A microfluidic array for large-scale ordering and orientation of embryos

Chung, Kwanghun; Kim, Yoosik; Kanodia, Jitendra; Gong, Emily; Shvartsman, Stanislav Y.; Lu, Hang

doi:10.1038/nmeth.1548

Cited by 141 publications

(148 citation statements)

References 30 publications

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“…For upright imaging, a Nikon 60× Plan-Apo oil objective was used, and images were collected at the focal plane ∼90 μm from the anterior or posterior pole of an embryo. End-on imaging was performed by using the microfluidics device described previously (57). Spatial patterns of Dl, dpERK, and Cic proteins, and of ind and lacZ mRNAs, were automatically extracted from raw confocal images as described elsewhere (58).…”

Section: δC40bmentioning

confidence: 99%

Kinetics of gene derepression by ERK signaling

Lim

Samper

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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ERK controls gene expression in development, but mechanisms that link ERK activation to changes in transcription are not well understood. We used high-resolution analysis of signaling dynamics to study transcriptional interpretation of ERK signaling during Drosophila embryogenesis, at a stage when ERK induces transcription of intermediate neuroblasts defective (ind), a gene essential for patterning of the nerve cord. ERK induces ind by antagonizing its repression by Capicua (Cic), a transcription factor that acts as a sensor of receptor tyrosine kinases in animal development and human diseases. A recent study established that active ERK reduces the nuclear levels of Cic, but it remained unclear whether this is required for the induction of Cic target genes. We provide evidence that Cic binding sites within the regulatory DNA of ind control the spatial extent and the timing of ind expression. At the same time, we demonstrate that ERK induces ind before Cic levels in the nucleus are reduced. Based on this, we propose that ERK-dependent relief of gene repression by Cic is a two-step process, in which fast reduction of repressor activity is followed by slower changes in nuclear localization and overall protein levels. This may be a common feature of systems in which ERK induces genes by relief of transcriptional repression.pattern formation | signal transduction | systems biology

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Section: δC40bmentioning

confidence: 99%

Kinetics of gene derepression by ERK signaling

Lim

Samper

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…The high-throughput automated platform positions the embryos vertically along their dorsoventral axis. This enables an efficient quantitative analysis of the patterns formed on the dorsoventral region, which serve as indicators of embryo morphogenesis 21 . During plant reproductive development, pollen tubes encounter chemical guidance signals from the ovules which allow the sperm cells to reach the egg cells and achieve fertilization.…”

Section: Developmental Biologymentioning

confidence: 99%

Microfluidics:A Boon for Biological Research

Mahesh

Vaidya²

2017

Current Science

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Microfluidics is an emerging new interdisciplinary field that deals with the manipulation of fluids at the microscale and nanoscale. Having its origins in other areas of science and technology, microfluidics is slowly beginning to make radical changes in various fields of biological sciences. The exclusivity of fluid behaviour at the microscale offers a large number of advantages in biological research such as miniaturization of assays, faster sample processing and rapid detection. This article provides a concise overview of the applications of microfluidics technology in some of the major disciplines of biological research. Furthermore, it also mentions the hurdles that microfluidics is facing and the solutions that are envisaged for the future to make it a widely available, reliable and costeffective technology.

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“…Embryos were collected, stained, and imaged together under the same microscope settings. End-on imaging was performed using the microfluidics device described previously (Chung et al, 2011). Images were collected at the focal plane ∼90 μm from the posterior pole of the embryo (see supplementary material Fig.…”

Section: Drosophila Embryo Microscopymentioning

confidence: 99%

Temporal ordering and registration of images in studies of developmental dynamics

Dsilva

Lim

et al. 2015

Development

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Progress of development is commonly reconstructed from imaging snapshots of chemical or mechanical processes in fixed tissues. As a first step in these reconstructions, snapshots must be spatially registered and ordered in time. Currently, image registration and ordering are often done manually, requiring a significant amount of expertise with a specific system. However, as the sizes of imaging data sets grow, these tasks become increasingly difficult, especially when the images are noisy and the developmental changes being examined are subtle. To address these challenges, we present an automated approach to simultaneously register and temporally order imaging data sets. The approach is based on vector diffusion maps, a manifold learning technique that does not require a priori knowledge of image features or a parametric model of the developmental dynamics. We illustrate this approach by registering and ordering data from imaging studies of pattern formation and morphogenesis in three model systems. We also provide software to aid in the application of our methodology to other experimental data sets.

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A microfluidic array for large-scale ordering and orientation of embryos

Cited by 141 publications

References 30 publications

Kinetics of gene derepression by ERK signaling

Kinetics of gene derepression by ERK signaling

Microfluidics:A Boon for Biological Research

Temporal ordering and registration of images in studies of developmental dynamics

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