Comparative effects of interferon alpha‐2b and pegylated interferon alpha‐2b on menstrual cycles and ovarian hormones in cynomolgus monkeys

BACKGROUND : The covalent modification of interferon (IFN) α2b with monomethyoxy polyethylene glycol (PEG) reduces its clearance rate and increases its half‐life. High doses of interferon (IFN) α2b have previously been shown to affect maintenance of pregnancy in rhesus monkeys. Given the role of ovarian hormones in reproductive function and pregnancy, this study was conducted to assess the effects of PEG‐IFNα2b or IFNα2b (comparative control) on ovarian hormones and menstrual cyclicity in cynomolgus monkeys. In addition, the potential for reversibility of PEG‐IFNα2b or IFNα2b‐related observations was assessed. METHODS : Monkeys were administered 3,105 µg/m² human recombinant (hr) IFNα2b or 52, 262, or 4,239 µg/m² PEG‐hr‐IFNα2b every other day for one menstrual cycle, followed by a post‐dose period of up to two menstrual cycles. RESULTS : Monkeys administered 3,105 µg/m² hr‐IFNα2b or 52, 262, or 4,239 µg/m² PEG‐hr‐IFNα2b exhibited transient decreases in food consumption, leukocyte and erythrocyte parameters. Monkeys administered 3,105 µg/m² hr‐IFNα2b exhibited lengthened menstrual cycles that were associated with a delay in reaching peak ovarian hormone levels and lower respective peak concentrations. Similarly, monkeys administered 4,239 µg/m² PEG‐hr‐IFNα2b exhibited lengthened menstrual cycles and a delay in reaching peak ovarian hormone levels and slightly lower respective peak concentrations. Post‐dosing menstrual cycle length, estradiol and progesterone profiles exhibited evidence of recovery in both the hr‐IFNα2b and the high‐dose PEG‐hr‐IFNα2b groups. CONCLUSIONS : Administration of hr‐IFNα2b or PEG‐hr‐IFNα2b at high doses to cynomolgus monkeys resulted in similar effects on menstrual cycles, estradiol and progesterone profiles, and exhibited evidence of reversibility upon cessation of dosing. These results suggest that the previously observed high‐dose IFNα‐related effects on the maintenance of pregnancy in monkeys are likely the result of altered ovarian function. Birth Defects Res (Part B) 86:29‐39, 2009. © 2009 Wiley‐Liss, Inc.     

Genetic connectivity and inter-population seed dispersal of Banksia hookeriana at the landscape scale

Background and Aims

Landscape genetics combines approaches from population genetics and landscape ecology, increasing the scope for conceptual advances in biology. Banksia hookeriana comprises clusters of individuals located on dune crests (geographical populations) physically separated by uninhabitable swales, with local extinctions common through frequent fire and/or severe drought.

Methods

A landscape genetics approach was used to explore landscape-scale genetic connectivity and structure among geographical populations of B. hookeriana on 18 physically separated dunes located within a heterogeneous landscape of 3 × 5 km. These geographical populations were separated by approx. 0·1 to >1 km of unsuitable intervening swale habitat. Using 11 highly variable microsatellite loci, we utilized a Bayesian approach to identify genetic discontinuities within and between these geographical populations. Population allocation tests were then used to detect inter-dune seed dispersal inferred from assignment of individuals to a source population other than that from which they were collected.

Key Results

For the modal number of genetically distinct clusters (n = 17 genetic populations), two coincided with the geographical (dune) populations, eight spanned two to four geographical populations, and the remaining seven were spread among various parts of the sampled dunes, so that most geographical populations were spatially defined mosaics of individuals (subpopulations) belonging to two or more genetic populations. We inferred 25 inter-dune immigrants among the 582 individuals assessed, with an average distance between sink and source dunes of 1·1 km, and a maximum of 3·3 km.

Conclusions

The results show that genetic structure in an apparently strongly spatially structured landscape is not solely dependent on landscape structure, and that many physically defined geographical populations were genetic mosaics. More strikingly, there were physically separated individuals and groups of individuals that were part of the same genetically defined populations. We attribute this mismatch between spatially and genetically defined population structure to the varying closeness of the dunes and the ability of seeds to disperse long distances.     

