Multispecies coexistence of trees in tropical forests: spatial signals of topographic niche differentiation increase with environmental heterogeneity

Neutral and niche theories give contrasting explanations for the maintenance of tropical tree species diversity. Both have some empirical support, but methods to disentangle their effects have not yet been developed. We applied a statistical measure of spatial structure to data from 14 large tropical forest plots to test a prediction of niche theory that is incompatible with neutral theory: that species in heterogeneous environments should separate out in space according to their niche preferences. We chose plots across a range of topographic heterogeneity, and tested whether pairwise spatial associations among species were more variable in more heterogeneous sites. We found strong support for this prediction, based on a strong positive relationship between variance in the spatial structure of species pairs and topographic heterogeneity across sites. We interpret this pattern as evidence of pervasive niche differentiation, which increases in importance with increasing environmental heterogeneity.     

Measurements of gross and net ecosystem productivity and water vapour exchange of a Pinus ponderosa ecosystem,and an evaluation of two generalized models

Net ecosystem productivity (NEP), net primary productivity (NPP), and water vapour exchange of a mature Pinus ponderosa forest (44°30′ N, 121°37′ W) growing in a region subject to summer drought were investigated along with canopy assimilation and respiratory fluxes. This paper describes seasonal and annual variation in these factors, and the evaluation of two generalized models of carbon and water balance (PnET‐II and 3‐PG) with a combination of traditional measurements of NPP, respiration and water stress, and eddy covariance measurements of above‐and below‐canopy CO₂ and water vapour exchange. The objective was to evaluate the models using two years of traditional and eddy covariance measurements, and to use the models to help interpret the relative importance of processes controlling carbon and water vapour exchange in a water‐limited pine ecosystem throughout the year. PnET‐II is a monthly time‐step model that is driven by nitrogen availability through foliar N concentration, and 3‐PG is a monthly time‐step quantum‐efficiency model constrained by extreme temperatures, drought, and vapour pressure deficits. Both models require few parameters and have the potential to be applied at the watershed to regional scale. There was 2/3 less rainfall in 1997 than in 1996, providing a challenge to modelling the water balance, and consequently the carbon balance, when driving the models with the two years of climate data, sequentially. Soil fertility was not a key factor in modelling processes at this site because other environmental factors limited photosynthesis and restricted projected leaf area index to ～1.6. Seasonally, GEP and LE were overestimated in early summer and underestimated through the rest of the year. The model predictions of annual GEP, NEP and water vapour exchange were within 1–39% of flux measurements, with greater disparity in 1997 because soil water never fully recharged. The results suggest that generalized models can provide insights to constraints on productivity on an annual basis, using a minimum of site data.     

SRA-Domain Proteins Required for DRM2-Mediated De Novo DNA Methylation

De novo DNA methylation and the maintenance of DNA methylation in asymmetrical sequence contexts is catalyzed by homologous proteins in plants (DRM2) and animals (DNMT3a/b). In plants, targeting of DRM2 depends on small interfering RNAs (siRNAs), although the molecular details are still unclear. Here, we show that two SRA-domain proteins (SUVH9 and SUVH2) are also essential for DRM2-mediated de novo and maintenance DNA methylation in Arabidopsis thaliana. At some loci, SUVH9 and SUVH2 act redundantly, while at other loci only SUVH2 is required, and this locus specificity correlates with the differing DNA-binding affinity of the SRA domains within SUVH9 and SUVH2. Specifically, SUVH9 preferentially binds methylated asymmetric sites, while SUVH2 preferentially binds methylated CG sites. The suvh9 and suvh2 mutations do not eliminate siRNAs, suggesting a role for SUVH9 and SUVH2 late in the RNA-directed DNA methylation pathway. With these new results, it is clear that SRA-domain proteins are involved in each of the three pathways leading to DNA methylation in Arabidopsis.     

The N terminus of the serpin, tengpin, functions to trap the metastable native state

Serpins fold to a metastable native state and are susceptible to undergoing spontaneous conformational change to more stable conformers, such as the latent form. We investigated conformational change in tengpin, an unusual prokaryotic serpin from the extremophile Thermoanaerobacter tengcongensis. In addition to the serpin domain, tengpin contains a functionally uncharacterized 56-amino-acid amino-terminal region. Deletion of this domain creates a variant--tengpinDelta51--which folds past the native state and readily adopts the latent conformation. Analysis of crystal structures together with mutagenesis studies show that the N terminus of tengpin protects a hydrophobic patch in the serpin domain and functions to trap tengpin in its native metastable state. A 13-amino-acid peptide derived from the N terminus is able to mimick the role of the N terminus in stabilizing the native state of tengpinDelta51. Therefore, the function of the N terminus in tengpin resembles protein cofactors that prevent mammalian serpins from spontaneously adopting the latent conformation.     

