No role for direct touch using the pectoral fins, as an information gathering strategy in a blind fish.

Blind Mexican cave fish (Astyanax fasciatus) lack a functional visual system and have been shown to sense their environment using a technique called hydrodynamic imaging, whereby nearby objects are detected by sensing distortions in the flow field of water around the body using the mechanosensory lateral line. This species has also been noted to touch obstacles, mainly with the pectoral fins, apparently using this tactile information alongside hydrodynamic imaging to sense their surroundings. This study aimed to determine the relative contributions of hydrodynamic and tactile information during wall following behaviour in blind Mexican cave fish. A wall was custom built with a 'netted' region in its centre, which provided very similar tactile information to a solid tank wall, but was undetectable using hydrodynamic imaging. The fish swam significantly closer to and collided more frequently with the netted region of this wall than the solid regions, indicating that the fish did not perceive the netted region as a solid obstacle despite being able to feel it as such with their pectoral fins. We conclude that the touching of objects with the pectoral fins may be an artefact of the intrinsic link between pectoral fin extensions and tail beating whilst swimming, and does not function to gather information. During wall following, hydrodynamic information appears to be used strongly in preference to tactile information in this non-visual system.

ChIPing away at global transcriptional regulation.

The regulation of gene expression impacts all aspects of cell biology and biochemistry. As we gain a greater understanding of the mechanisms involved in this process, we also begin to unveil its complexities. The delicate balancing act played out by the multitude of DNA interacting proteins can easily become unhinged. The implications of this may potentially lead to cell death or a diseased state. Recent microarray technologies are now allowing scientists to begin the journey into characterizing the relationship between gene expression and DNA modifying proteins. For example, genome-wide studies of protein-DNA interactions, such as Chromatin Immunoprecipitation on arrays (also referred to as ChIP-chip), allow for a global view of where and when DNA binding proteins interact. A number of microarray based genome wide methodologies have emerged based upon these same principles. Here, we outline a methodology that we have developed using the ChIP-chip technique. Application of this methodology is easily adaptable to different cell types, antibodies, and to a variety of array platforms.

Identification and characterization of a novel gene, dapr, involved in skeletal muscle differentiation and protein kinase B signaling.

The phosphatidylinositol 3-kinase (PI3K) signaling pathway has been associated with a variety of cellular functions ranging from cell cycle regulation to tissue development. Although years of research have extensively characterized this signaling pathway, little is known as to how specific cellular events are coordinated by its activation. Here we demonstrate that Dapr (differentiation-associated protein), a novel protein, appears to focus one aspect of this pathway by acting as a putative scaffold protein during skeletal muscle differentiation. We present for the first time a description of this protein using in silico analysis. dapr was discovered through a previous study employing chromatin immunoprecipitation and CpG microarray analysis experiments as being regulated by myocyte-enhancing factor 2, a key transcription factor involved in the differentiation of skeletal muscle tissue. In this study we show that during the course of differentiation, Dapr binds to the PI3K signaling pathway member protein kinase B (PKB). In C2C12 myoblast cells before differentiation Dapr is localized to the cytosol, migrating with PKB to the membrane after initiation of muscle differentiation. Knockdown of Dapr by RNAi resulted in inhibition of myotube formation. Our findings indicate that Dapr is a key component required by myoblasts for orchestrating their differentiation during myogenesis. Furthermore, it appears that Dapr is involved in the PI3K signaling cascade, potentially acting as a scaffold protein for PKB and coordinating its compartmentalization during differentiation.

Identification of MEF2-regulated genes during muscle differentiation.

Although a great deal has been elucidated concerning the mechanisms regulating muscle differentiation, little is known about transcription factor-specific gene regulation. Our understanding of the genetic mechanisms regulating cell differentiation is quite limited. Much of what has been defined centers on regulatory signaling cascades and transcription factors. Surprisingly few studies have investigated the association of genes with specific transcription factors. To address these issues, we have utilized a method coupling chromatin immunoprecipitation and CpG microarrays to characterize the genes associated with MEF2 in differentiating C(2)C(12) cells. Results demonstrated a defined binding pattern over the course of differentiation. Filtered data demonstrated 9 clones to be elevated at 0 h, 792 at 6 h, 163 by 1 day, and 316 at 3 days. Using unbiased selection parameters, we selected a subset of 291 prospective candidates. Clones were sequenced and filtered for removal of redundancy between clones and for the presence of repetitive elements. We were able to place 50 of these on the mouse genome, and 20 were found to be located near well-annotated genes. From this list, previously undefined associations with MEF2 were discovered. Many of these genes represent proteins involved in neurogenesis, neuromuscular junctions, signaling and metabolism. The remaining clones include many full-length cDNA and represent novel gene targets. The results of this study provides for the first time, a unique look at gene regulation at the level of transcription factor binding in differentiating muscle.