Testing a simple rule for dominance in resource competition

Competition for limiting resources long has been considered an important factor generating community structure. A minimal model of resource competition predicts that the species that reduces the limiting resource R to the lowest level ([Formula: see text]) will exclude its competitors. Whether this "[Formula: see text] rule" is robust to violations of model assumptions remains largely unknown. I conducted a competition experiment with four species of bacterivorous protists in laboratory microcosms and predicted the outcome from each species' [Formula: see text] value. I also examined how the outcome of competition, species abundances, and the effect of protists on bacterial density varied with productivity. Microcosms were unstirred batch cultures containing a variety of bacteria, challenging the robustness of the simplest competition models. Protists with low [Formula: see text] values were less affected by competition, although competing protists often coexisted. The values of [Formula: see text] can predict competitive dominance, even in the absence of competitive exclusion. Other model predictions were less robust. Contrary to expectation, densities of grazed bacteria increased with productivity, and the effect of some protists on bacterial density did not vary with productivity. Bacterial heterogeneity may account for deviations from model predictions. Further experiments should examine the conditions under which simple rules can be expected to identify dominant species.     

The amitochondriate eukaryote Trichomonas vaginalis contains a divergent thioredoxin-linked peroxiredoxin antioxidant system

Trichomonas is an amitochondriate parasitic protozoon specialized for an anaerobic lifestyle. Nevertheless, it is exposed to oxygen and is able to cope with the resultant oxidative stress. In the absence of glutathione, cysteine has been thought to be the major antioxidant. We now report that the parasite contains thioredoxin reductase, which functions together with thioredoxin and thioredoxin peroxidase to detoxify potentially damaging oxidants. Thioredoxin reductase and thioredoxin also reduce cystine and so may play a role in maintaining the cellular cysteine levels. The importance of the thioredoxin system as one of the major antioxidant defense mechanisms in Trichomonas was confirmed by showing that the parasite responds to environmental changes resulting in increased oxidative stress by up-regulating thioredoxin and thioredoxin peroxidases levels. Sequence data indicate that the thioredoxin reductase of Trichomonas differs fundamentally in structure from that of its human host and thus may represent a useful drug target. The protein is generally similar to thioredoxin reductases present in other lower eukaryotes, all of which probably originated through horizontal gene transfer from a prokaryote. The phylogenetic signal in thioredoxin peroxidase is weak, but evidence from trees suggests that this gene has been subject to repeated horizontal gene transfers from different prokaryotes to different eukaryotes. The data are thus consistent with the complexity hypothesis that predicts that the evolution of simple pathways such as the thioredoxin cascade are likely to be affected by horizontal gene transfer between species.     

The anaerobic biodegradation of diethanolamine by a nitrate reducing bacterium

The ability of bacterial cultures to degrade diethanolamine under anoxic conditions with nitrate as an electron acceptor was investigated. A mixed culture capable of anaerobic degradation of diethanolamine was obtained from river sediments by enrichment culture. From this a single bacterial strain was isolated which could use diethanolamine, monoethanolamine, triethanolamine and N-methyl diethanolamine as its sole carbon and energy sources either aerobically or anaerobically. Growth on diethanolamine was faster in the absence of oxygen. The accumulation of possible metabolites in the culture medium was determined as was the ability to grow on certain putative intermediates in the degradation of diethanolamine. A possible pathway for the degradation of ethanolamines by this organism is suggested.     

Should conservation strategies consider spatial generality? Farmland birds show regional not national patterns of habitat association

A key assumption underlying any management practice implemented to aid wildlife conservation is that it will have similar effects on target species across the range it is applied. However, this basic assumption is rarely tested. We show that predictors [nearly all associated with agri-environment scheme (AES) options known to affect European birds] had similar effects for 11 bird species on sites with differing farming practice (pastoral vs. mixed farming) or which differed in the density at which the species was found. However, predictors from sites in one geographical region tended to have different effects in other areas suggesting that AES options targeted at a regional scale are more likely to yield beneficial results for farmland birds than options applied uniformly in national schemes. Our study has broad implications for designing conservation strategies at an appropriate scale, which we discuss.     

Detecting the coevolution of biosequences--an example of RNA interaction prediction

A probabilistic graphical model is proposed in order to detect the coevolution between different sites in biological sequences. The model extends the continuous-time Markov process of sequence substitution for single nucleic or amino acids and imposes general constraints regarding simultaneous changes on the substitution rate matrix. Given a multiple sequence alignment for each molecule of interest and a phylogenetic tree, the model can predict potential interactions within or between nucleic acids and proteins. Initial validation of the model is carried out using tRNA and 16S rRNA sequence data. The model accurately identifies the secondary interactions of tRNA as well as several known tertiary interactions. In addition, results on 16S rRNA data indicate this general and simple coevolutionary model outperforms several other parametric and nonparametric methods in predicting secondary interactions. Furthermore, the majority of the putative predictions exhibit either direct contact or proximity of the nucleotide pairs in the 3-dimensional structure of the Thermus thermophilus ribosomal small subunit. The results on RNA data suggest a general model of coevolution might be applied to other types of interactions between protein, DNA, and RNA molecules.     

