Toward Automatic Annotation of in situ mRNA Expression Patterns of Drosophila Embryos

2006 ◽  
Author(s):  
Jie Zhou ◽  
Hanchuan Peng
Keyword(s):  
Mrna Expression ◽  
Expression Patterns ◽  
Automatic Annotation ◽  
Drosophila Embryos

mRNA expression patterns of the IGF system during mouse limb bud development, determined by whole mount in situ hybridization

1998 ◽  
Vol 138 (1-2) ◽  
pp. 151-161 ◽  
Author(s):  
Marjolein van Kleffens ◽  
Cora Groffen ◽  
Roberto R. Rosato ◽  
Stefan M. van den Eijnde ◽  
Johan W. van Neck ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Mrna Expression ◽  
Expression Patterns ◽  
Limb Bud ◽  
Bud Development ◽  
Igf System ◽  
Whole Mount ◽  
Mouse Limb

scholarly journals In Situ Studyof Abundant Expression of Proinflammatory Chemokines and Cytokines inPulmonary Granulomas That Develop in Cynomolgus MacaquesExperimentally Infected with Mycobacteriumtuberculosis

2003 ◽  
Vol 71 (12) ◽  
pp. 7023-7034 ◽  
Author(s):  
Craig L. Fuller ◽  
JoAnne L. Flynn ◽  
Todd A. Reinhart
Keyword(s):  
16S Rrna ◽  
Mrna Expression ◽  
Expression Patterns ◽  
Public Health Problem ◽  
Granuloma Formation ◽  
Major Public Health Problem ◽  
Cytokine Mrna ◽  
Granulomatous Lesions ◽  
Ifn Γ

ABSTRACT Tuberculosis remains a major public health problem worldwide. Chemokines and cytokines organize and direct infiltrating cells to sites of infection, and these molecules likely play crucial roles in granuloma formation and maintenance. To address this issue, we used in situ hybridization (ISH) to measure chemokine and cytokine mRNA expression levels and patterns directly in lung tissues from cynomolgus macaques (Macaca fascicularis) experimentally infected with a low dose of virulent Mycobacterium tuberculosis. We examined more than 300 granulomas and observed abundant expression of gamma interferon (IFN-γ)-inducible chemokine mRNAs (CXCL9/monokine induced by IFN-γ, CXCL10/IFN-γ-inducible protein, and CXCL11/IFN-γ-inducible T-cell α-chemoattractant) within solid and caseous granulomas, and there was only minimal expression in nongranulomatous regions of tissue. The mRNA expression patterns of IFN-γ and tumor necrosis factor alpha were examined in parallel, and the results revealed that cytokine mRNA+ cells were abundant and generally localized to the granulomas. Mycobacterial 16S rRNA expression was also measured by ISH, and the results revealed that there was localization predominantly to the granulomas and that the highest signal intensity was in caseous granulomas. We observed several granulomatous lesions with exceptionally high levels of RNA for mycobacterial 16S rRNA, IFN-γ, and IFN-γ-inducible chemokines, suggesting that the local presence of mycobacteria is partially responsible for the upregulation of IFN-γ-inducible chemokines and recruitment of CXCR3+ cells, which were also abundant in granulomatous lesions. These results suggest that expression of CXCR3 ligands and the subsequent recruitment of CXCR3+ cells are involved in granuloma formation and maintenance.

scholarly journals From simplicity to complexity: The gain or loss of spot rows underlies the morphological diversity of three Drosophila species

2020 ◽  
Author(s):  
William A. Dion ◽  
Mujeeb O. Shittu ◽  
Tessa E. Steenwinkel ◽  
Komal K. B. Raja ◽  
Prajakta P. Kokate ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Expression Patterns ◽  
Morphological Diversity ◽  
Fruit Flies ◽  
Drosophila Species ◽  
Dopa Decarboxylase ◽  
Color Patterns ◽  
Evolutionary Time ◽  
Pupal Development

