0000000000143230
AUTHOR
Jie Shen
showing 10 related works from this author
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction
2015
Background Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. Results We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being …
Postnatal Deletion of Numb/Numblike Reveals Repair and Remodeling Capacity in the Subventricular Neurogenic Niche
2006
Neural stem cells are retained in the postnatal subventricular zone (SVZ), a specialized neurogenic niche with unique cytoarchitecture and cell-cell contacts. Although the SVZ stem cells continuously regenerate, how they and the niche respond to local changes is unclear. Here we generated nestin-creERtm transgenic mice with inducible Cre recombinase in the SVZ, and removed Numb/Numblike, key regulators of embryonic neurogenesis from postnatal SVZ progenitors and ependymal cells. This resulted in severe damage to brain lateral ventricle integrity, and identified previously unknown roles for Numb/Numblike in regulating ependymal wall integrity and SVZ neuroblast survival. Surprisingly, the ve…
Fluorescent Core/Shell Nanoparticles for Specific Cell‐Nucleus Staining
2008
The highly fluorescent perylene-3,4,9,10-tetracarboxdiimide (PDI) chromophore is a popular dye and pigment because of its excellent chemical, thermal, and photochemical stability. Due to these outstanding properties, there have been several successful applications of PDI chromophores in various fields. Water-soluble and fluorescent PDI dyes have been used in biological applications such as the in vitro staining of cells and proteins. The combination of water solubility and high fluorescence quantum yield still represents a challenging goal since PDI dyes have a strong tendency to form aggregates in aqueous solution even at very low concentrations. Water solubility and high fluorescence quan…
Fold formation at the compartment boundary of Drosophila wing requires Yki signaling to suppress JNK dependent apoptosis
2016
AbstractCompartment boundaries prevent cell populations of different lineage from intermingling. In many cases, compartment boundaries are associated with morphological folds. However, in the Drosophila wing imaginal disc, fold formation at the anterior/posterior (A/P) compartment boundary is suppressed, probably as a prerequisite for the formation of a flat wing surface. Fold suppression depends on optomotor-blind (omb). Omb mutant animals develop a deep apical fold at the A/P boundary of the larval wing disc and an A/P cleft in the adult wing. A/P fold formation is controlled by different signaling pathways. Jun N-terminal kinase (JNK) and Yorkie (Yki) signaling are activated in cells alo…
Optomotor-blind negatively regulates Drosophila eye development by blocking Jak/STAT signaling
2015
Organ formation requires a delicate balance of positive and negative regulators. In Drosophila eye development, wingless (wg) is expressed at the lateral margins of the eye disc and serves to block retinal development. The T-box gene optomotor-blind (omb) is expressed in a similar pattern and is regulated by Wg. Omb mediates part of Wg activity in blocking eye development. Omb exerts its function primarily by blocking cell proliferation. These effects occur predominantly in the ventral margin. Our results suggest that the primary effect of Omb is the blocking of Jak/STAT signaling by repressing transcription of upd which encodes the Jak receptor ligand Unpaired.
T-Box Genes in Drosophila Limb Development
2017
T-box genes are essential for limb development in vertebrates and arthropods. The Drosophila genome encodes eight T-box genes, six of which are expressed in limb ontogenesis. The Tbx20-related gene pair midline and H15 is essential for dorso-ventral patterning of the Drosophila legs. The three Tbx6-related Dorsocross genes are required for epithelial remodeling during wing development. The Drosophila gene optomotor-blind (omb) is the only member of the Tbx2 subfamily in the fly and is predominantly involved in wing development. Omb is essential for wing development and is sufficient to promote the development of a second wing pair. Targeted manipulations of omb expression have shown that th…
Dpp signaling inhibits proliferation in the Drosophila wing by Omb-dependent regional control of bantam
2013
The control of organ growth is a fundamental aspect of animal development but remains poorly understood. The morphogen Dpp has long been considered as a general promoter of cell proliferation during Drosophila wing development. It is an ongoing debate whether the Dpp gradient is required for the uniform cell proliferation observed in the wing imaginal disc. Here, we investigated how the Dpp signaling pathway regulates proliferation during wing development. By systematic manipulation of Dpp signaling we observed that it controls proliferation in a region-specific manner: Dpp, via omb, promoted proliferation in the lateral and repressed proliferation in the medial wing disc. Omb controlled th…
Spatial discontinuity of Optomotor-blind expression in the Drosophila wing imaginal disc disrupts epithelial architecture and promotes cell sorting
2010
Abstract Background Decapentaplegic (Dpp) is one of the best characterized morphogens, required for dorso-ventral patterning of the Drosophila embryo and for anterior-posterior (A/P) patterning of the wing imaginal disc. In the larval wing pouch, the Dpp target gene optomotor-blind (omb) is generally assumed to be expressed in a step function above a certain threshold of Dpp signaling activity. Results We show that the transcription factor Omb forms, in fact, a symmetrical gradient on both sides of the A/P compartment boundary. Disruptions of the Omb gradient lead to a re-organization of the epithelial cytoskeleton and to a retraction of cells toward the basal membrane suggesting that the O…
optomotor-blind suppresses instability at the A/P compartment boundary of the Drosophila wing.
2008
Formation and function of the A/P compartment boundary of the Drosophila wing have been studied intensely. The boundary prevents mingling of A and P cells, is characterized by an expression discontinuity of several genes like engrailed, Cubitus interruptus, hedgehog and decapentaplegic and is essential for patterning the wing. Compared with segmental or compartmental boundaries in several other systems which generally manifest as folds or clefts, the wing A/P boundary is morphologically inconspicuous in both the larval and adult stage. We show here that the Drosophila wing A/P boundary, too, is susceptible to fold and cleft formation and that these processes are suppressed by the T-box tran…
The Dorsocross T-box transcription factors promote tissue morphogenesis in the Drosophila wing imaginal disc.
2012
The Drosophila wing imaginal disc is subdivided into notum, hinge and blade territories during the third larval instar by formation of several deep apical folds. The molecular mechanisms of these subdivisions and the subsequent initiation of morphogenic processes during metamorphosis are poorly understood. Here, we demonstrate that the Dorsocross (Doc) T-box genes promote the progression of epithelial folds that not only separate the hinge and blade regions of the wing disc but also contribute to metamorphic development by changing cell shapes and bending the wing disc. We found that Doc expression was restricted by two inhibitors, Vestigial and Homothorax, leading to two narrow Doc stripes…