikhonov M

PROVIDER: S-EPMC4680620 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Only accessible information is useful: insights from gradient-mediated patterning.

Tikhonov Mikhail M Little Shawn C SC Gregor Thomas T

Royal Society open science 20151125 11

Information theory is gaining popularity as a tool to characterize performance of biological systems. However, information is commonly quantified without reference to whether or how a system could extract and use it; as a result, information-theoretic quantities are easily misinterpreted. Here, we take the example of pattern-forming developmental systems which are commonly structured as cascades of sequential gene expression steps. Such a multi-tiered structure appears to constitute sub-optimal ...[more]

PMID: 26716005

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Project description:BackgroundSlipped upper femoral epiphysis is an adolescent hip disorder requiring rapid surgical intervention. Faced with the prospect of their child undergoing surgery, many fearful parents will turn to the internet to provide information and reassurance. Previous studies have shown the orthopaedic information can be difficult to comprehend.ObjectiveAssess the readability of healthcare websites regarding slipped upper femoral epiphysis.MethodsThe term Slipped Upper Femoral Epiphysis was searched in Google, Bing and Yahoo. The websites were evaluated using readability software with seven specialised readability tests including the Flesch-Kincaid Reading Grade Level, the Flesch Reading Ease Score, the Simple Measure of Gobbledygook, Coleman-Liau Index, Automated Readability Index and the Gunning Fog Index. The reading grade level (RGL) was also calculated.A Flesich Read Ease Score (FRES) score above 65 and an RGL of sixth grade and under was considered acceptable. Websites were also assessed for translation services.Results21 unique websites were assessed. The average FRES was 52.5±15.4. Only 3 websites scored 65 or higher (14%). There was a statistically significant difference between website scores based on affiliation, with physician websites having the overall highest mean(p=0.004).The average RGL was 8.67±1.8. Only two websites met the accepted RGL criteria (9.5%) while five websites were marked as extremely difficult to understand (23.8%). Only five websites offered translations (23.8%). There was no statistically significant difference in readability scores between websites which offered translation and those which did not.One-sample t-tests showed that both the RGL (p<0.001; CI 1.83 to 3.49) and the FRES (p<0.001, CI -19.4 to -5.4) scores were significantly different from the accepted standard.ConclusionMost websites reviewed were above the recommended RGL, making content inaccessible. Improving readability and translation services would enhance the internet's usability as a healthcare tool for parents.

Project description:Micropatterning techniques provide direct control over the spatial organization of cells at the sub-mm scale. Regulation of these spatial parameters is important for controlling cell fate and cell function. While micropatterning has proved a powerful technique for understanding the impact of cell organization on cell behaviour, current methods for micropatterning cells require complex, specialized equipment that is not readily accessible in most biological and bioengineering laboratories. In addition, currently available methods require significant protocol optimization to ensure reliable and reproducible patterning. The inaccessibility of current methods has severely limited the widespread use of micropatterning as a tool in both biology and tissue engineering laboratories. Here we present a simple, cheap, and fast method to micropattern mammalian cells into stripes and circular patterns using Parafilm™, a common material found in most biology and bioengineering laboratories. Our method does not require any specialized equipment and does not require significant method optimization to ensure reproducible patterning. Although our method is limited to simple patterns, these geometries are sufficient for addressing a wide range of biological problems. Specifically, we demonstrate i) that using our Parafilm™ insert method we can pattern and co-pattern ARPE-19 and MDCK epithelial cells into circular and stripe micropatterns in tissue culture polystyrene (TCPS) wells and on glass slides, ii) that we can contain cells in the desired patterns for more than one month and iii) that upon removal of the Parafilm™ insert we can release the cells from the containment pattern and allow cell migration outward from the original pattern. We also demonstrate that we can exploit this confinement release feature to conduct an epithelial cell wound healing assay. This novel micropatterning method provides a reliable and accessible tool with the flexibility to address a wide range of biological and engineering problems that require control over the spatial and temporal organization of cells.

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Only accessible information is useful: insights from gradient-mediated patterning.

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Only accessible information is useful: insights from gradient-mediated patterning.

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