Community‐level spatial structure supports a model of stochastic geometry in species‐rich shrublands

In some ecosystems a small suite of species can determine community‐level patterns of species richness by acting as either ‘accumulators’ or ‘repellers’; that is, the richness of the immediate neighbourhood of such species departs from that expected on the basis of a given null model. Using the individual species‐area approach, we evaluated community‐level spatial pattern in four species‐rich shrublands (two 40 × 40 m and two 30 × 30 m plots) by assessing the frequency of accumulator and repeller species and whether any such species were associated with specific life‐history characteristics. Few species departed from the expectations of the null spatial model that we used, although, at three of the four sites, accumulators were more common than repellers. Departures from the null model we assessed were most prevalent within just 1 m of focal individuals and were not consistently associated with specific life‐history traits. Model‐based clustering suggests that there are distinct sub‐communities in each of the four communities, but while internally spatially cohesive, these sub‐communities intermingle and their membership is not predictable from the life‐history traits of their constituent species. Comparable analyses in other species‐rich systems have also detected a similar absence of spatial interactions. The disturbance regime in the shrubland communities we consider is markedly different from those in the forest ecosystems where previous studies have been concentrated (recurrent fire versus infrequent gap‐phase dynamics) and resources are more limiting. Thus, our results provide further support for the generality of a model of stochastic geometry, likely underpinned by stochastic dilution effects, in species‐rich plant communities.     

Nucleotide sequence analysis of the lemur beta-globin gene family: evidence for major rate fluctuations in globin polypeptide evolution

Lemur beta-related globin genes have been isolated and sequenced. Orthology of prosimian and human epsilon-, gamma-, and beta-related globin genes was established by dot-matrix analysis. All of these lemur globin genes potentially encode functional beta-related globin polypeptides, though precisely when the gamma-globin gene is expressed remains unknown. The organization of the 18-kb brown lemur beta-globin gene cluster (5' epsilon-gamma-[psi eta-delta]-beta 3') is consistent with its evolution by contraction via unequal crossing-over from the putative ancestral mammalian beta-globin gene cluster (5' epsilon-gamma- eta-delta-beta 3'). The dwarf lemur nonadult globin genes are arranged as in the brown lemur. Similar levels of synonymous (silent) nucleotide substitutions and noncoding DNA sequence differences have accumulated between species in all of these genes, suggesting a uniform rate of noncoding DNA divergence throughout primate beta-globin gene clusters. These differences are comparable with those observed in the nonfunctional psi eta pseudogene and have therefore accumulated at the presumably maximal neutral rate. In contrast, nonsynonymous (replacement) nucleotide substitutions show a significant heterogeneity in distribution for both the same gene in different lineages and different genes in the same lineage. These major fluctuations in replacement but not silent substitution rates cannot be attributed to changes in mutation rate, suggesting that changes in the rate of globin polypeptide evolution in primates is not governed solely by variable mutation rates.      

Species delimitation of the liquorice tribe (Leguminosae: Glycyrrhizeae) based on phylogenomic and machine learning analyses

The liquorice tribe Glycyrrhizeae is a leguminous herbaceous group of plants comprised of the genera Glycyrrhiza and Glycyrrhizopsis. Some Glycyrrhiza taxa contain glycyrrhizin, a pharmacologically significant sweet substance that also has applications in crafting industrial materials. Here, we utilized an expanded taxon sampling of Glycyrrhizeae to reconstruct the phylogenetic relationships in the tribe based on genome skimming data, including whole chloroplast genomes, nuclear ribosomal DNA, and low-copy nuclear DNA. We also launched machine learning analysis (MLA) for one species pair with controversial taxonomic boundary. The integrated results indicated Glycyrrhizopsis should be split from Glycyrrhiza, while the former genus Meristotropis should be treated as part of Glycyrrhiza. Glycyrrhizopsis includes two species, Glycyrrhizopsis asymmetrica and Glycyrrhizopsis flavescens, and we recognize 13 species in Glycyrrhiza: Glycyrrhiza acanthocarpa, Glycyrrhiza astragalina, Glycyrrhiza bucharica, Glycyrrhiza echinata, Glycyrrhiza foetida, Glycyrrhiza glabra, Glycyrrhiza gontscharovii, Glycyrrhiza lepidota, Glycyrrhiza macedonica, Glycyrrhiza pallidiflora, Glycyrrhiza squamulosa, Glycyrrhiza triphylla, and Glycyrrhiza yunnanensis. We propose a broader G. glabra that includes former Glycyrrhiza aspera, G. glabra s.s., Glycyrrhiza inflata, and Glycyrrhiza uralensis, and represents the glycyrrhizin-contained medicinal group. Our ancestral state inferences show the ancestor of Glycyrrhiza lacked glycyrrhizin, and the presence of glycyrrhizin evolved twice within Glycyrrhiza during the last one million years. Our integrative phylogenomics-MLA study not only provides new insights into long-standing taxonomic controversies of Glycyrrhizeae, but also represents a useful approach for future taxonomic studies on other plant taxa.     

