This paper applies methods of multiple resolution map comparison to quantify characteristics for 13 applications of 9 different popular peer-reviewed land change models. Each modeling application simulates change of land categories in raster maps from an initial time to a subsequent time. For each modeling application, the statistical methods compare: (1) a reference map of the initial time, (2) ence map of the subsequent time, and (3) a prediction map of the subsequent time. The three possible two-map comparisons for each application characterize: (1) the dynamics of the landscape, (2) the behavior of the model, and (3) the accuracy of the prediction. The three-map comparison for each application specifies the amount of the prediction's accuracy that is attributable to land persistence versus land change. Results show that the amount of error is larger than the amount of correctly predicted change for 12 of the 13 applications at the resolution of the raw data. The applications are summarized and compared using two statistics: the null resolution and the figure of merit. According to the figure of merit, the more accurate applications are the 123Comparing the input, output, and validation maps for several models of land change 13 ones where the amount of observed net change in the reference maps is larger. This paper facilitates communication among land change modelers, because it illustrates the range of results for a variety of models using scientifically rigorous, generally applicable, and intellectually accessible statistical techniques. JEL Classification

Despite recent advances in characterizing the regulation of histone H3 lysine 4 (H3-K4) methylation at the GAL1 gene by the H2B-K123-specific deubiquitinase activity of Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-acetyltransferase)-associated Ubp8p, our knowledge on the general role of Ubp8p at the SAGA-dependent genes is lacking. For this study, using a formaldehyde-based in vivo cross-linking and chromatin immunoprecipitation (ChIP) assay, we have analyzed the role of Ubp8p in the regulation of H3-K4 methylation at three other SAGA-dependent yeast genes, namely, PHO84, ADH1, and CUP1. Like that at GAL1, H3-K4 methylation is increased at the PHO84 core promoter in the UBP8 deletion mutant. We also show that H3-K4 methylation remains invariant at the PHO84 open reading frame in the ⌬ubp8 mutant, demonstrating a highly localized role of Upb8p in regulation of H3-K4 methylation at the promoter in vivo. However, unlike that at PHO84, H3-K4 methylation at the two other SAGA-dependent genes is not controlled by Ubp8p. Interestingly, Ubp8p and H3-K4 methylation are dispensable for preinitiation complex assembly at the core promoters of these genes. Our ChIP assay further demonstrates that the association of Ubp8p with SAGA is mediated by Sgf11p, consistent with recent biochemical data. Collectively, the data show that Ubp8p differentially controls H3-K4 methylation at the SAGA-dependent promoters, revealing a complex regulatory network of histone methylation in vivo.Transcription is a highly coordinated and orchestrated process. It takes place on the DNA template that is packaged into chromatin in the nucleus. The chromatin is an array of nucleosomes in which 146 base pairs of DNA (in each nucleosome) are wrapped around the histone octamer (27). Each octamer consists of two molecules each of the histones H2A, H2B, H3, and H4 (27). Nucleosomal arrays fold into a 30-nm fiber upon incorporation of the linker histone H1 (19,22).Histones are subject to posttranslational modifications such as acetylation, phosphorylation, ubiquitination, and methylation, and these modifications are known to play important roles in epigenetic regulation of transcription (33,44). Most modifications were originally observed on the N-terminal tails of histones, with the exception of ubiquitination, which occurs on the C-terminal tails of H2A and H2B (13). However, several novel posttranslational modifications have been identified recently in the core region of the histones (45). Histone modifications alter DNA-histone interactions within and between nucleosomes, and thus they affect the higher-order chromatin structure. Alternatively, combinations of histone modifications present an interaction surface for other proteins that translate the so-called "histone code" into a gene expression pattern (42), explaining how the same chemical modification can have different functional consequences depending on the target amino acid residue.Methylation of histone H3 at lysine 4 (K4) is associated with active chromatin in a wide range of eukaryotic organis...

Elevated atmospheric CO2 (eCO2) enhances the yield of vegetables and could also affect their nutritional quality. We conducted a meta-analysis using 57 articles consisting of 1,015 observations and found that eCO2 increased the concentrations of fructose, glucose, total soluble sugar, total antioxidant capacity, total phenols, total flavonoids, ascorbic acid, and calcium in the edible part of vegetables by 14.2%, 13.2%, 17.5%, 59.0%, 8.9%, 45.5%, 9.5%, and 8.2%, respectively, but decreased the concentrations of protein, nitrate, magnesium, iron, and zinc by 9.5%, 18.0%, 9.2%, 16.0%, and 9.4%. The concentrations of titratable acidity, total chlorophyll, carotenoids, lycopene, anthocyanins, phosphorus, potassium, sulfur, copper, and manganese were not affected by eCO2. Furthermore, we propose several approaches to improving vegetable quality based on the interaction of eCO2 with various factors, including species, cultivars, CO2 levels, growth stages, light, O3 stress, nutrient, and salinity. Finally, we present a summary of the eCO2 impact on the quality of three widely cultivated crops, namely, lettuce, tomato, and potato.

SummaryA system where archaeal gene expression could be controlled by simple manipulation of growth conditions would enable the construction of conditional lethal mutants in essential genes, and permit the controlled overproduction of proteins in their native host. As tools for the genetic manipulation of Haloferax volcanii are well developed, we set out to identify promoters with a wide dynamic range of expression in this organism. Tryptophan is the most costly amino acid for the cell to make, so we reasoned that tryptophan-regulated promoters might be good candidates. Microarray analysis of H. volcanii gene expression in the presence and absence of tryptophan identified a tryptophanase gene (tna) that showed strong induction in the presence of tryptophan. qRT-PCR revealed a very fast response and an up to 100-fold induction after tryptophan addition. This result has been confirmed using three independent reporter genes (cct1, pyrE2 and bgaH). Vectors containing this promoter will be very useful for investigating gene function in H. volcanii and potentially in other halophilic archaea. To demonstrate this, we used the promoter to follow the consequences of depletion of the essential chaperonin protein CCT1, and to determine the ability of heterologous CCT proteins to function in H. volcanii.