Additional hox clusters in the zebrafish: divergent expression patterns belie equivalent activities of duplicate hoxB5 genes

SUMMARY The evolution of metazoan body plans has involved changes to the Hox genes, which are involved in patterning the body axis and display striking evolutionary conservation of structure and expression. Invertebrates contain a single Hox cluster whereas tetrapods possess four clusters. The zebrafish has seven unlinked hox clusters, a finding that is difficult to reconcile with the notion that genomic complexity, reflected by Hox cluster number, and morphological complexity are causally linked, as the body plan of the zebrafish is not obviously more complex than that of the mouse or human. Why have the additional hox genes in zebrafish been conserved? To address the role of these additional zebrafish hox genes, we have examined the duplicate hoxB5 genes, hoxB5a, and hoxB5b. Conservation of gene duplicates can occur when one gene acquires a new function (neofunctionalization), or when the ancestral function is divided between the two duplicates (subfunctionalization). hoxB5a and hoxB5b are expressed in distinct domains, and their combined expression domain is strikingly similar to that of single Hoxb5 genes in other species. The biochemical functions encoded by the two genes were studied by overexpression, which resulted in identical developmental defects in the anterior hindbrain and cranial neural crest, suggesting strongly that hoxB5a and hoxB5b have equivalent biochemical properties with respect to early development. From these studies, we conclude that conservation of hoxB5a and hoxB5b is likely the result of division of the ancestral Hoxb5 function between the two genes, without significant changes in biochemical activity. These results suggest a resolution to the conundrum of the extra hox genes and clusters in the zebrafish, since if any of the additional hox genes in the zebrafish are similarly subfunctionalized, they are unlikely to supply novel genetic functions. Thus, the morphological complexity potentially conferred by the majority of additional zebrafish hox clusters may not be substantially greater than that conferred by the four tetrapod clusters.     

The sym plasmid pRP2JI and at least two other loci of Rhizobium leguminosarum biovar phaseoli can confer resistance to infection by the virulent bacteriophage RL38

Abstract The virulent Rhizobium bacteriophage RL38 did not form plaques on R.leguminosarum by phaseoli but did so at high efficiency on a derivative of that strain lacking its symbiotic plasmid pRP2JI. Other strains with large deletions in pRP2JI which removed many nod and nif genes retained resistance to RL38, showing that the gene which confers phage resistance lies elsewhere on the plasmid. Although the wild-type strain of R. leguminosarum bv. phaseoli failed to plate RL38, it was possible to transduce chromosomal markers into this strain, indicating that the 'block' was not at an early stage in the infection process. Two different recombinant plasmids obtained from a clone bank of genomic DNA of R. leguminosarum bv. phaseoli , which appeared to have no DNA in common, both conferred resistance to RL38. Surprisingly, the DNA cloned in each of these plasmids did not originate from pRP2JI. Therefore, several different loci both on the Sym plasmid and elsewhere on the bacterial genome can be involved in conferring resistance to this bacteriophage.     

Differences in the Activation of the Mitochondrial Permeability Transition Among Brain Regions in the Rat Correlate with Selective Vulnerability

Mitochondria from different regions of the brain were prepared, and the activation of the mitochondrial permeability transition (MPT) by calcium was investigated by monitoring the associated mitochondrial swelling. In general, the properties of the MPT in brain mitochondria were found to be qualitatively similar to those observed in liver and heart mitochondria. Thus, swelling was inhibited by adenine nucleotides (AdNs) and low pH (<7.0), whereas thiol reagents and alkalosis facilitated swelling. Cyclosporin A and its nonimmunosuppressive analogue N-methyl-Val-4-cyclosporin A (PKF 220-384) both inhibited swelling and prevented the translocation of cyclophilin D from the matrix to the membranes of cortical mitochondria. However, the calcium sensitivity of the MPT differed in mitochondria from three brain regions (hippocampus > cortex > cerebellum) and is correlated with the susceptibility of these regions to ischemic damage. Depleting mitochondria of AdNs by treatment with pyrophosphate ions sensitized the MPT to [Ca2+] and abolished regional differences, implying regional differences in mitochondrial AdN content. This was confirmed by measurements showing significant differences in AdN content among regions (cerebellum > cortex > hippocampus). Our data add to recent evidence that the MPT may be involved in neuronal death.     