Estrogen controls embryonic stem cell proliferation via store-operated calcium entry and the nuclear factor of activated T-cells (NFAT)

Embryonic stem cells (ESCs) can self-renew indefinitely and differentiate into all cell lineages. Calcium is a universal second messenger which regulates a number of cellular pathways. Previous studies showed that store-operated calcium channels (SOCCs) but not voltage-operated calcium channels are present in mouse ESCs (mESCs). In this study, store-operated calcium entry (SOCE) was found to exist in mESCs using confocal microscopy. SOCC blockers lanthanum, 2-aminoethoxydiphenyl borate (2-APB) and SKF-96365 reduced mESC proliferation in a concentration-dependent manner, suggesting that SOCE is important for ESC proliferation. Pluripotent markers, Sox-2, Klf-4, and Nanog, were down-regulated by 2-APB, suggesting that self-renewal property of mESCs relies on SOCE. 17β-estradiol (E2) enhanced mESC proliferation. This enhanced proliferation was associated with an increment of SOCE. Both stimulated proliferation and increased SOCE could be reversed by SOCC blockers suggesting that E2 mediates its stimulatory effect on proliferation via enhancing SOCE. Also, cyclosporin A and INCA-6, inhibitors of calcineurin [phosphatase that de-phosphorylates and activates nuclear factor of activated T-cells (NFAT)], reversed the proliferative effect of E2, indicating that NFAT is involved in E2-stimulated proliferation. Interestingly, E2 caused the nuclear translocation of NFATc4, and this could be reversed by 2-APB. These results suggested that NFATc4 is the downstream target of E2-induced SOCE. The present investigation provides the first line of evidence that SOCE and NFAT are crucial for ESCs to maintain their unique characteristics. In addition, the present investigation also provides novel information on the mechanisms of how E2, an important female sex hormone, affects ESC proliferation.     

Assessing Musical Abilities Objectively: Construction and Validation of the Profile of Music Perception Skills

A common approach for determining musical competence is to rely on information about individuals’ extent of musical training, but relying on musicianship status fails to identify musically untrained individuals with musical skill, as well as those who, despite extensive musical training, may not be as skilled. To counteract this limitation, we developed a new test battery (Profile of Music Perception Skills; PROMS) that measures perceptual musical skills across multiple domains: tonal (melody, pitch), qualitative (timbre, tuning), temporal (rhythm, rhythm-to-melody, accent, tempo), and dynamic (loudness). The PROMS has satisfactory psychometric properties for the composite score (internal consistency and test-retest r>.85) and fair to good coefficients for the individual subtests (.56 to.85). Convergent validity was established with the relevant dimensions of Gordon’s Advanced Measures of Music Audiation and Musical Aptitude Profile (melody, rhythm, tempo), the Musical Ear Test (rhythm), and sample instrumental sounds (timbre). Criterion validity was evidenced by consistently sizeable and significant relationships between test performance and external musical proficiency indicators in all three studies (.38 to.62, p<.05 to p<.01). An absence of correlations between test scores and a nonmusical auditory discrimination task supports the battery’s discriminant validity (−.05, ns). The interrelationships among the various subtests could be accounted for by two higher order factors, sequential and sensory music processing. A brief version of the full PROMS is introduced as a time-efficient approximation of the full version of the battery.     

Negative effects of agrocin 84-encoding Agrobacterium plasmids on symbiotic properties of Rhizobium meliloti

Two plasmids, pAgK84::Tn5-Mob from Agrobacterium radiobacter carrying genes for the production of agrocin 84, and RP4-4 from E. coli were inserted either separately or together into a strain of Rhizobium meliloti. Each of these plasmid-containing R. meliloti transconjugants was less effective than the wild type strain in their ability to fix nitrogen in Medicago tornata. The pAgK84::Tn5-Mob-containing transconjugant was significantly less effective than that containing RP4-4. The transconjugant strains were inferior to the wild type strain in their ability to nodulate seedlings and to compete for nodulation.