On the ratio of intercellular to ambient CO2 (c i/c a) derived from ecosystem flux.

The ratio of intercellular to ambient CO2 concentrations (c i/c a) plays a key role in ecophysiology, micrometeorology, and global climatic change. However, systematic investigation on c i/c a variation and its determinants are rare. Here, the c i/c a was derived from measuring ecosystem fluxes in an even-aged monoculture of rubber trees (Hevea brasiliensis). We tested whether c i/c a is constant across environmental gradients and if not, which dominant factors control c i/c a variations. Evidence indicates that c i/c a is not a constant. The c i/c a exhibits a clear "V"-shaped diurnal pattern and varies across the environmental gradient. Water vapor pressure deficit (D) is the dominant factor controls over the c i/c a variations. c i/c a consistently decreases with increasing D. c i/c a decreases with square root of D as predicted by the optimal stomatal model. The D-driving single-variable model could simulate c i/c a as well as that of sophisticated model. Many variables function on longer timescales than a daily cycle, such as soil water content, could improve c i/c a model prediction ability. Ecosystem flux can be effectively used to calculate c i/c a and use it to better understand various natural cycles.

Use of fluorescent DNA-templated gold/silver nanoclusters for the detection of sulfide ions.

We have developed a one-pot approach to prepare fluorescent DNA-templated gold/silver nanoclusters (DNA-Au/Ag NCs) from Au(3+), Ag(+), and DNA (5'-CCCTTAATCCCC-3') in the presence of NaBH(4) in order to detect sulfide (S(2-)) ions on the basis of fluorescence quenching. The as-prepared DNA-Au/Ag NCs have been characterized by UV-vis absorption, fluorescence, circular dichroism, X-ray photoelectron spectroscopy, and electrospray ionization-mass spectrometry measurements. Relative to DNA-Ag NCs, DNA-Au/Ag NCs are much more stable in high ionic strength media (e.g., 200 mM NaCl). The quantum yield of the as-prepared DNA-Au/Ag NCs is 4.5%. We have demonstrated that the fluorescence of DNA-Au/Ag NCs is quenched by S(2-) ions through the interaction between sulfide ions and gold/silver atoms/ions, a result which leads to changes in the conformation of the templated DNA from packed hairpin to random coil structures. These changes in fluorescence intensity allow sensitive detection of S(2-) ions at concentrations as low as 0.83 nM. To minimize interference from I(-) ions for the detection of S(2-) ions using the DNA-Au/Ag NCs, the addition of sodium peroxydisulfate to the solution is essential. We have validated the practicality of this probe for the detection of S(2-) ions in hot spring and seawater samples, demonstrating its advantages of simplicity, sensitivity, selectivity, and low cost.

Characterization and application to the detection of single-stranded DNA binding protein of fluorescent DNA-templated copper/silver nanoclusters.

A simple strategy for the preparation of strongly fluorescent and stable DNA-Cu/Ag NCs from reduction of AgNO(3) and Cu(NO(3))(2) by NaBH(4) in the presence of DNA having a sequence 5'-CCCTTAATCCCC-3' has been demonstrated. Fluorescence, absorption, X-ray photoelectron spectroscopy (XPS), and electrospray ionization-mass spectrometry (ESI-MS) measurements have been applied to the characterization of the DNA-Cu/Ag NCs. The ESI-MS data reveal that each DNA-Cu/Ag NC contained 2 Ag and 1 Cu atoms. The interactions among DNA with the Ag and Cu atoms are further supported by the data of low-temperature fluorescence. In the presence of Cu(2+) ions, the reaction time is 1.5 h, which is much shorter than that (120 h) for the preparation of Ag-DNA NCs that are prepared in a mixture of AgNO(3), NaBH(4) and DNA without containing Cu(2+) ions. Relative to the DNA-Ag NCs, the DNA-Cu/Ag NCs have greater fluorescence (quantum yield 51.2% vs. 11.5%). The DNA-Cu/Ag NCs are highly sensitive and selective for the detection of single-stranded DNA binding protein (SSB), with a linear range 1-50 nM and a limit of detection 0.2 nM at a signal-to-ratio of 3.

Detection of copper ions through recovery of the fluorescence of DNA-templated copper/silver nanoclusters in the presence of mercaptopropionic acid.

We have developed a simple and homogeneous fluorescence assay, comprised of 3-mercaptopropionic acid (MPA) and DNA-Cu/Ag nanoclusters (NCs) in aqueous solution, for the detection of Cu(2+) ions. The fluorescence of the DNA-Cu/Ag NCs was quenched by MPA, which was recovered in the presence of Cu(2+) ions. This MPA-induced fluorescence quenching arises through changes in the DNA conformation that occur after interactions between MPA and the Cu/Ag clusters. The MPA-induced fluorescence quenching displayed typical characteristics in Stern-Volmer plots; it followed a static quenching mechanism. The presence of Cu(2+) ions resulted in the oxidation of MPA to form a disulfide compound, leading to recovery of the fluorescence of the DNA-Cu/Ag NCs. The fluorescence of the DNA-Cu/Ag NCs in the presence of MPA increased upon increasing the concentration of Cu(2+) ions over the range from 5 to 200 nM. The DNA-Cu/Ag NC probe provided the limit of detection (at a signal-to-noise ratio of 3) for Cu(2+) ions of 2.7 nM, with high selectivity (by at least 2300-fold over other tested metal ions). We validated the practicality of using this probe for the detection of Cu(2+) ions in environmental samples through analyses of Montana soil and pond water samples.

