Evolutionary history and distance dependence control survival of dipterocarp seedlings

One important hypothesis to explain tree-species coexistence in tropical forests suggests that increased attack by natural enemies near conspecific trees gives locally rare species a competitive advantage. Host ranges of natural enemies generally encompass several closely related plant taxa suggesting that seedlings should also do poorly around adults of closely related species. We investigated the effects of adult Parashorea malaanonan on seedling survival in a Bornean rain forest. Survival of P. malaanonan seedlings was highest at intermediate distances from parent trees while heterospecific seedlings were unaffected by distance. Leaf herbivores did not drive this relationship. Survival of seedlings was lowest for P. malaanonan , and increased with phylogenetic dissimilarity from this species, suggesting that survival of close relatives of common species is reduced. This study suggests that distance dependence contributes to species coexistence and highlights the need for further investigation into the role of shared plant enemies in community dynamics.
Ecology Letters (2010) 13: 51–59     

Biofilm formation in environmental bacteria is influenced by different macromolecules depending on genus and species

The formation of biofilms by diverse bacteria isolated from contaminated soil and groundwater on model substrata with different surface properties was assessed in a multifactorial screen. Diverse attachment phenotypes were observed as measured by crystal violet dye retention and confocal laser scanning microscopy (CLSM). Bulk measurements of cell hydrophobicity had little predictive ability in determining whether biofilms would develop on hydrophobic or hydrophilic substrata. Therefore selected pairs of bacteria from the genera Rhodococcus, Pseudomonas and Sphingomonas that exhibited different attachment phenotypes were examined in more detail using CLSM and the lipophilic dye, Nile Red. The association of Rhodococcus sp. cell membranes with lipids was shown to influence the attachment properties of these cells, but this approach was not informative for Pseudomonas and Sphingomonas sp. Confocal Raman Microspectroscopy of Rhodococcus biofilms confirmed the importance of lipids in their formation and indicated that in Pseudomonas and Sphingomonas biofilms, nucleic acids and proteins, respectively, were important in identifying the differences in attachment phenotypes of the selected strains. Treatment of biofilms with DNase I confirmed a determining role for nucleic acids as predicted for Pseudomonas. This work demonstrates that the attachment phenotypes of microbes from environmental samples to different substrata varies markedly, a diverse range of macromolecules may be involved and that these differ significantly between genera. A combination of CLSM and Raman spectroscopy distinguished between phenotypes and could be used to identify the key macromolecules involved in cell attachment to surfaces for the specific cases studied.     

Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage

The similarity of two nucleotide sequences is often expressed in terms of evolutionary distance, a measure of the amount of change needed to transform one sequence into the other. Given two sequences with a small distance between them, can their similarity be explained by their base composition alone? The nucleotide order of these sequences contributes to their similarity if the distance is much smaller than their average permutation distance, which is obtained by calculating the distances for many random permutations of these sequences. To determine whether their similarity can be explained by their dinucleotide and codon usage, random sequences must be chosen from the set of permuted sequences that preserve dinucleotide and codon usage. The problem of choosing random dinucleotide and codon-preserving permutations can be expressed in the language of graph theory as the problem of generating random Eulerian walks on a directed multigraph. An efficient algorithm for generating such walks is described. This algorithm can be used to choose random sequence permutations that preserve (1) dinucleotide usage, (2) dinucleotide and trinucleotide usage, or (3) dinucleotide and codon usage. For example, the similarity of two 60-nucleotide DNA segments from the human beta-1 interferon gene (nucleotides 196-255 and 499-558) is not just the result of their nonrandom dinucleotide and codon usage.      

The influence of the parasitic angiosperm Striga gesnerioides on the growth and photosynthesis of its host, Vigna unguiculata

Cowpea plants (Vigna unguiculata) infected with the root hemiparasiticangiosperm Striga gesnerioides accumulated less biomass thanuninfected plants over a growth period of 60 d. The allometricrelationship between shoot and root dry weight was similar inparasitized plants relative to control plants, as was the proportionof dry matter partitioned into leaf, stem and root tissue. However,infected plants failed to make any significant investment ofdry matter in pods. The rate of photosynthesis of the youngestfully expanded leaf of parasitized plants was significantlylower than for control plants. The lower rates of photosynthesiswere not attributable to stomatal limitation, a loss of chlorophyllor to an accumulation of carbohydrate. The depression of photosynthesisin the young leaves was transient. As control leaves aged, photosynthesisdeclined. This also occurred in Striga infected plants, butto a lesser extent resulting in higher rates of photosynthesisin mature leaves when compared to those of uninfected plants.The foliar nitrogen content of parasitized plants was higherthan control plants consistent with the slower rate of photosyntheticdecline of older leaves. The data are discussed with respectto the influence of parasitic weeds on host growth and photosynthesis. Key words: Cowpea, hemiparasite, allometry, nitrogen     

The electrical responses of the retinal receptors and the lamina in the visual system of the fly musca

Slow electrical responses were recorded from receptors and from the lamina of the visual pathway of the fly Musca.

