Differential expression and regulation of expansin gene family members during fruit growth and development of ‘Shijia’ longan fruit

In this work, five expansin cDNAs (DlExp1–5) from ‘Shijia’ longan fruit were isolated and characterized. Moreover, the expression profiles of five expansin genes and the effect of naphthalene acetic acid (NAA) and thidiazuron (TDZ) on their expressions were investigated. The results showed that five expansins exhibited different expression patterns during fruit growth and development. DlExp1 was constitutively expressed in the pericarp while the levels of DlExp1 mRNA in the aril were very high at early stage of fruit development, and decreased gradually from 28 to 77 days after anthesis (DAA). DlExp2 and DlExp4 were related to the growth of pericarp, whereas the expression of DlExp2 and DlExp5 in the aril decreased from 28 to 77 DAA. In addition, NAA and TDZ applied at the stage of rapid pericarp (21 DAA) or aril growth (56 DAA) increased the accumulations of DlExp1 and DlExp2 mRNA in the pericarp and aril, while NAA and TDZ had no or little effect on the accumulations of DlExp3, DlExp4 and DlExp5. DlExp1 and DlExp2 also accumulated highly in rapidly growing tissues, such as young stems and leaves. These findings indicated that Exp genes played a different role in longan fruit growth and showed different response to plant growth substances.     

The effects of diet and caloric restriction on adipose tissue fatty acid signatures of tufted puffin (<Emphasis Type="Italic">Fratercula cirrhata</Emphasis>) nestlings

Fatty acid (FA) signature analysis is a powerful tool to investigate foraging ecology and food web dynamics in marine ecosystems. However, use of FA signatures to qualitatively or quantitatively infer diets is potentially complicated by effects of nutritional state on lipid metabolism. Estimation of diets using the quantitative fatty acid signature analysis (QFASA) model requires the use of calibration coefficients to account for predator metabolism of individual FAs. We conducted a captive feeding experiment to determine the effects of a 50% reduction in food intake on growth rate and adipose tissue FA signatures of tufted puffin (Fratercula cirrhata) nestlings, a species that routinely experiences food restriction during growth. FA signatures of chicks fed low- and high-calorie diets both exhibited a change in composition in response to the dietary shift with the direction of change in the composition of individual FAs matching the direction of change in the dietary FAs. Despite a growth rate in the restricted nestlings that was 38% of those in the well-fed group, rates of FA turnover were not different between high and low-calorie treatments, and turnover was close to, but not entirely complete, after 27 days on both high-calorie and restricted diets. FA signatures of tufted puffin nestlings were significantly affected by caloric restriction, but these effects were much less pronounced than those of dietary turnover, and calibration coefficients of puffins fed low and high-calorie diets were highly correlated. Our results demonstrate that changes in physiological state can affect FA metabolism, but future research is required to better understand whether the size of these effects is sufficient to substantially alter diet estimation using the QFASA model.     

Use of plate-wash samples to monitor the fates of culturable bacteria in mercury- and trichloroethylene-contaminated soils

With the ultimate aim of developing bioremediation technology that use the optimum bacterial community for each pollutant, we performed polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis and identified communities of culturable bacteria in HgCl(2)- and trichloroethylene (TCE)-contaminated soil microcosms. PCR-DGGE band patterns were similar at 0 and 1 ppm HgCl(2), but changes in specific bands occurred at 10 ppm HgCl(2). Band patterns appearing at 10 and 100 ppm TCE were very different from those at 0 ppm. Phylogenetic analysis showed four bacterial groups in the HgCl(2)-contaminatied cultures: Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes. Most high-density bands, decreased-density bands, and common bands were classified into the phyla Proteobacteria, Actinobacteria, and Firmicutes, respectively; the effects of HgCl(2) on culturable bacteria appeared to differ among phyla. Duganella violaceinigra [98.4% similarity to DNA Data Bank of Japan (DDBJ) strain], Lysobacter koreensis (98.2%), and Bacillus panaciterrae (98.6%) were identified as bacteria specific to HgCl(2)-contaminated soils. Bacteria specific to TCE-contaminated soils were distributed into three phyla (Firmicutes, Proteobacteria, and Actinobacteria), but there was no clear relationship between phylum and TCE effects on culturable bacteria. Paenibacillus kobensis (97.3%), Paenibacillus curdlanolyticus (96.3%), Paenibacillus wynnii (99.8%), and Sphingomonas herbicidovorans (99.4%) were identified as bacteria specific to TCE-contaminated soils. These bacteria may be involved in pollutant degradation.     

