Published in Methods
Planar cell polarity (PCP) is the polarity of epithelial cells in the plane orthogonal to the apical-basal axis, and is controlled by a partially defined signaling system (McNeill, 2010; Singh and Mlodzik, 2012). PCP related signaling also plays roles in cell migration, tissue re-organization and stem cell differentiation during embryonic developme...
Published in Methods
modENCODE was a 5year NHGRI funded project (2007–2012) to map the function of every base in the genomes of worms and flies characterizing positions of modified histones and other chromatin marks, origins of DNA replication, RNA transcripts and the transcription factor binding sites that control gene expression. Here we describe the Drosophila modEN...
Published in Methods
The TGF-beta pathway is an evolutionarily conserved signal transduction module that mediates diverse biological processes in animals. In Drosophila, both the BMP and Activin branches are required for viability. Studies rooted in classical and molecular genetic approaches continue to uncover new developmental roles for TGF-beta signaling. We present...
Published in Methods
The Mitogen-Activated Protein Kinase (MAPK) pathway represents one of the most conserved signaling cascades in multicellular organisms, since its cytoplasmic components can also be found in single-celled eukaryotic organisms such as yeast. With this broad view in mind, we can ask ourselves not only what are the seminal features and functions of the...
Published in Methods
We review the properties and uses of cell lines in Drosophila research, emphasizing the variety of lines, the large body of genomic and transcriptional data available for many of the lines, and the variety of ways the lines have been used to provide tools for and insights into the developmental, molecular, and cell biology of Drosophila and mammals...
Published in Methods
The gastrointestinal (GI) tract harbors an essential barrier epithelium that separates an organism from its changing external environment. As such, the gut epithelium is a fascinating nexus of stem cell biology, tissue homeostasis, physiology and immunology. Investigators have sought to mine this rich interface for new biological and mechanistic in...
Published in Methods
The development and molecular composition of muscle tissue is evolutionarily conserved. Drosophila is a powerful in vivo model system to investigate muscle morphogenesis and function. Here, we provide a short and comprehensive overview of the important developmental steps to build Drosophila body muscle in embryos, larvae and pupae. We describe key...
Published in Methods
In situ hybridization is an important technique for measuring the spatial expression patterns of mRNA in cells, tissues, and whole animals. However, mRNA levels cannot be compared across experiments using typical protocols. Here we present a semi-quantitative method to compare mRNA levels of a gene across multiple samples. This method yields an est...
Published in Methods
Circadian rhythms have a profound influence on most bodily functions: from metabolism to complex behaviors. They ensure that all these biological processes are optimized with the time-of-day. They are generated by endogenous molecular oscillators that have a period that closely, but not exactly, matches day length. These molecular clocks are synchr...
Published in BMC Systems Biology
BackgroundIn computational biology, a novel knowledge has been obtained mostly by identifying 'intra-relation,' the relation between entities on a specific biological level such as from gene expression or from microRNA (miRNA) and many such researches have been successful. However, intra-relations are not fully explaining complex cancer mechanisms ...