Negative cross-talk between salicylate- and jasmonate-mediated pathways in the Wassilewskija ecotype of Arabidopsis thaliana

Plants often respond to attack by insect herbivores and necrotrophic pathogens with induction of jasmonate-dependent resistance traits, but respond to attack by biotrophic pathogens with induction of salicylate-dependent resistance traits. To assess the degree to which the jasmonate- and salicylate-dependent pathways interact, we compared pathogenesis-related protein activity and bacterial performance in four mutant Arabidopsis thaliana lines relative to their wild-type backgrounds. We found that two salicylate-dependent pathway mutants (cep1, nim1-1) exhibited strong effects on the growth of the generalist biotrophic pathogen, Pseudomonas syringae pv. tomato, whereas two jasmonate-dependent pathway mutants (fad3-2fad7-2fad8, jar1-1) did not. Leaf peroxidase and exochitinase activity were negatively correlated with bacterial growth, whereas leaf polyphenol oxidase activity and trypsin inhibitor concentration were not. Interestingly, leaf total glucosinolate concentration was positively correlated with bacterial growth. In the same experiment, we also found that application of jasmonic acid generally increased leaf peroxidase activity and trypsin inhibitor concentration in the mutant lines. However, the cep1 mutant, shown previously to overexpress salicylic acid, exhibited no detectable biological or chemical responses to jasmonic acid, suggesting that high levels of salicylic acid may have inhibited a plant response. In a second experiment, we compared the effect of jasmonic acid and/or salicylic acid on two ecotypes of A. thaliana. Application of salicylic acid to the Wassilewskija ecotype decreased bacterial growth. However, this effect was not observed when both salicylic acid and jasmonic acid were applied, suggesting that jasmonic acid negated the beneficial effect of salicylic acid. Collectively, our results confirm that the salicylate-dependent pathway is more important than the jasmonate-dependent pathway in determining growth of P. syringae pv. tomato in A. thaliana, and suggest important negative interactions between these two major defensive pathways in the Wassilewskija ecotype. In contrast, the Columbia ecotype exhibited little evidence of negative interactions between the two pathways, suggesting intraspecific variability in how these pathways interact in A. thaliana.     

Epigenetic characteristics and development of embryos cloned from donor cells treated by trichostatin A or 5-aza-2'-deoxycytidine

Development to blastocyst following nuclear transfer is dependent on the donor cell's ability to reprogram its genome to that of a zygote. This reprogramming step is inefficient and may be dependent on a number of factors, including chromatin organization. Trichostatin A (TSA; 0-5 microM), a histone deacetylase inhibitor, was used to increase histone acetylation and 5-aza-2'-deoxycytidine (5-aza-dC; 0-5 microM), a DNA methyl-transferase inhibitor, was used to decrease methylation of chromatin in donor cells in an attempt to improve their reprogrammability. Adult fibroblast cells treated with 1.25 or 5 microM TSA had elevated histone H3 acetylation compared to untreated controls. Cells treated with 0.3 microM 5-aza-dC had decreased methylation compared to untreated controls. Both drugs at 0.08 microM caused morphological changes of the donor cells. Development to blastocysts by embryos cloned from donor cells after 0.08 or 0.3 microM 5-aza-dC treatments was lower than in embryos cloned from untreated control cells (9.7% and 4.2%, respectively, vs. 25.1%), whereas 0.08 microM TSA treatment of donor cells increased blastocyst development compared to controls (35.1% vs. 25.1%). These results indicate that partial erasure of preexisting epigenetic marks of donor cells improves subsequent in vitro development of cloned embryos.     

COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics

SUMMARY: We present a database of fully sequenced and published genomes to facilitate the re-distribution of data and ensure reproducibility of results in the field of computational genomics. For its design we have implemented an extremely simple yet powerful schema to allow linking of genome sequence data to other resources. AVAILABILITY: http://maine.ebi.ac.uk:8000/services/cogent/