Inferring angiosperm phylogeny from EST data with widespread gene duplication

Background

Most studies inferring species phylogenies use sequences from single copy genes or sets of orthologs culled from gene families. For taxa such as plants, with very high levels of gene duplication in their nuclear genomes, this has limited the exploitation of nuclear sequences for phylogenetic studies, such as those available in large EST libraries. One rarely used method of inference, gene tree parsimony, can infer species trees from gene families undergoing duplication and loss, but its performance has not been evaluated at a phylogenomic scale for EST data in plants.

Results

A gene tree parsimony analysis based on EST data was undertaken for six angiosperm model species and Pinus, an outgroup. Although a large fraction of the tentative consensus sequences obtained from the TIGR database of ESTs was assembled into homologous clusters too small to be phylogenetically informative, some 557 clusters contained promising levels of information. Based on maximum likelihood estimates of the gene trees obtained from these clusters, gene tree parsimony correctly inferred the accepted species tree with strong statistical support. A slight variant of this species tree was obtained when maximum parsimony was used to infer the individual gene trees instead.

Conclusion

Despite the complexity of the EST data and the relatively small fraction eventually used in inferring a species tree, the gene tree parsimony method performed well in the face of very high apparent rates of duplication.

     

Drought’s impact on Ca,Fe, Mg,Mo and S concentration and accumulation patterns in the plants and soil of a Mediterranean evergreen <Emphasis Type="Italic">Quercus </Emphasis><Emphasis Type="Italic">ilex</Emphasis> forest

We conducted a 6-year field manipulation drought experiment in an evergreen Quercus ilex forest where we simulated the drought predicted by GCM and ecophysiological models for the coming decades (an average of 15% soil moisture reduction). We thereby tested the hypothesis that enhanced drought will change Ca, Fe, Mg, Mo and S availability, concentrations and accumulation patterns in Mediterranean ecosystems. The strongest effects of drought occurred in the soil. Drought increased the total soil concentrations of S, the soil extract concentrations of Fe, Mg and S, the Mg saturation in the soil exchangeable complex and tended to increase the percentage base saturation of the soil exchangeable complex. These increased soil concentrations were related to a decrease of plant uptake capacity and not to an increase of soil enzyme activity, which in fact decreased under drier conditions. Drought increased leaf Mg concentrations in the three dominant species although only significantly in Quercus ilex and Arbutus unedo (20 and 14%, respectively). In contrast, drought tended to decrease Ca in Phillyrea latifolia (18%) and Ca and Fe concentrations in the wood of all three species. Drought increased Ca and Fe concentrations in the roots of Quercus ilex (26 and 127%). There was a slight general trend to decrease total biomass accumulation of nutrients that depend on water flux such as Mg, Fe and S. This effect was related to a decrease of soil moisture that reduced soil flow, and to a decrease in photosynthetic capacity, sap flow, transpiration and growth, and therefore plant uptake capacity under drought observed in Quercus ilex and Arbutus unedo. On the contrary, drought increased Mo accumulation in aboveground biomass in Phillyrea latifolia and reduced Mo accumulation in Arbutus unedo by reducing growth and wood Mo concentrations (51%). Phillyrea latifolia showed a great capacity to adapt to drier conditions, with no decrease in growth, an increase of Mo uptake capacity and a decrease in leaf Ca concentration, which was related to a decrease in transpiration under drought. The results indicate asymmetrical changes in species capacity to accumulate these elements, which are likely to produce changes in inter-specific competitive relations among dominant plant species and in their nutritional quality as food sources. The results also indicate that drought tended to decrease nutrient content in aboveground biomass, mainly through the decrease in growth and transpiration of the most sensitive species and caused an increase in the availability of these nutrients in soil. Thus, drought decreased the ecosystem’s capacity to retain Mg, Fe and S, facilitating their loss in torrential rainfalls.     

