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BCIT Citations Collection

Shaped singular spectrum analysis for quantifying gene expression, with application to the early drosophila embryo
In recent years, with the development of automated microscopy technologies, the volume and complexity of image data on gene expression have increased tremendously. The only way to analyze quantitatively and comprehensively such biological data is by developing and applying new sophisticated mathematical approaches. Here, we present extensions of 2D singular spectrum analysis (2D-SSA) for application to 2D and 3D datasets of embryo images. These extensions, circular and shaped 2D-SSA, are applied to gene expression in the nuclear layer just under the surface of the Drosophila (fruit fly) embryo. We consider the commonly used cylindrical projection of the ellipsoidal Drosophila embryo. We demonstrate how circular and shaped versions of 2D-SSA help to decompose expression data into identifiable components (such as trend and noise), as well as separating signals from different genes. Detection and improvement of under- and overcorrection in multichannel imaging is addressed, as well as the extraction and analysis of 3D features in 3D gene expression patterns., Peer-reviewed article, Published. Received 4 July 2014; Revised 10 September 2014; Accepted 10 September 2014.
Spatial bistability generates hunchback expression sharpness in the drosophila embryo
During embryonic development, the positional information provided by concentration gradients of maternal factors directs pattern formation by providing spatially dependent cues for gene expression. In the fruit fly, Drosophila melanogaster, a classic example of this is the sharp on-off activation of the hunchback (hb) gene at midembryo, in response to local concentrations of the smooth anterior-posterior Bicoid (Bcd) gradient. The regulatory region for hb contains multiple binding sites for the Bcd protein as well as multiple binding sites for the Hb protein. Some previous studies have suggested that Bcd is sufficient for properly sharpened Hb expression, yet other evidence suggests a need for additional regulation. We experimentally quantified the dynamics of hb gene expression in flies that were wild-type, were mutant for hb self-regulation or Bcd binding, or contained an artificial promoter construct consisting of six Bcd and two Hb sites. In addition to these experiments, we developed a reaction-diffusion model of hb transcription, with Bcd cooperative binding and hb self-regulation, and used Zero Eigenvalue Analysis to look for multiple stationary states in the reaction network. Our model reproduces the hb developmental dynamics and correctly predicts the mutant patterns. Analysis of our model indicates that the Hb sharpness can be produced by spatial bistability, in which hb self-regulation produces two stable levels of expression. In the absence of self-regulation, the bistable behavior vanishes and Hb sharpness is disrupted. Bcd cooperative binding affects the position where bistability occurs but is not itself sufficient for a sharp Hb pattern. Our results show that the control of Hb sharpness and positioning, by hb self-regulation and Bcd cooperativity, respectively, are separate processes that can be altered independently. Our model, which matches the changes in Hb position and sharpness observed in different experiments, provides a theoretical framework for understanding the data and in particular indicates that spatial bistability can play a central role in threshold-dependent reading mechanisms of positional information., Peer-reviewed article, Published. Received October 16, 2007; Accepted August 13, 2008; Published September 26, 2008.
Stochastic dynamics of gene expression in developing fly embryos
Proceedings of 2017 International Conference on Noise and Fluctuations (ICNF), Vilnius, Lithuania on 20-23 June 2017. Segmentation of the developing insect body is preceded by cell-specific gene expression. In fruit flies (Drosophila), pair-rule genes are expressed in spatial stripes specifying segment fates. Transcription of the even-skipped (eve) pair-rule gene was recently shown to proceed in noisy bursts. Here, we develop a stochastic model of eve transcription from DNA to mRNA. This indicates that eve transcription proceeds at two rates, with a slow rate providing basal production and a fast rate allowing for high mRNA output. This two-rate transcription may afford more reliability in mRNA output, and therefore the protein levels which specify cell type, than a simple on-off (one-rate) mechanism., Conference paper, Published.