AbstractTo understand how novel animal patterning emerged, one needs to ask how the development of color patterns has changed among diverging species. Here we examine three species of fruit flies – Drosophila guttifera (D. guttifera), Drosophila palustris (D. palustris), and Drosophila subpalustris (D. subpalustris) – displaying a varying number of abdominal spot rows that were either gained or lost throughout evolutionary time. Through in situ hybridization, we examine the mRNA expression patterns for the pigmentation genes Dopa decarboxylase (Ddc), tan (t), and yellow (y) during pupal development. Our results show that Ddc, t, and y are co-expressed in identical patterns, each foreshadowing the adult abdominal spots in D. guttifera, D. palustris, and D. subpalustris.

scholarly journals RNAScope in situ Hybridization as a Novel Technique for the Assessment of c-KIT mRNA Expression in Canine Mast Cell Tumor

2021 ◽  
Vol 8 ◽  
Author(s):  
Davide De Biase ◽  
Francesco Prisco ◽  
Giuseppe Piegari ◽  
Arianna Ilsami ◽  
Ilaria d'Aquino ◽  
...  
Keyword(s):  
Mast Cell ◽  
Mrna Expression ◽  
Messenger Rna ◽  
Histological Grade ◽  
Expression Patterns ◽  
Cell Tumor ◽  
Specific Method ◽  
Mast Cell Tumor ◽  
Canine Mast Cell Tumor

RNA is considered as an indicator of the dynamic genetic expression changes in a cell. RNAScope is a commercially available in situ hybridization assay for the detection of RNA in formalin-fixed paraffin-embedded tissue. In this work, we describe the use of RNAScope as a sensitive and specific method for the evaluation of c-KIT messenger RNA (mRNA) in canine mast cell tumor. We investigated the expression of c-KIT mRNA with RNAscope in 60 canine mast cell tumors (MCTs), comparing it with the histological grade and KIT immunohistochemical expression patterns. Our results showed an overall good expression of c-KIT mRNA in neoplastic cells if compared with control probes. We also observed a statistically significant correlation between histological grade and c-KIT mRNA expression. No correlations were found between KIT protein immunohistochemical distribution pattern and c-KIT mRNA expression or histological grade. Our results provide a reference basis to better understand c-KIT mRNA expression in canine MCTs and strongly encourage further studies that may provide useful information about its potential and significant role as a prognostic and predictive biological marker for canine MCTs clinical outcome.

Detection and mapping of interactions between chromatin and the nuclear envelope in drosophila embryos

1995 ◽  
Vol 53 ◽  
pp. 764-765
Author(s):  
W.F. Marshall ◽  
A.F. Dernburg ◽  
B. Harmon ◽  
J.W. Sedat
Keyword(s):  
Nuclear Envelope ◽  
Chromatin Condensation ◽  
Three Dimensional ◽  
Physiological Role ◽  
Nuclear Surface ◽  
Intact Cells ◽  
Molecular Determinants ◽  
Surface Harmonic ◽  
Drosophila Embryos

Interactions between chromatin and nuclear envelope (NE) have been implicated in chromatin condensation, gene regulation, nuclear reassembly, and organization of chromosomes within the nucleus. To further investigate the physiological role played by such interactions, it will be necessary to determine which loci specifically interact with the nuclear envelope. This will not only facilitate identification of the molecular determinants of this interaction, but will also allow manipulation of the pattern of chromatin-NE interactions to probe possible functions. We have developed a microscopic approach to detect and map chromatin-NE interactions inside intact cells.Fluorescence in situ hybridization (FISH) is used to localize specific chromosomal regions within the nucleus of Drosophila embryos and anti-lamin immunofluorescence is used to detect the nuclear envelope. Widefield deconvolution microscopy is then used to obtain a three-dimensional image of the sample (Fig. 1). The nuclear surface is represented by a surface-harmonic expansion (Fig 2). A statistical test for association of the FISH spot with the surface is then performed.

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