Monosubstituted γ-lactam and conformationally constrained 1,3-diaminopropan-2-ol transition-state isostere inhibitors of β-secretase (BACE)

The synthesis, evaluation, and structure-activity relationships of a class of γ-lactam 1,3-diaminopropan-2-ol transition-state isostere inhibitors of BACE are discussed. Two strategies for optimizing lead compound 1a are presented. Reducing the overall size of the inhibitors resulted in the identification of γ-lactam 1i, whereas the introduction of conformational constraint on the prime-side of the inhibitor generated compounds such as the 3-hydroxypyrrolidine inhibitor 28n. The full in vivo profile of 1i in rats and 28n in Tg 2576 mice is presented.     

The environmental basis of North American species richness patterns among Epicauta (Coleoptera: Meloidae)

Understanding regional variability in species richness is necessary for conservation efforts to succeed in the face of large-scale environmental deterioration. Several analyses of North American vertebrates have shown that climatic energy provides the best explanation of contemporary species richness patterns. The paucity of analyses of insect diversity patterns, however, remains a serious obstacle to a general hypothesis of spatial variation in diversity. We collected species distribution data on a North American beetle genus, Epicauta (Coleoptera: Meloidae) and tested several major diversity hypotheses. These beetles are generally grasshopper egg predators as larvae, and angiosperm herbivores as adults. Epicauta richness is highest in the hot, dry American southwest, and decreases north and east, consistent with the species richness-energy hypothesis. Potential evapotranspiration, which is also the best predictor of richness patterns among North American vertebrates, explains 80.2% of the variability in Epicauta species richness. Net primary productivity and variables measuring climatic heat energy only (such as PET) are not generally comparable, though they are sometimes treated as if they were equivalent. We conclude that the species richness-energy hypothesis currently provides a better overall explanation for Epicauta species richness patterns in North America than other major diversity hypotheses. The observed relationship between climatic energy and regional species richness may provide significant insight into the response of ecological communities to climate change.     

Distant segments of Saccharomyces cerevisiae scR1 RNA promote assembly and function of the signal recognition particle

The conserved signal recognition particle targets ribosomes synthesizing presecretory proteins to the endoplasmic reticulum membrane. Key to the activity of SRP is its ability to bind the ribosome at distant locations, the signal sequence exit and elongation factor-binding sites. These contacts are made by the S and Alu domains of SRP, respectively. We tested earlier secondary structure predictions of the Saccharomyces cerevisiae SRP RNA, scR1, and provide and test a consensus structure. The structure contains four non-conserved insertions, helices 9-12, into the core SRP RNA fold, and an extended helix 7. Using a series of scR1 mutants lacking part or all of these structural elements, we find that they are important for the RNA in both function and assembly of the RNP. About 20% of the RNA, corresponding to the outer regions of these helices, is dispensable for function. Further, we examined the role of several features within the S-domain section of the core, helix 5, and find that its length and flexibility are important for proper SRP function and become essential in the absence of helix 10, 11 and/or 7 regions. Overall, the genetic data indicate that regions of scR1 distant in both primary sequence and secondary structure have interrelated roles in the function of the complex, and possibly mediate communication between Alu and S domains during targeting.     

Rapid evolution of spermathecal duct length in the Allonemobius socius complex of crickets: species, population and Wolbachia effects

The three species in the Allonemobius socius complex of crickets have recently diverged and radiated across North America. Interestingly, the only barriers to gene flow between these species in zones of secondary contact appear to be associated with fertilization traits - e.g., conspecific sperm precedence and the ability of males to induce females to lay eggs. Other traits, such as the length of female's reproductive tract, may also influence fertilization success and be associated with species boundaries. However, the underlying variation in this duct has not been assessed across populations and species. Moreover, the effects of reproductive parasites like Wolbachia on these morphological features have yet to be addressed, even though its infections are concentrated in reproductive tissues. I evaluated both the natural variation in and the effects of Wolbachia infection on spermathecal duct length among several populations of two species in the Allonemobius socius complex. My results suggest the following: (1) spermathecal duct length varies between species and is associated with species boundaries, (2) there is considerable variation among populations within species, (3) there is a Wolbachia infection-by-population interaction effect on the length of the spermathecal duct, and (4) experimental curing of Wolbachia recovers the uninfected morphology. These findings suggest the following hypotheses: (1) spermathecal duct length, like other fertilization traits in Allonemobius, is evolving rapidly and influences reproductive isolation and (2) Wolbachia-induced modifications of this duct could influence the dynamics of male-female coevolution. Further experiments are needed, however, to explicitly test these latter two hypotheses.     

Metabonomics in pharmaceutical R&D

This minireview is based on a lecture given at the First Maga Circe Conference on metabolomics held at Sabaudia, Italy, in March 2006 in which the analytical and statistical techniques used in metabonomics, efforts at standardization and some of the major applications to pharmaceutical research and development are reviewed. Metabonomics involves the determination of multiple metabolites simultaneously in biofluids, tissues and tissue extracts. Applications to preclinical drug safety studies are illustrated by the Consortium for Metabonomic Toxicology, a collaboration involving several major pharmaceutical companies. This consortium was able, through the measurement of a dataset of NMR spectra of rodent urine and serum samples, to build a predictive expert system for liver and kidney toxicity. A secondary benefit was the elucidation of the endogenous biochemicals responsible for the classification. The use of metabonomics in disease diagnosis and therapy monitoring is discussed with an exemplification from coronary artery disease, and the concept of pharmaco-metabonomics as a way of predicting an individual's response to treatment is exemplified. Finally, some advantages and perceived difficulties of the metabonomics approach are summarized.