Marsupials and monotremes sort genome treasures from junk

A recent landmark paper demonstrates the unique contribution of marsupials and monotremes to comparative genome analysis, filling an evolutionary gap between the eutherian mammals (including humans) and more distant vertebrate species.     

fw2.2 directly affects the size of developing tomato fruit, with secondary effects on fruit number and photosynthate distribution

fw2.2 is a quantitative trait locus responsible for approximately 30% of the difference in fruit size between large, domesticated tomatoes (Lycopersicon esculentum Mill.) and their small-fruited wild relatives. The gene underlying this quantitative trait locus was cloned recently and shown to be associated with altered cell division in ovaries (Frary et al., 2000). However, it was not known whether the change in fruit size is associated with other changes in plant morphology or overall fruit yield-changes that could potentially cause the fruit weight phenotype. To shed light on this issue, a detailed comparison was made between nearly isogenic lines differing for alleles at this locus to search for pleiotropic effects associated with fw2.2. Field observations show that although the small-fruited nearly isogenic line produced smaller ovaries and fruit as expected, this was compensated by a larger number of fruit-due mainly to a significantly greater number of inflorescences-but with no net change in total fruit mass yield. This strongly suggests that fw2.2 may have a pleiotropic effect on how the plant distributes photosynthate among fruit. In a flower removal experiment to control for differences in inflorescence size and number, fruit size remained significantly different between the nearly isogenic lines. These observations indicate that the primary effect of fw2.2 is in controlling ovary and fruit size, and that other associated phenotypic effects are secondary.     

Identification of a novel phosphonocarboxylate inhibitor of Rab geranylgeranyl transferase that specifically prevents Rab prenylation in osteoclasts and macrophages

Nitrogen-containing bisphosphonate drugs inhibit bone resorption by inhibiting FPP synthase and thereby preventing the synthesis of isoprenoid lipids required for protein prenylation in bone-resorbing osteoclasts. NE10790 is a phosphonocarboxylate analogue of the potent bisphosphonate risedronate and is a weak anti-resorptive agent. Although NE10790 was a poor inhibitor of FPP synthase, it did inhibit prenylation in J774 macrophages and osteoclasts, but only of proteins of molecular mass approximately 22-26 kDa, the prenylation of which was not affected by peptidomimetic inhibitors of either farnesyl transferase (FTI-277) or geranylgeranyl transferase I (GGTI-298). These 22-26-kDa proteins were shown to be geranylgeranylated by labelling J774 cells with [(3)H]geranylgeraniol. Furthermore, NE10790 inhibited incorporation of [(14)C]mevalonic acid into Rab6, but not into H-Ras or Rap1, proteins that are modified by FTase and GGTase I, respectively. These data demonstrate that NE10790 selectively prevents Rab prenylation in intact cells. In accord, NE10790 inhibited the activity of recombinant Rab GGTase in vitro, but did not affect the activity of recombinant FTase or GGTase I. NE10790 therefore appears to be the first specific inhibitor of Rab GGTase to be identified. In contrast to risedronate, NE10790 inhibited bone resorption in vitro without markedly affecting osteoclast number or the F-actin "ring" structure in polarized osteoclasts. However, NE10790 did alter osteoclast morphology, causing the formation of large intracellular vacuoles and protrusion of the basolateral membrane into large, "domed" structures that lacked microvilli. The anti-resorptive activity of NE10790 is thus likely due to disruption of Rab-dependent intracellular membrane trafficking in osteoclasts.     

Prolonged in vivo residence times of antibody fragments associated with albumin

Antibody fragments can be expressed at a high level in microbial systems, but they may have limited therapeutic value because they are rapidly eliminated from the body. We demonstrate here that site-specific conjugation or binding of bacterially derived Fab' to the long-lived protein serum albumin allows full retention of the antibody's binding characteristics while imparting the albumin's longevity in vivo. In rats the area under the curve for Fab' conjugated to rat serum albumin was 17-fold greater than for the control of Fab' conjugated to cysteine. Again, a bispecific F(ab')(2) with specificity for rat serum albumin showed an area under the curve about 8-fold greater than did a F(ab')(2) without specificity to albumin. Genetic fusions of scFv to albumin were similarly long-lived and could be expressed in yeast to provide the basis of a cost-effective production system.     

Strain dependent response of circadian rhythms during exposure to continuous illumination

Enzymes activities were measured, at three hours intervals, during 30 hours, in various tissues of C57BL/6J and A/J male mice. The measurements, were carried out on mice which were exposed for two, five and twenty one days to continuous illumination. Identical measurements were performed also on mice which were kept in alternating 14 hours light: 10 hours dark. Activity patterns of each group were analysed to test the presence, or absence, of rhythm characteristics. The results of the experiments with C57BL/6J have been previously reported. The comparison of the results, which were obtained from the two strains revealed that under exposure to alternating light: dark conditions all activity patterns exhibited a significant circadian rhythm. Except for one enzyme (thymus GAPD), the times of peak activity (acrophase) were identical for all other examined enzymes, in both strains. On the other hand when the two strains were exposed to continuous illumination they differed in their response to the effect of continuous light. The activity of the same enzyme exhibited different periodicity and/or different acrophase in each of the two strains. This variability reflects the existence of genetic differences, between the strains in the free running behavior of these enzymes' activity rhythms.     

773. GINKGO BILOBA – Connections with people and art across a thousand years

We review the representation of Ginkgo biloba L., a quintessentially Chinese plant, in the art of those Western botanists who first encountered it in China and Japan. We also show how several later representations of Ginkgo, in both the West and the East, were inspired and made possible by specimens of Ginkgo in cultivation.     

Ecologically functional landscapes and the role of dingoes as trophic regulators in south‐eastern Australia and other habitats

Large carnivores can play a pivotal role in maintaining healthy, balanced ecosystems. By suppressing the abundances and hence impacts of herbivores and smaller predators, top predators can indirectly benefit the species consumed by herbivores and smaller predators. Restoring and maintaining the ecosystem services that large carnivores provide has been identified as a critical step required to sustain biodiversity and maintain functional, resilient ecosystems. Recent research has shown that Australia's largest terrestrial predator, the Dingo (Canis lupus dingo), has strong effects on ecosystems in arid Australia and that these effects are beneficial for the conservation of small mammals and vegetation. Similarly, there is evidence from south‐eastern Australia that dingoes suppress the abundance of macropods and red Fox (Vulpes vulpes). It is likely that dingoes in south‐eastern Australia also generate strong indirect effects on the prey of foxes and macropods, as has been observed in the more arid parts of the continent. These direct and indirect effects of dingoes have the potential to be harnessed as passive tools to assist biodiversity conservation through the maintenance of ecologically functional dingo populations. However, research is required to better understand dingoes' indirect effects on ecosystems and the development of dingo management strategies that allow for both the preservation of dingoes and protection of livestock.     

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background

Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.

Results

Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.

Conclusions

Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.