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Find video protocols related to scientific articles indexed in Pubmed.
Comparative gene expression analysis of Dtg, a novel target gene of Dpp signaling pathway in the early Drosophila melanogaster embryo.
Gene
PUBLISHED: 07-19-2013
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In the early Drosophila melanogaster embryo, Dpp, a secreted molecule that belongs to the TGF-? superfamily of growth factors, activates a set of downstream genes to subdivide the dorsal region into amnioserosa and dorsal epidermis. Here, we examined the expression pattern and transcriptional regulation of Dtg, a new target gene of Dpp signaling pathway that is required for proper amnioserosa differentiation. We showed that the expression of Dtg was controlled by Dpp and characterized a 524-bp enhancer that mediated expression in the dorsal midline, as well as, in the differentiated amnioserosa in transgenic reporter embryos. This enhancer contained a highly conserved region of 48-bp in which bioinformatic predictions and in vitro assays identified three Mad binding motifs. Mutational analysis revealed that these three motifs were necessary for proper expression of a reporter gene in transgenic embryos, suggesting that short and highly conserved genomic sequences may be indicative of functional regulatory regions in D. melanogaster genes. Dtg orthologs were not detected in basal lineages of Dipterans, which unlike D. melanogaster develop two extra-embryonic membranes, amnion and serosa, nevertheless Dtg orthologs were identified in the transcriptome of Musca domestica, in which dorsal ectoderm patterning leads to the formation of a single extra-embryonic membrane. These results suggest that Dtg was recruited as a new component of the network that controls dorsal ectoderm patterning in the lineage leading to higher Cyclorrhaphan flies, such as D. melanogaster and M. domestica.
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Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators.
Biometals
PUBLISHED: 02-24-2011
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Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophilic bacterium that obtains its energy from the oxidation of ferrous iron, elemental sulfur, or reduced sulfur minerals. This capability makes it of great industrial importance due to its applications in biomining. During the industrial processes, A. ferrooxidans survives to stressing circumstances in its environment, such as an extremely acidic pH and high concentration of transition metals. In order to gain insight into the organization of A. ferrooxidans regulatory networks and to provide a framework for further studies in bacterial growth under extreme conditions, we applied a genome-wide annotation procedure to identify 87 A. ferrooxidans transcription factors. We classified them into 19 families that were conserved among diverse prokaryotic phyla. Our annotation procedure revealed that A. ferrooxidans genome contains several members of the ArsR and MerR families, which are involved in metal resistance and detoxification. Analysis of their sequences revealed known and potentially new mechanism to coordinate gene-expression in response to metal availability. A. ferrooxidans inhabit some of the most metal-rich environments known, thus transcription factors identified here seem to be good candidates for functional studies in order to determine their physiological roles and to place them into A. ferrooxidans transcriptional regulatory networks.
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Genome-wide identification of new Wnt/beta-catenin target genes in the human genome using CART method.
BMC Genomics
PUBLISHED: 06-01-2010
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The importance of in silico predictions for understanding cellular processes is now widely accepted, and a variety of algorithms useful for studying different biological features have been designed. In particular, the prediction of cis regulatory modules in non-coding human genome regions represents a major challenge for understanding gene regulation in several diseases. Recently, studies of the Wnt signaling pathway revealed a connection with neurodegenerative diseases such as Alzheimers. In this article, we construct a classification tool that uses the transcription factor binding site motifs composition of some gene promoters to identify new Wnt/beta-catenin pathway target genes potentially involved in brain diseases.
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Genes encoding novel secreted and transmembrane proteins are temporally and spatially regulated during Drosophila melanogaster embryogenesis.
BMC Biol.
PUBLISHED: 07-15-2009
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Morphogenetic events that shape the Drosophila melanogaster embryo are tightly controlled by a genetic program in which specific sets of genes are up-regulated. We used a suppressive subtractive hybridization procedure to identify a group of developmentally regulated genes during early stages of D. melanogaster embryogenesis. We studied the spatiotemporal activity of these genes in five different intervals covering 12 stages of embryogenesis.
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Overexpression of amyloid precursor protein increases copper content in HEK293 cells.
Biochem. Biophys. Res. Commun.
PUBLISHED: 03-06-2009
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Amyloid precursor protein (APP) is a transmembrane glycoprotein widely expressed in mammalian tissues and plays a central role in Alzheimers disease. However, its physiological function remains elusive. Cu(2+) binding and reduction activities have been described in the extracellular APP135-156 region, which might be relevant for cellular copper uptake and homeostasis. Here, we assessed Cu(2+) reduction and (64)Cu uptake in two human HEK293 cell lines overexpressing APP. Our results indicate that Cu(2+) reduction increased and cells accumulated larger levels of copper, maintaining cell viability at supra-physiological levels of Cu(2+) ions. Moreover, wild-type cells exposed to both Cu(2+) ions and APP135-155 synthetic peptides increased copper reduction and uptake. Complementation of function studies in human APP751 transformed Fre1 defective Saccharomyces cerevisiae cells rescued low Cu(2+) reductase activity and increased (64)Cu uptake. We conclude that Cu(2+) reduction activity of APP facilitates copper uptake and may represent an early step in cellular copper homeostasis.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.