Image-Level and Group-Level Models for Drosophila Gene Expression Pattern Annotation

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison. Results: We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach. Conclusion: In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation

Exploring the Potential of Laser Capture Microdissection Technology in Integrated Oral BioSciences

Laser capture microdissection (LCM) is a high end research and diagnostic technology that helps in obtaining pure cell populations for the purpose of cell or lesion specific genomic and proteomic analysis. Literature search on the application of LCM in oral tissues was made through PUBMED. There is ample evidence to substantiate the utility of LCM in understanding the underlying molecular mechanism involving an array of oral physiological and pathological processes, including odontogenesis, taste perception, eruptive tooth movement, oral microbes, and cancers of the mouth and jaw tumors. This review is aimed at exploring the potential application of LCM in oral tissues as a high-throughput tool for integrated oral sciences. The indispensable application of LCM in the construction of lesion specific genomic libraries with emphasis on some of the novel molecular markers thus discovered is also highlighted. This article is protected by copyright. All rights reserved

Localization and Androgen Regulation of Metastasis-Associated Protein 1 in Mouse Epididymis

BACKGROUND: Metastasis-associated protein 1 (MTA1), the founding member of the MTA family of genes, can modulate transcription by influencing the status of chromatin remodeling. Despite its strong correlation with the metastatic potential of cancer cells, MTA1 can also regulate crucial cellular pathways by modifying the acetylation status. We have previously reported the presence of MTA1/MTA1 in human and mouse testes, providing the evidence for its involvement in the regulation of testicular function during murine spermatogenesis. The objective of present study was to further assess the localization of MTA1 in mouse epididymis on both transcriptional and translational level, and then to explore whether MTA1 expression is regulated by androgens and postnatal epididymal development. METHODOLOGY/PRINCIPAL FINDINGS: Mice were deprived of circulating androgen by bilaterally castration and were then supplemented with exogenous testosterone propionate for one week. MTA1 was immunolocalized in the epithelium of the entire epididymis with the maximal expression in the nuclei of principal cells and of clear cells in proximal region. Its expression decreased gradually after castration, whereas testosterone treatment could restore the expression, indicating that the expression of this gene is dependent on androgen. During postnatal development, the protein expression in the epididymis began to appear from day 7 to day 14, increased dramatically from postnatal day 28, and peaked at adulthood onwards, coinciding with both the well differentiated status of epididymis and the mature levels of circulating androgens. This region- and cell-specific pattern was also conservative in normal human epididymis. CONCLUSIONS: Our data suggest that the expression of MTA1 protein could be regulated by androgen pathway and its expression level is closely associated with the postnatal development of the epididymis, giving rise to the possibility that this gene plays a potential role in sperm maturation and fertility

Gene Knockout Study Reveals That Cytosolic Ascorbate Peroxidase 2(OsAPX2) Plays a Critical Role in Growth and Reproduction in Rice under Drought, Salt and Cold Stresses

<div><p>Plant ascorbate peroxidases (APXs), enzymes catalyzing the dismutation of H₂O₂ into H₂O and O₂, play an important role in reactive oxygen species homeostasis in plants. The rice genome has eight <i>OsAPXs</i>, but their physiological functions remain to be determined. In this report, we studied the function of <i>OsAPX2</i> gene using a T-DNA knockout mutant under the treatment of drought, salt and cold stresses. The <i>Osapx2</i> knockout mutant was isolated by a genetic screening of a rice T-DNA insertion library under 20% PEG-2000 treatment. Loss of function in <i>OsAPX2</i> affected the growth and development of rice seedlings, resulting in semi-dwarf seedlings, yellow-green leaves, leaf lesion mimic and seed sterility. <i>OsAPX2</i> expression was developmental- and spatial-regulated, and was induced by drought, salt, and cold stresses. <i>Osapx2</i> mutants had lower APX activity and were sensitive to abiotic stresses; overexpression of <i>OsAPX2</i> increased APX activity and enhanced stress tolerance. H₂O₂ and MDA levels were high in <i>Osapx2</i> mutants but low in <i>OsAPX2</i>-OX transgenic lines relative to wild-type plants after stress treatments. Taken together, the cytosolic ascorbate peroxidase OsAPX2 plays an important role in rice growth and development by protecting the seedlings from abiotic stresses through scavenging reactive oxygen species.</p> </div

H₂O₂ content assay of wild-type, <i>Osapx2</i>, complementation and <i>OsAPX2</i>-OX plants at different developmental stages.

<p>H₂O₂ content assay was performed in wild-type, <i>Osapx2</i>, independent complementation lines (cp1 and cp2) and independent <i>OsAPX2</i>-OX lines (OX1 and OX2) at different developmental stages. Different letters (a–c) indicate significant differences (<i>P</i><0.05) between lines.</p

The phenotype of the PEG-sensitive T-DNA insertional rice line.

<p>After two days germination, wild-type (WT) (A) and mutant lines (B) were treated with 20% PEG2000. WT and mutant lines were treated with mock (C and D) and 20% PEG2000 (E and F) respectively, for 48 h. Seedlings of treated WT (G) and mutant seedlings (H) were recovered for 4 days. Bar = 1 cm.</p

The expression of <i>OsAPX1</i> in <i>Osapx2</i>.

<p>The expression of <i>OsAPX1</i> was detected in leaves of wild-type and <i>Osapx2</i> mutant seedlings under normal condition and after stress treatments. Data represent means ± SD of three replicates.</p

<i>OsAPX2</i> expression response to drought, cold and salt stresses.

<p>A: <i>OsAPX2</i> expression response to salt stress. B,C: Time course of <i>OsAPX2</i> expression during drought and cold treatments. <i>Actin</i> was used as an internal control. Data represent means ± SD of three replicates.</p