Insects on the rise

The Insect Genomics Workshop was held in Arlington, Virginia, from 28 to 30 October 2001.     

Chordate evolution in a new light

Gene expression studies in embryos often provide insights into evolutionary relationships across phyla. In this issue of Cell, Lowe et al. examine the patterning of the bilaterian nervous system by studying gene expression in a hemichordate, the acorn worm. Although these animals have an unstructured nervous system, they show surprisingly conserved gene expression domains, shedding new light on the evolution of the central nervous system and the phylogenetic placement of chordates.     

The role of Suppressor of Hairless in Notch mediated signalling during zebrafish somitogenesis

Suppressor of Hairless (Su(H)) codes for a protein that interacts with the intracellular domain of Notch to activate the target genes of the Delta-Notch signalling pathway. We have cloned the zebrafish homologue of Su(H) and have analysed its function by morpholino mediated knockdown. While there are at least four notch and four delta homologues in zebrafish, there appears to be only one complete Su(H) homologue. We have analysed the function of Su(H) in the somitogenesis process and its influence on the expression of notch pathway genes, in particular her1, her7, deltaC and deltaD. The cyclic expression of her1, her7 and deltaC in the presomitic mesoderm is disrupted by the Su(H) knockdown mimicking the expression of these genes in the notch1a mutant deadly seven. deltaD expression is similarly affected by Su(H) knockdown like deltaC but shows in addition an ectopic expression in the developing neural tube. The inactivation of Su(H) in a fss/tbx24 mutant background leads furthermore to a clear breakdown of cyclic her1 and her7 expression, indicating that the Delta-Notch pathway is required for the creation of oscillation and not only for the synchronisation between neighbouring cells. The strongest phenotypes in the Su(H) knockdown embryos show a loss of all somites posterior to the first five to seven ones. This phenotype is stronger than the known amorphic phenotypes for notch1 (des) or deltaD (aei) in zebrafish, but mimicks the knockout phenotype of RBP-Jkappa gene in the mouse, which is the homologue of Su(H). This suggests that there is some functional redundancy among the Notch and Delta genes. This fact that the first five to seven somites are only weakly affected by Su(H) knockdown indicates that additional genetic pathways may be active in the specification of the most anterior somites.     

Worker piping in honey bee swarms and its role in preparing for liftoff

Worker piping, previously reported only in hives, was observed in swarms as they prepared to liftoff to fly to a new home. Pipers are excited bees which scramble through the swarm cluster, pausing every second or so to emit a pipe. Each pipe consists of a sound pulse which lasts 0.82 +/- 0.43 s and rises in fundamental frequency from 100-200 Hz to 200-250 Hz. Many. if not all, of the pipers are nest-site scouts. The scouts pipe when it is time to stimulate the non-scouts to warm themselves to a flight-ready temperature (35 degrees C) in preparation for liftoff. The time-course of worker piping matches that of swarm warming, both start at a low level, about an hour before liftoff, and both build to a climax at liftoff. When we excluded pipers from bees hanging in the cool, outermost layer of a swarm cluster, we found that these bees did not warm up. The form of worker piping that we have studied in swarms differs from the form of worker piping that others have studied in hives. We call the two forms "wings-together piping" (in swarms) and "wings-apart piping" (in hives).     

A genetic uncertainty problem

The existence of genes that, when knocked out, result in no obvious phenotype has puzzled biologists for many years. The phenomenon is often ascribed to redundancy in regulatory networks, caused by duplicated genes. However, a recent systematic analysis of data from the yeast genome projects does not support a link between gene duplications and redundancies. An alternative explanation suggests that genes might also evolve by very weak selection, which would mean that their true function cannot be studied in normal laboratory experiments. This problem is comparable to Heisenberg's uncertainty relationship in physics. It is possible to formulate an analogous relationship for biology, which, at its extreme, predicts that the understanding of the full function of a gene might require experiments on an evolutionary scale, involving the entire effective population size of a given species.     

A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages

Macroevolutionary trends traditionally are studied by fossil analysis, comparative morphology or evo-devo approaches. With the availability of genome sequences and associated data from an increasing diversity of taxa, it is now possible to add an additional level of analysis: genomic phylostratigraphy. As an example of this approach, we use a phylogenetic framework and embryo expression data from Drosophila to show that grouping genes by their phylogenetic origin can uncover footprints of important adaptive events in evolution.     

Strategies for developing protein tyrosine phosphatase inhibitors

Protein tyrosine phosphatases (PTPs) play vital roles in numerous cellular processes and are implicated in a growing number of human diseases, ranging from cancer to cardiovascular, immunological, infectious, neurological, and metabolic diseases. Here we present methods for developing small molecule inhibitors for these enzymes, starting with how to set up a high throughput chemical library screening for PTP inhibitors, how to confirm and prioritize hits, and how to circumnavigate possible pitfalls. Next, we present the relatively new hit generating method of in silico or virtual screening. We give an overview of existing software tools, describe how to choose and generate protein target structures and illustrate the procedure with examples. We then discuss how three-dimensional PTP structures can be analyzed in terms of their potential to bind small molecule inhibitors selectively over homologous proteins and how computer tools can be applied for lead optimization efforts. We finish with a perspective of how well these PTP inhibitors might perform as future drugs to treat human disease.