Intraspecific chemical variability of the leaf essential oil of Juniperus phoenicea subsp. turbinata from Corsica

The composition of 50 samples of essential oil of individual plants of Juniperus phoenicea subsp. turbinata from Corsica was investigated by GC, GC-MS and 13C NMR. alpha-Pinene, beta-phellandrene, alpha-terpinyl acetate, Delta-3-carene, myrcene and alpha-phellandrene were found to be the main constituents. The results were submitted to cluster analysis and discriminant analysis which allowed two groups of essential oils to be distinguished with respect to the content of alpha-pinene, beta-phellandrene and alpha-terpinyl acetate.     

An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters

Background  

Many studies have provided algorithms or methods to assess a statistical significance in quantitative proteomics when multiple replicates for a protein sample and a LC/MS analysis are available. But, confidence is still lacking in using datasets for a biological interpretation without protein sample replicates. Although a fold-change is a conventional threshold that can be used when there are no sample replicates, it does not provide an assessment of statistical significance such as a false discovery rate (FDR) which is an important indicator of the reliability to identify differentially expressed proteins. In this work, we investigate whether differentially expressed proteins can be detected with a statistical significance from a pair of unlabeled protein samples without replicates and with only duplicate LC/MS injections per sample. A FDR is used to gauge the statistical significance of the differentially expressed proteins.     

Sequence and structure of Brassica rapa chromosome A3

Background

The species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species.

Results

We have determined and analyzed the sequence of B. rapa chromosome A3. We obtained 31.9 Mb of sequences, organized into nine contigs, which incorporated 348 overlapping BAC clones. Annotation revealed 7,058 protein-coding genes, with an average gene density of 4.6 kb per gene. Analysis of chromosome collinearity with the A. thaliana genome identified conserved synteny blocks encompassing the whole of the B. rapa chromosome A3 and sections of four A. thaliana chromosomes. The frequency of tandem duplication of genes differed between the conserved genome segments in B. rapa and A. thaliana, indicating differential rates of occurrence/retention of such duplicate copies of genes. Analysis of 'ancestral karyotype' genome building blocks enabled the development of a hypothetical model for the derivation of the B. rapa chromosome A3.

Conclusions

We report the near-complete chromosome sequence from a dicotyledonous crop species. This provides an example of the complexity of genome evolution following polyploidy. The high degree of contiguity afforded by the clone-by-clone approach provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.     

The co-distribution of Plasmodium falciparum and hookworm among African schoolchildren

Background

On the island of Bioko (Equatorial Guinea), insecticide-treated nets (ITNs) have been the main tool used to control malaria over the last 13 years. In 2004, started an indoor residual spraying (IRS) campaign to control malaria. The purpose of this study is to asses the impact of the two control strategies on the island of Bioko (Equatorial Guinea), with regards to Plasmodium infection and anaemia in the children under five years of age.

Methods

Two transversal studies, the first one prior to the start of the IRS campaign and the second one year later. Sampling was carried out by stratified clusters. Malaria infection was measured by means of thick and thin film, and the packed cell volume (PCV) percentage. Data related to ITN use and information regarding IRS were collected. The Pearson's chi-square and logistic regression statistical tests were used to calculate odds ratios (OR)

Results

In the first survey, 168 children were sampled and 433 children in the second one. The prevalence of infection was 40% in 2004, and significantly lower at 21.7% in 2005. PCV was 41% and 39%, respectively. 58% of the children surveyed in 2004 and 44.3% in 2005 had slept under an ITN. 78% of the dwellings studied in 2005 had been sprayed. In the 2005 survey, sleeping without a mosquito net meant a risk of infection 3 times greater than sleeping protected with a net hanged correctly and with no holes (p < 0.05).

Conclusion

IRS and ITNs have proven to be effective control strategies on the island of Bioko. The choice of one or other strategy is, above all, a question of operational feasibility and availability of local resources.     

Streamlining genomes: toward the generation of simplified and stabilized microbial systems

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Highlights? Top-down and bottom-up approaches to genome streamlining. ? Computational support for constructing and refactoring streamlined genomes. ? From genome engineering to metabolic reprogramming. ? Perspectives in applied genome engineering.     

Morphophysiological differences in leaves of <Emphasis Type="Italic">Lavoisiera campos</Emphasis>-<Emphasis Type="Italic">portoana</Emphasis> (Melastomataceae) enhance higher drought tolerance in water shortage events

Lavoisiera campos-portoana Barreto (Melastomataceae) has two kinds of leaves, pubescent and glabrous, and branches may have one or both types of leaves at the same moment. The plant is endemic to high altitude rocky fields in Brazil where rainfall is very seasonal. We predicted that these two leaf types are adaptations to different regimes of water availability. In experimental conditions of drought stress, we measured relative water content (RWC), photosynthetic pigments, chlorophyll a fluorescence and osmotic potential, and we counted stomates and measured stomatal conductance on both sides of leaves and compared these between the two leaf types. Stomatal conductance and electron transport rate at a given photosynthetic photon flux were greater in pubescent leaves than in glabrous leaves, and both declined during drought stress. Excessive photon flux density in glabrous leaves was greater during stress and after rehydration. Photosynthetic pigment content and RWC did not change between leaves, and values reduced during the stress period. Both types of leaves showed osmotic adjustment capacity, which occurred earlier in glabrous ones. These morphophysiological differences highlight the adaptation strategies of this plant to withstand drought, since the glabrous portion of the plant presents a preventive behavior, while the pubescent portion only shows the same responses in more advanced stages of drought stress.     

Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including ‘ARMAN'' (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O₂ concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO₂, CH₄, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called ‘ARMAN''-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H₂, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H₂ in acidic suboxic macroscopic growths.     

Vegetative hyphal fusion is not essential for plant infection by Fusarium oxysporum

Vegetative hyphal fusion (VHF) is a ubiquitous phenomenon in filamentous fungi whose biological role is poorly understood. In Neurospora crassa, the mitogen-activated protein kinase (MAPK) Mak-2 and the WW domain protein So are required for efficient VHF. A MAPK orthologous to Mak-2, Fmk1, was previously shown to be essential for root penetration and pathogenicity of the vascular wilt fungus Fusarium oxysporum. Here we took a genetic approach to test two hypotheses, that (i) VHF and plant infection have signaling mechanisms in common and (ii) VHF is required for efficient plant infection. F. oxysporum mutants lacking either Fmk1 or Fso1, an orthologue of N. crassa So, were impaired in the fusion of vegetative hyphae and microconidial germ tubes. Δfmk1 Δfso1 double mutants exhibited a more severe fusion phenotype than either single mutant, indicating that the two components function in distinct pathways. Both Δfso1 and Δfmk1 strains were impaired in the formation of hyphal networks on the root surface, a process associated with extensive VHF. The Δfso1 mutants exhibited slightly reduced virulence in tomato fruit infection assays but, in contrast to Δfmk1 strains, were still able to perform functions associated with invasive growth, such as secretion of pectinolytic enzymes or penetration of cellophane sheets, and to infect tomato plants. Thus, although VHF per se is not essential for plant infection, both processes have some signaling components in common, suggesting an evolutionary relationship between the underlying cellular mechanisms.