CONDOR: a database resource of developmentally associated conserved non-coding elements

Background  

Comparative genomics is currently one of the most popular approaches to study the regulatory architecture of vertebrate genomes. Fish-mammal genomic comparisons have proved powerful in identifying conserved non-coding elements likely to be distal cis-regulatory modules such as enhancers, silencers or insulators that control the expression of genes involved in the regulation of early development. The scientific community is showing increasing interest in characterizing the function, evolution and language of these sequences. Despite this, there remains little in the way of user-friendly access to a large dataset of such elements in conjunction with the analysis and the visualization tools needed to study them.     

The influence of 1-hydroxyethane-1,1-diphosphonate and dichloromethanediphosphonate on lysine hydroxylation and cross-link formation in rat bone, cartilage and skin collagen.

The effects in vivo of dichloromethanediphosphonate and 1-hydroxyethane 1,1-diphosphonate on collagen solubility, hydroxylation of lysine and proline and on the formation of collagen intermolecular cross-links were studied by using rat bone, cartilage and skin tissues. Dichloromethanediphosphonate decreased bone collagen solubility both in acetic acid and after pepsin treatment. Although none of the diphosphonates had any effect on the hydroxylation of proline, dichloromethane-diphosphonate, but not 1-hydroxyethane-1,1-diphosphonate, increased the number of hydroxylysine residues in the alpha-chains of bone, skin and cartilage collagen. The stimulatory effect was dose-dependent. The dichloromethanediphosphonate-mediated increase in hydroxylysine residues in bone and cartilage was manifested in an increase of dihydroxylysinonorleucine, the cross-link that is formed by the condensation of two hydroxylysine residues. The cross-link hydroxylysinonorleucine, a condensation product of hydroxylysine and lysine, on the other hand, was decreased. The total number of intermolecular cross-links was not changed by the diphosphonate.     

Lens development depends on a pair of highly conserved Sox21 regulatory elements

Highly conserved non-coding elements (CNEs) linked to genes involved in embryonic development have been hypothesised to correspond to cis-regulatory modules due to their ability to induce tissue-specific expression patterns. However, attempts to prove their requirement for normal development or for the correct expression of the genes they are associated with have yielded conflicting results. Here, we show that CNEs at the vertebrate Sox21 locus are crucial for Sox21 expression in the embryonic lens and that loss of Sox21 function interferes with normal lens development. Using different expression assays in zebrafish we find that two CNEs linked to Sox21 in all vertebrates contain lens enhancers and that their removal from a reporter BAC abolishes lens expression. Furthermore inhibition of Sox21 function after the injection of a sox21b morpholino into zebrafish leads to defects in lens development. These findings identify a direct link between sequence conservation and genomic function of regulatory sequences. In addition to this we provide evidence that putative Sox binding sites in one of the CNEs are essential for induction of lens expression as well as enhancer function in the CNS. Our results show that CNEs identified in pufferfish-mammal whole-genome comparisons are crucial developmental enhancers and hence essential components of gene regulatory networks underlying vertebrate embryogenesis.     

Inter‐ and intraspecific effects of body size on habitat use among sexually‐dimorphic macropodids

Body size affects key life‐history parameters including dietary requirements and predation risk. We examined these effects on diel habitat use in a community of three sexually‐dimorphic macropodid marsupial species: western grey kangaroo Macropus fuliginosus, red‐necked wallaby M. rufogriseus and swamp wallaby Wallabia bicolor. In particular, our study seeks evidence of these effects operating concurrently at the intra‐ and interspecific levels. We used radio‐tracking to quantify habitat use and characterised each used location by recording the cover of plant functional groups and the presence of plant species. During nocturnal foraging periods we predicted that smaller animals (between and within species) should use habitats with higher‐quality forage, which is often less abundant, than larger animals, as metabolic demand scales with body size. During diurnal resting periods we predicted that smaller animals (between and within species), being more vulnerable to predation, should use greater concealment cover than larger animals. Western grey kangaroos and swamp wallabies behaved as predicted during foraging periods, but red‐necked wallabies did not, using more open, poorer‐quality habitats than expected. Only western grey kangaroos showed a within‐species effect on habitat use: the relatively smaller females foraged in higher‐quality patches. Habitats used by animals during the resting period generally offered greater concealment cover than those used during the foraging period, but there were no clear body size effects on the density of vegetation used. In our system, body size alone could not explain all of the observed patterns, suggesting that there may also be individual differences in habitat requirements influenced by factors such as reproductive costs, predation risk and social facilitation.     

Increase in fatty acid oxidation in calvaria cells cultured with diphosphonates.