Regulation of Cadherin Trafficking

Cadherins are a large family of cell–cell adhesion molecules that tether cytoskeletal networks of actin and intermediate filaments to the plasma membrane. This function of cadherins promotes tissue organization and integrity, as demonstrated by numerous disease states that are characterized by the loss of cadherin-based adhesion. However, plasticity in cell adhesion is often required in cellular processes such as tissue patterning during development and epithelial migration during wound healing. Recent work has revealed a pivotal role for various membrane trafficking pathways in regulating cellular transitions between quiescent adhesive states and more dynamic phenotypes. The regulation of cadherins by membrane trafficking is emerging as a key player in this balancing act, and studies are beginning to reveal how this process goes awry in the context of disease. This review summarizes the current understanding of how cadherins are routed and how the interface between cadherins and membrane trafficking pathways regulates cell surface adhesive potential. Particular emphasis is placed on the regulation of cadherin trafficking by catenins and the interplay between growth factor signaling pathways and cadherin endocytosis.     

Minimizing the cost of environmental management decisions by optimizing statistical thresholds

Environmental management decisions are prone to expensive mistakes if they are triggered by hypothesis tests using the conventional Type I error rate (α) of 0.05. We derive optimal α‐levels for decision‐making by minimizing a cost function that specifies the overall cost of monitoring and management. When managing an economically valuable koala population, it shows that a decision based on α = 0.05 carries an expected cost over $5 million greater than the optimal decision. For a species of such value, there is never any benefit in guarding against the spurious detection of declines and therefore management should proceed directly to recovery action. This result holds in most circumstances where the species’ value substantially exceeds its recovery costs. For species of lower economic value, we show that the conventional α‐level of 0.05 rarely approximates the optimal decision‐making threshold. This analysis supports calls for reversing the statistical ‘burden of proof’ in environmental decision‐making when the cost of Type II errors is relatively high.     

Biosynthesis of trichothecene mycotoxins: cell-free epoxidation of a trichodiene derivative

A cell-free enzyme system from cultures of Fusarium culmorum catalyses the 12,13-epoxidation of semi-synthetic 9 beta,10 beta-epoxytrichodiene to 9 beta,10 beta;12,13-diepoxytrichodiene. This enzyme activity may be involved in the biosynthesis of trichothecene mycotoxins and since the 12,13-epoxide is known to be essential for toxicity, the enzyme activity probably confers the toxic properties associated with this group of mycotoxins. The epoxidase requires NADPH and molecular oxygen, is inhibited by carbon monoxide, and thus appears to be a cytochrome P-450-dependent mono-oxygenase. Whole cell cultures of the fungus carry out the same biotransformation, and in addition hydroxylate the diepoxide product at position 3, yielding 3 alpha-hydroxy-9 beta,10 beta;12,13-diepoxytrichodiene.     

Isolation from sugarcane cultures of variants resistant to antimetabolites

Variants resistant to antimetabolites are useful for investigating metabolic regulation and biochemical genetics in organisms. In this study, suspensions of mutagenized sugarcane ( Saccharum sp.) cells, originating from a stalk parenchyma explain of the Hawaiian variety 50–7209, were used to investigate the feasibility of isolating variants resistant to l -canavanine, glyphosate [N-(phosphonomethyl)glycine], ophiobolin A and orthovanadate. Rigorous retesting of clones which grew on selection media led to the identification of three cell lines, two of which were resistant to glyphosate and one to orthovanadate. No variants were isolated which showed a persistent resistance either to l -canavanine or ophiobolin A.
The results demonstrate that resistant variants do occur, or can be induced, in sugarcane cell suspensions and that they can be rescued and cultivated.