1. Receptors 1 to 6 in the retinal ommatidia are identified by their response dichroic sensitivity planes. The half-width of their angular sensitivity distributions is estimated 2.5° in dark adaptation, and found not to vary with ambient illumination. The retinula cells are only excited by light that enters the eye through their overlying corneal facets.
2. The responses of the lamina show no detectable dichroic sensitivity, though in favourable cases their angular sensitivity distributions may be as narrow as those of the receptors. It is shown that these responses are excited by light that enters the six facets of the corneal projection of the single lamina cartridge synapse. The retinula fibres of passage through the lamina, originating from ommatidial cells 7 and 8, evidently do not contribute excitation to the responses.
3. It is shown that the separate responses contributed by the individual receptors of the projection are added linearly at the lamina response compartment over a wide range of light intensities.

     

Electron paramagnetic resonance- (EPR-) resolved kinetics of cryogenic nitric oxide recombination to cytochrome c oxidase and myoglobin.

By the electron paramagnetic resonance (EPR) technique, recovery kinetics for nitric oxide (NO) to heme following cryogenic photolysis were studied for the nitrosylferrocytochrome a3 center in cytochrome c oxidase and for myoglobin. The recovery was nonexponential, as has been observed in previous cryogenic CO and O2 rebinding to heme systems. NO rebinding to heme a3 started near a temperature of 50 K and was related to a distribution of thermal activation energies. At the peak of the distribution the activation energy was 3.1 kcal/mol, and the preexponential in the recovery rate was 10(9.9) s-1. For recovery of NO back to the a3 heme, the activation energy was threefold less than that for CO where CO binds to nearby Cua3 following photolysis from heme a3, but was larger than the activation energy for CO, O2, and probably NO rebinding to myoglobin. NO ligand rebinding to myoglobin occurred at a temperature as low as 15 K and in a temperature regime where tunneling could occur. However, the rate of NO rebinding to myoglobin did increase with temperature in the 15-25 K range.     

Photosynthesis in localised regions of oat leaves infected with crown rust (Puccinia coronata): quantitative imaging of chlorophyll fluorescence

Localised changes in photosynthesis in oat leaves infected with the biotrophic rust fungus Puccinia coronata Corda were examined at different stages of disease development by quantitative imaging of chlorophyll fluorescence. Following inoculation of oat leaves with crown rust the rate of whole-leaf gas exchange declined. However, crown rust formed discrete areas of infection which expanded as the disease progressed and these localised regions of infection gave rise to heterogeneous changes in photosynthesis. To quantify these changes, images of chlorophyll fluorescence were taken 5, 8 and 11 d after inoculation and used to calculate images representing two parameters; Φ_II, a measure of PSII photochemical efficiency and ΔFm/Fm′, a measure of non-photochemical energy dissipation (qN). Five days after inoculation, disease symptoms appeared as yellow flecks which were correlated with the extent of the fungal mycelium within the leaf. At this stage, Δ_II was slightly reduced in the infected regions but, in uninfected regions of the leaf, values of Φ_II were similar to those of healthy leaves. In contrast, qN (ΔFm/Fm′) was greatly reduced throughout the infected leaf in comparison to healthy leaves. We suggest that the low value of qN in an infected leaf reflects a high demand for ATP within these leaves. At sporulation, 8 d after inoculation, Φ_II was reduced throughout the infected leaf although the reduction was most marked in areas invaded by fungal mycelium. In the infected leaf the pattern of non-photochemical quenching was complex; qN was low within invaded regions, perhaps reflecting high metabolic activity, but was now much higher in uninfected regions of the infected leaf, in comparison to healthy leaves. Eleven days after inoculation “green islands” formed in regions of the leaf associated with the fungal mycelium. At this stage, photosynthesis was severely inhibited over the entire leaf; however, heterogeneity was still apparent. In the region not invaded by the fungal mycelium, Φ_II and qN were very low and these regions of the leaf were highly fluorescent, indicating that the photosynthetic apparatus was severely damaged. In the greenisland tissue, Φ_II was low but detectable, indicating that some photosynthetic processes were still occurring. Moreover, qN was high and fluorescence low, indicating that the cells in this region were not dead and were capable of significant quenching of chlorophyll fluorescence.