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- Creators: Barton, C. Michael
- Member of: Programs and Communities
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.
Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.
Results
We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/.
Conclusions
Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.
PowerPoint presentation to the Santa Fe Institute, October 2004.
Dramatic changes in land use were associated with the rise of agriculture in the mid Holocene in the Mediterranean region. Both surface properties and drainage networks were changed along with direct modifications to surface properties (vegetation removal and change, sediment liberation and compaction); consequent drainage alteration (terracing, canals) and up and downstream responses in the watersheds communicated these changes throughout the landscape.
The magnitude, rate, and feedbacks with the growing human populations are critical questions in our effort to assess human-landscape interactions. To investigate these relationships, recent field work in the Penaguila Valley of southeast Spain included landform mapping, alluvial deposit description, and sample collection emphasizing areas of active erosion, remnant land surfaces and their relation to archaeological sites.
We have updated our geomorphic maps by refining the delineation of alluvial terraces, steep-walled (40m deep) drainages ("barrancos"), and hollows ("barrancos de fondo plano"). Hollows are curved, elongate, flat-bottomed gullies with steep walls (2-30m tall) and extend headward from the main barrancos. This work enables more accurate terrace correlations necessary for both landscape evolution modeling and interpretation of the development history of the basin.
Alluvial terraces are crucial to this research because they record periods of past stable topography. In the Penaguila, sites dating back to late Mesolithic and early Neolithic (around 6600 BP) and subsequent periods (Chalcolithic and Bronze Age) are exposed on a prominent terrace surface mapped as Terrace A. This broad low relief surface is scarred by deep barrancos and hollow formation that expose bedrock marls and overlying alluvial deposits. Stratigraphic profiles and texture analyses of Terrace A deposits reveal overland flow facies and channel networks in reworked and CaCO3-encrusted marls, and several organic-rich paleosols. Small remnant surfaces mapped as Terrace Z (below Terrace A) were observed within the main barrancos and indicate a later, brief accumulation period with subsequent incision to the modern channel.
Holocene landscape development in the Penaguila appears to have progressed from a period of stability to slope denudation with aggradation (stream infilling) followed by rapid incision which initiated sometime near the time of occupation. This change from a low relief alluvial surface to one cut by narrow channels may have been an important shift for local populations. Their response to that environmental modification may be associated with the horticulturalist to agricultural intensification noted in the archaeological record. Tighter chronology and better understanding of the driving processes for barranco incision and hollow formation will improve our ability to correlate the changing landscape with land use practices. Such an improved correlation leads to better understanding of human-landscape interactions.
Microsoft PowerPoint presentation about data management and access issues for the research project, "Land-Use and Landscape Socioecology in the Mediterranean Basin."
