Methods for acquisition of quantitative data from confocal images of gene expression in situ

Surkova, Svetlana; Myasnikova, Ekaterina; Kozlov, Konstantin; Samsonova, A. A.; Reinitz, John; Samsonova, Maria

doi:10.1134/s1990519x08020156

Cited by 12 publications

(10 citation statements)

References 29 publications

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“…The quantitative gene expression data and integrated patterns for each temporal class of cycle 14A were obtained as previously described [33], [69], [71], [72] using recently developed packages ProStack and BREReA [73], [74]. The one-dimensional integrated patterns of gene expression in wild type were taken from FlyEx database (http://urchin.spbcas.ru/flyex/, [75]).…”

Section: Methodsmentioning

confidence: 99%

Modeling of Gap Gene Expression in Drosophila Kruppel Mutants

et al. 2012

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The segmentation gene network in Drosophila embryo solves the fundamental problem of embryonic patterning: how to establish a periodic pattern of gene expression, which determines both the positions and the identities of body segments. The gap gene network constitutes the first zygotic regulatory tier in this process. Here we have applied the systems-level approach to investigate the regulatory effect of gap gene Kruppel (Kr) on segmentation gene expression. We acquired a large dataset on the expression of gap genes in Kr null mutants and demonstrated that the expression levels of these genes are significantly reduced in the second half of cycle 14A. To explain this novel biological result we applied the gene circuit method which extracts regulatory information from spatial gene expression data. Previous attempts to use this formalism to correctly and quantitatively reproduce gap gene expression in mutants for a trunk gap gene failed, therefore here we constructed a revised model and showed that it correctly reproduces the expression patterns of gap genes in Kr null mutants. We found that the remarkable alteration of gap gene expression patterns in Kr mutants can be explained by the dynamic decrease of activating effect of Cad on a target gene and exclusion of Kr gene from the complex network of gap gene interactions, that makes it possible for other interactions, in particular, between hb and gt, to come into effect. The successful modeling of the quantitative aspects of gap gene expression in mutant for the trunk gap gene Kr is a significant achievement of this work. This result also clearly indicates that the oversimplified representation of transcriptional regulation in the previous models is one of the reasons for unsuccessful attempts of mutant simulations.

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Section: Methodsmentioning

confidence: 99%

Modeling of Gap Gene Expression in Drosophila Kruppel Mutants

et al. 2012

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“…Not only in developmental studies but also in all fields of genetic studies, signal extraction and noise reduction are regarded as important tasks since genetic data are often characterized by the existence of considerable noise. Many methods are utilized for signal extraction, such as machine learning algorithms [15,16] and different background removal techniques [17–19] . In this paper we evaluate the use of powerful and popular signal processing techniques which include both parametric and nonparametric methods to provide a sound extraction of Bcd signal.…”

Section: Introductionmentioning

confidence: 99%

Bicoid Signal Extraction with a Selection of Parametric and Nonparametric Signal Processing Techniques

Ghodsi

Silva

Hassani

2015

Genomics, Proteomics &Amp; Bioinformatics

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The maternal segmentation coordinate gene bicoid plays a significant role during Drosophila embryogenesis. The gradient of Bicoid, the protein encoded by this gene, determines most aspects of head and thorax development. This paper seeks to explore the applicability of a variety of signal processing techniques at extracting bicoid expression signal, and whether these methods can outperform the current model. We evaluate the use of six different powerful and widely-used models representing both parametric and nonparametric signal processing techniques to determine the most efficient method for signal extraction in bicoid. The results are evaluated using both real and simulated data. Our findings show that the Singular Spectrum Analysis technique proposed in this paper outperforms the synthesis diffusion degradation model for filtering the noisy protein profile of bicoid whilst the exponential smoothing technique was found to be the next best alternative followed by the autoregressive integrated moving average.

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“…The volume measurement process was automated using an image processing algorithm to prevent human bias and to achieve better accuracy. A peak detection method was employed on the histogram of these images to segment the tumor signal from the background [ 35 , 36 ]. After obtaining a binary z-stack image which represents the tumor voxels, the volume of liver tumor was calculated from the voxels count.…”

Section: Resultsmentioning

confidence: 99%

Visualizing Photodynamic Therapy in Transgenic Zebrafish Using Organic Nanoparticles with Aggregation-Induced Emission

Manghnani

et al. 2018

Nano-Micro Lett.

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Photodynamic therapy (PDT) employs accumulation of photosensitizers (PSs) in malignant tumor tissue followed by the light-induced generation of cytotoxic reactive oxygen species to kill the tumor cells. The success of PDT depends on optimal PS dosage that is matched with the ideal power of light. This in turn depends on PS accumulation in target tissue and light administration time and period. As theranostic nanomedicine is driven by multifunctional therapeutics that aim to achieve targeted tissue delivery and image-guided therapy, fluorescent PS nanoparticle (NP) accumulation in target tissues can be ascertained through fluorescence imaging to optimize the light dose and administration parameters. In this regard, zebrafish larvae provide a unique transparent in vivo platform to monitor fluorescent PS bio-distribution and their therapeutic efficiency. Using fluorescent PS NPs with unique aggregation-induced emission characteristics, we demonstrate for the first time the real-time visualization of polymeric NP accumulation in tumor tissue and, more importantly, the best time to conduct PDT using transgenic zebrafish larvae with inducible liver hyperplasia as an example.Electronic supplementary materialThe online version of this article (10.1007/s40820-018-0214-4) contains supplementary material, which is available to authorized users.

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Methods for acquisition of quantitative data from confocal images of gene expression in situ

Cited by 12 publications

References 29 publications

Modeling of Gap Gene Expression in Drosophila Kruppel Mutants

Modeling of Gap Gene Expression in Drosophila Kruppel Mutants

Bicoid Signal Extraction with a Selection of Parametric and Nonparametric Signal Processing Techniques

Visualizing Photodynamic Therapy in Transgenic Zebrafish Using Organic Nanoparticles with Aggregation-Induced Emission

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