Leaf Litter Decomposition and Monodominance in the Peltogyne Forest of Marací Island, Brazil1

The forest type dominated by Peltogyne gracilipes (Caesalpiniaceae) on the riverine Marací Island is the least speciesrich of any recorded for Brazilian Amazonia. Because the forest has high soil and foliar Mg concentrations, and Mg is known to be toxic to plant growth at high concentrations, this study tested the hypothesis that dominance by Peltogyne is related to Mg leaf litter amounts and decomposition. We predicted that decomposition of Peltogyne leaves would differ from that of other species, and that their decomposition would result in a pulse of Mg release. Three plots (50 × 50 m) were established in each of three forest types: Peltogyne‐rich forest (PRF; dominated by P. gracilipes),Peltogyne‐poor forest (PPF), and forest without Peltogyne (FWP). Three leaf litter decomposition experiments tested if decomposition of mixed leaf litter in coarse‐ mesh (CM) litterbags differed among forests (experiment 1); whether or not decomposition and nutrient release of Ecclinusa guianensis, Lueheopsis duckeana, and Peltogyne in CM litterbags differed among forests and species (experiment 2); and using fine‐mesh (FM) litterbags, investigated the differences in the influence of fauna! activity on Ecclinusa and Peltogyne decomposition (experiment 3). Decomposition was independent of the presence and dominance of Peltogyne, since decomposition rates in both PRF and FWP were in general lower than in PPF. These differences appeared to be related to fauna] activity. The decomposition of Peltogyne leaves was lower than that of the other species tested and was more affected by microbial and physical action. It is possible that the monodominance of Peltogyne is related to its deciduousness and faster decomposition in the dry season, which coincides with a large leaf fall. Magnesium was lost quickly from the Peltogyne leaves and the resultant pulses of Mg into the soil during the heavy rains at the beginning of the wet season may be deleterious for other species that are not adapted to high solution Mg concentrations. Results obtained were consistent with the hypothesis that Peltogyne dominance is related to the pattern of its leaf decomposition and the seasonal pulses of toxic Mg.     

Quantitative analysis of protein interaction network dynamics in yeast

Many cellular functions are mediated by protein–protein interaction networks, which are environment dependent. However, systematic measurement of interactions in diverse environments is required to better understand the relative importance of different mechanisms underlying network dynamics. To investigate environment‐dependent protein complex dynamics, we used a DNA‐barcode‐based multiplexed protein interaction assay in Saccharomyces cerevisiae to measure in vivo abundance of 1,379 binary protein complexes under 14 environments. Many binary complexes (55%) were environment dependent, especially those involving transmembrane transporters. We observed many concerted changes around highly connected proteins, and overall network dynamics suggested that “concerted” protein‐centered changes are prevalent. Under a diauxic shift in carbon source from glucose to ethanol, a mass‐action‐based model using relative mRNA levels explained an estimated 47% of the observed variance in binary complex abundance and predicted the direction of concerted binary complex changes with 88% accuracy. Thus, we provide a resource of yeast protein interaction measurements across diverse environments and illustrate the value of this resource in revealing mechanisms of network dynamics.     

An integrated platform of genomic assays reveals small-molecule bioactivities

Bioactive compounds are widely used to modulate protein function and can serve as important leads for drug development. Identifying the in vivo targets of these compounds remains a challenge. Using yeast, we integrated three genome-wide gene-dosage assays to measure the effect of small molecules in vivo. A single TAG microarray was used to resolve the fitness of strains derived from pools of (i) homozygous deletion mutants, (ii) heterozygous deletion mutants and (iii) genomic library transformants. We demonstrated, with eight diverse reference compounds, that integration of these three chemogenomic profiles improves the sensitivity and specificity of small-molecule target identification. We further dissected the mechanism of action of two protein phosphatase inhibitors and in the process developed a framework for the rational design of multidrug combinations to sensitize cells with specific genotypes more effectively. Finally, we applied this platform to 188 novel synthetic chemical compounds and identified both potential targets and structure-activity relationships.     

Vegetation and soil and plant chemistry on ultramafic rocks in the tropical Far East

The tropical Far East has many outcrops of ultramafic rock including very large areas in Sulawesi (c. 8000 km²) and New Caledonia (c. 5500 km²). The outcrops occur under several different climates, and give rise to a range of soils, the characteristics of which are reviewed. The vegetation on them is very varied. Under the same climate one can find grassland, scrub, and both short and tall rain forests. The variation in species richness on the ultramafics is difficult to explain. The degree of endemism varies too; it is probably less dependent on soil characteristics than on historical factors. The causes of the various unusual types of vegetation on ultramafic outcrops are discussed. It is possible that the somewhat dwarfed forests result from a shortage of one or more major nutrients or from very high soil Mg/Ca quotients or high Ni concentrations. The distinct ‘maquis’ vegetation of New Caledonia, and probably ultramafic scrub elsewhere, has evolved in relation to not only the soil chemical factors just listed but also periodic fire and varying degrees of drought. Fires are certainly more important than was once thought and the adverse soil factors may have a role in delaying recolonisation. The plant chemistry is notable for the presence of species which hyperaccumulate certain elements, notably Ni. This phenomenon is discussed in relation to its ecological importance, which may be protection of the hyperaccumulators against herbivores. The need for a conservation policy for the ultramafic areas is stressed, and mention is made of the restoration work on sites damaged by nickel mining in New Caledonia.     

Staphylococcus aureus ClpC ATPase is a late growth phase effector of metabolism and persistence

Staphylococcus aureus Clp ATPases (molecular chaperones) alter normal physiological functions including an aconitase‐mediated effect on post‐stationary growth, acetate catabolism, and entry into death phase (Chatterjee et al., J. Bacteriol. 2005, 187, 4488–4496). In the present study, the global function of ClpC in physiology, metabolism, and late‐stationary phase survival was examined using DNA microarrays and 2‐D PAGE followed by MALDI‐TOF MS. The results suggest that ClpC is involved in regulating the expression of genes and/or proteins of gluconeogenesis, the pentose‐phosphate pathway, pyruvate metabolism, the electron transport chain, nucleotide metabolism, oxidative stress, metal ion homeostasis, stringent response, and programmed cell death. Thus, one major function of ClpC is balancing late growth phase carbon metabolism. Furthermore, these changes in carbon metabolism result in alterations of the intracellular concentration of free NADH, the amount of cell‐associated iron, and fatty acid metabolism. This study provides strong evidence for ClpC as a critical factor in staphylococcal energy metabolism, stress regulation, and late‐stationary phase survival; therefore, these data provide important insight into the adaptation of S. aureus toward a persister state in chronic infections.