Size-class effect contributes to tree species assembly through influencing dispersal in tropical forests.

We have investigated the processes of community assembly using size classes of trees. Specifically our work examined (1) whether point process models incorporating an effect of size-class produce more realistic summary outcomes than do models without this effect; (2) which of three selected models incorporating, respectively environmental effects, dispersal and the joint-effect of both of these, is most useful in explaining species-area relationships (SARs) and point dispersion patterns. For this evaluation we used tree species data from the 50-ha forest dynamics plot in Barro Colorado Island, Panama and the comparable 20 ha plot at Bubeng, Southwest China. Our results demonstrated that incorporating an size-class effect dramatically improved the SAR estimation at both the plots when the dispersal only model was used. The joint effect model produced similar improvement but only for the 50-ha plot in Panama. The point patterns results were not improved by incorporation of size-class effects using any of the three models. Our results indicate that dispersal is likely to be a key process determining both SARs and point patterns. The environment-only model and joint-effects model were effective at the species level and the community level, respectively. We conclude that it is critical to use multiple summary characteristics when modelling spatial patterns at the species and community levels if a comprehensive understanding of the ecological processes that shape species' distributions is sought; without this results may have inherent biases. By influencing dispersal, the effect of size-class contributes to species assembly and enhances our understanding of species coexistence.

Strong neutral spatial effects shape tree species distributions across life stages at multiple scales.

Traditionally, ecologists use lattice (regional summary) count data to simulate tree species distributions to explore species coexistence. However, no previous study has explicitly compared the difference between using lattice count and basal area data and analyzed species distributions at both individual species and community levels while simultaneously considering the combined scenarios of life stage and scale. In this study, we hypothesized that basal area data are more closely related to environmental variables than are count data because of strong environmental filtering effects. We also address the contribution of niche and the neutral (i.e., solely dependent on distance) factors to species distributions. Specifically, we separately modeled count data and basal area data while considering life stage and scale effects at the two levels with simultaneous autoregressive models and variation partitioning. A principal coordinates of neighbor matrix (PCNM) was used to model neutral spatial effects at the community level. The explained variations of species distribution data did not differ significantly between the two types of data at either the individual species level or the community level, indicating that the two types of data can be used nearly identically to model species distributions. Neutral spatial effects represented by spatial autoregressive parameters and the PCNM eigenfunctions drove species distributions on multiple scales, different life stages and individual species and community levels in this plot. We concluded that strong neutral spatial effects are the principal mechanisms underlying the species distributions and thus shape biodiversity spatial patterns.

One-pot synthesis of fluorescent oligonucleotide Ag nanoclusters for specific and sensitive detection of DNA.

In this study, we prepared fluorescent, functional oligonucleotide-stabilized silver nanoclusters (FFDNA-Ag NCs) through one-pot synthesis and then employed them as probes for single nucleotide polymorphisms (SNPs). The FFDNA-Ag NCs were obtained through the NaBH(4)-mediated reduction of AgNO(3) in the presence of a DNA strand having the sequence 5'-C(12)-CCAGATACTCACCGG-3'. The specific DNA scaffold combines a fluorescent base motif (C(12)) and a specific sequence (CCAGATACTCACCGG) that recognizes a gene for fumarylacetoacetate hydrolase (FAH). The sensing mechanism of our new probe is based on the FFDNA-Ag NCs having different stabilities (fluorescence intensities) in solutions containing 150 mM NaCl in the absence and presence of perfect match DNA (DNA(pmt)). Under the optimal conditions (150 mM NaCl, 20 mM phosphate solution, pH 7.0), the fluorescence ratios of the FFDNA-Ag NC probes in the presence and absence of DNA(pmt), plotted against the concentration of DNA(pmt), was linear over the range 25-1000 nM (R(2)=0.98), with a limit of detection (S/N=3) of 14 nM. This cost-effective and simple FFDNA-Ag NC probe is sensitive and selective for SNPs of a gene for FAH.

Silver nanoclusters as fluorescent probes for selective and sensitive detection of copper ions.

Fluorescent DNA-Ag NCs are demonstrated as novel, label-free, and turn-on fluorescence probes for Cu(2+) ions sensors. We also used this novel fluorescent probe to determine Cu(2+) ions in Montana soil (SRM 2710) and pond water.

Nanomaterial-based surface-assisted laser desorption/ionization mass spectrometry of peptides and proteins.

We have investigated six nanomaterials for their applicability as surfaces for the analyses of peptides and proteins using surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS). Gold nanoparticles (NPs) were useful nanomaterials for small analytes (e.g., glutathione); Pt nanosponges and Fe(3)O(4) NPs were efficient nanomaterials for proteins, with an upper detectable mass limit of ca. 25 kDa. Nanomaterials have several advantages over organic matrices, including lower limits of detection for small analytes and lower batch-to-batch variations (fewer problems associated with "sweet spots"), when used in laser desorption/ionization mass spectrometry.