Zero erucic acid trait of rapeseed (<Emphasis Type="Italic">Brassica napus</Emphasis> L.) results from a deletion of four base pairs in the <Emphasis Type="Italic">fatty acid elongase 1</Emphasis> gene

The fatty acid elongase 1 (FAE1) gene is a key gene in the erucic acid biosynthesis in rapeseed. The complete coding sequences of the FAE1 gene were isolated separately from eight high and zero erucic acid rapeseed cultivars (Brassica napus L.). A four base pair deletion between T1366 and G1369 in the FAE1 gene was found in a number of the cultivars, which leads to a frameshift mutation and a premature stop of the translation after the 466th amino acid residue. This deletion was predominantly found in the C-genome and rarely in the A-genome of B. napus. Expression of the gene isoforms with the four base pair deletion in a yeast system generated truncated proteins with no enzymatic activity and could not produce very long chain fatty acids as the control with an intact FAE1 gene did in yeast cells. In the developing rape seeds the FAE1 gene isoforms with the four base pair deletion were transcribed normally but failed to translate proteins to form a functional complex. The four base pair deletion proved to be a mutation responsible for the low erucic acid trait in rapeseed and independent from the point mutation reported by Han et al. (Plant Mol Biol 46:229–239, 2001). Gang Wu, Yuhua Wu contribute equally to this article.     

Characterization of Protein–Protein Interfaces

We analyze the characteristics of protein–protein interfaces using the largest datasets available from the Protein Data Bank (PDB). We start with a comparison of interfaces with protein cores and non-interface surfaces. The results show that interfaces differ from protein cores and non-interface surfaces in residue composition, sequence entropy, and secondary structure. Since interfaces, protein cores, and non-interface surfaces have different solvent accessibilities, it is important to investigate whether the observed differences are due to the differences in solvent accessibility or differences in functionality. We separate out the effect of solvent accessibility by comparing interfaces with a set of residues having the same solvent accessibility as the interfaces. This strategy reveals residue distribution propensities that are not observable by comparing interfaces with protein cores and non-interface surfaces. Our conclusions are that there are larger numbers of hydrophobic residues, particularly aromatic residues, in interfaces, and the interactions apparently favored in interfaces include the opposite charge pairs and hydrophobic pairs. Surprisingly, Pro-Trp pairs are over represented in interfaces, presumably because of favorable geometries. The analysis is repeated using three datasets having different constraints on sequence similarity and structure quality. Consistent results are obtained across these datasets. We have also investigated separately the characteristics of heteromeric interfaces and homomeric interfaces.     

The decomposition of α-aminophosphine oxides to phosphonic acid derivatives (P<Superscript>III</Superscript>)

Aminophosphine oxides and aminophosphonates are, in general, very stable compounds. However, following phosphorus–carbon bond cleavage in aqueous acidic media these compounds sometimes decompose to phosphonic acids derivatives (P^III). Despite some controversy in the literature, careful analysis supported by theoretical studies leads to the conclusion that decomposition to P^III derivatives proceeds via an elimination reaction. Figure The decomposition of α-aminophosphine oxides to phosphonic acid derivatives (P^III)     

Phenanthrene stimulates the degradation of pyrene and fluoranthene by <Emphasis Type="Italic">Burkholderia</Emphasis> sp. VUN10013

Pyrene and fluoranthene, when supplied as the sole carbon source, were not degraded by Burkholderia sp. VUN10013. However, when added in a mixture with phenanthrene, both pyrene and fluoranthene were degraded in liquid broth and soil. The amounts of pyrene and fluoranthene in liquid media (initial concentrations of 50 mg l⁻¹ each) decreased to 42.1% and 41.1%, respectively, after 21 days. The amounts of pyrene and fluoranthene in soil (initial concentrations of 75 mg kg⁻¹ dry soil each) decreased to 25.8% and 12.1%, respectively, after 60 days. None of the high molecular weight (HMW) polycylic aromatic hydrocarbons (PAHs) tested adversely affected phenanthrene degradation by this bacterial strain and the amount of phenanthrene decreased rapidly within 3 and 15 days of incubation in liquid broth and soil, respectively. Anthracene also stimulated the degradation of pyrene or fluoranthene by Burkholderia sp. VUN10013, but to a lesser extent than phenanthrene. The extent of anthracene degradation decreased in the presence of these HMW PAHs.