1. Cultured calvaria cells oxidized palmitate and octanoate to CO2 and water-soluble products. 2. When these cells were treated for 6 days with 0.025 and 0.25 mM-dichloromethanediphosphonate, oxidation of palmitate was increased, whereas that of octanoate was influenced less. 3. When the rate of oxidation was raised by increasing the palmitate concentration in the medium, the effect of the diphosphonate was decreased and finally disappeared. 4. 1-Hydroxyethane-1,1-diphosphonate had only minor effects. 5. The increase in palmitate oxidation appeared 2 days after the addition of dichloromethanediphosphonate, simultaneously with a fall in lactate production. (Inhibition of glycolysis by diphosphonates has already been shown.) 6. Cycloheximide, an inhibitor of protein synthesis, did not influence the effect of dichloromethanediphosphonate on the oxidation of palmitate and the production of lactate. 7. Cells cultured with dichloromethanediphosphonate showed a faster uptake of palmitic acid than did control cells. However, this observation did not explain the increased palmitate oxidation, since uptake was much faster than oxidation, and was therefore not the rate-limiting step. 8. 2-Bromopalmitate, an inhibitor of fatty acid oxidation, did not influence the inhibition of glycolysis by the diphosphonates. This inhibition, therefore, did not result from the increased oxidation of palmitate. It is also unlikely that the increased oxidation of palmitate is connected with the inhibition of glycolysis.     

No inbreeding depression in laboratory‐reared individuals of the parasitoid wasp Allotropa burrelli

Inbreeding depression is a major concern in almost all human activities relating to plant and animal breeding. The biological control of pests with natural enemies is no exception, because populations of biocontrol agents experience a series of bottlenecks during importation, rearing, and introduction. A classical biological control program for the Comstock mealybug Pseudococcus comstocki (Hemiptera: Pseudococcidae) was initiated in France in 2008, based on the introduction of an exotic parasitoid, Allotropa burrelli Mues. (Hymenoptera: Platygastridae), a haplodiploid parasitoid imported from Japan. We evaluated the sensitivity of A. burrelli to inbreeding, to optimize rearing and release strategies. We compared several morphological and life‐history traits between the offspring of siblings and the offspring of unrelated parents. We took into account the low level of genetic variability due to the relatively small size of laboratory‐reared populations by contrasting two types of pedigree: one for individuals from a strain founded from a single field population, and the other generated by hybridizing individuals from two strains founded from two highly differentiated populations. Despite this careful design, we obtained no evidence for a negative impact of inbreeding on laboratory‐reared A. burrelli. We discussed the results in light of haplodiploid sex determination and parasitoid mating systems, and classical biological control practices.     

Web damage and feeding experience influence web site tenacity in the orb-web spider Argiope keyserlingi Karsch

For orb-web spiders, the decision to remain at a particular site or to relocate elsewhere will ultimately depend on the quality of the site. In the past, the quality of the site has been measured in terms of prey availability; spiders experiencing large numbers of prey items are less likely to relocate. However, regular web damage caused by larger nonprey animals may also contribute to the quality of a particular site. Laboratory experiments revealed that the frequency and extent of web relocation by the orb-web spider Argiope keyserlingi was influenced by the feeding regime and the rate of nonprey web damage. Daily movement patterns were influenced by web damage, and these movements were in the direction away from the source of damage. However, the cumulative distance moved during the 7 days of the experiment was influenced by the frequency with which spiders were fed. Spiders that were not given prey moved further than spiders that obtained prey. These data indicate that spiders respond to web damage on a daily basis, but the cumulative movement of spiders over a longer period is influenced mostly by the history of prey ingestion rate. Copyright 2000 The Association for the Study of Animal Behaviour.     

Novel microsatellite markers suggest the mechanism of parthenogenesis in Extatosoma tiaratum is automixis with terminal fusion

Parthenogenetic reproduction is taxonomically widespread and occurs through various cytological mechanisms, which have different impact on the genetic variation of the offspring. Extatosoma tiaratum is a facultatively parthenogenetic Australian insect (Phasmatodea), in which females oviposit continuously throughout their adult lifespan irrespective of mating. Fertilized eggs produce sons and daughters through sexual reproduction and unfertilized eggs produce female offspring via parthenogenesis. Here, we developed novel microsatellite markers for E. tiaratum and characterized them by genotyping individuals from a natural population. We then used the microsatellite markers to infer the cytological mechanism of parthenogenesis in this species. We found evidence suggesting parthenogenesis in E. tiaratum occurs through automixis with terminal fusion, resulting in substantial loss of microsatellite heterozygosity in the offspring. Loss of microsatellite heterozygosity may be associated with loss of heterozygosity in fitness related loci. The mechanism of parthenogenetic reproduction can therefore affect fitness outcomes and needs to be considered when comparing costs and benefits of sex versus parthenogenesis.     

Cryptic castes,social context and colony defence in a social bee,Tetragonula carbonaria

Division of labour in social insect colonies is facilitated in two ways: through temporal sharing of tasks or by morphologically specialised castes. In casteless species, colony defence is maintained by morphologically indistinct workers, who lack the obvious defensive specialisation of polymorphic species. Discrimination of intruders is carried out via antenna, which also detects defensive social cues such as alarm pheromones. Despite their functional importance however, antennal morphology is rarely considered in studies of nestmate recognition. We investigated antennal morphology and the necessity of social cues in mediating defensive behaviour across differentially tasked workers of a casteless social bee, Tetragonula carbonaria. Our results suggest that the current understanding of division of labour in casteless worker species remains poorly understood, with differences in antennal morphology and aggression creating morphologically and behaviourally distinct ‘cryptic castes’. Further, we found that defensive behaviour was only elicited near nest odours, highlighting the importance of mediating aggression among workers.