Quantitative Trait Loci Mapping and The Genetic Basis of Heterosis in Maize and Rice

Despite its importance to agriculture, the genetic basis of heterosis is still not well understood. The main competing hypotheses include dominance, overdominance, and epistasis. NC design III is an experimental design that. has been used for estimating the average degree of dominance of quantitative trait 106 (QTL) and also for studying heterosis. In this study, we first develop a multiple-interval mapping (MIM) model for design III that provides a platform to estimate the number, genomic positions, augmented additive and dominance effects, and epistatic interactions of QTL. The model can be used for parents with any generation of selling. We apply the method to two data sets, one for maize and one for rice. Our results show that heterosis in maize is mainly due to dominant gene action, although overdominance of individual QTL could not completely be ruled out due to the mapping resolution and limitations of NC design III. For rice, the estimated QTL dominant effects could not explain the observed heterosis. There is evidence that additive X additive epistatic effects of QTL could be the main cause for the heterosis in rice. The difference in the genetic basis of heterosis seems to be related to open or self pollination of the two species. The MIM model for NC design III is implemented in Windows QTL Cartographer, a freely distributed software.

Can native vegetation recover after slash pine cultivation in the Brazilian Savanna?

There is a widespread view that forest plantations with exotic species are green deserts, unable to sustain biodiversity. Few studies have demonstrated, however, that planted stands of exotic trees have a greater negative effect on the plant diversity of savanna vegetation. We compared the native woody flora under four stands of slash pine of about 45 years old with four stands where the previously existing native Cerrado vegetation was preserved and protected from disturbances for the same period, has changed into dense vegetation - the ""cerradao"", at Assis municipality, Sao Paulo State, Brazil. Aiming at understanding the potential ecological filters driving these communities, we assessed air and soil humidity, light availability and classified the native species on the basis of shade tolerance, dispersal syndrome and biomes in which they occur (Atlantic Forest or Cerrado). We recorded an average of 70 (+/- 13) species under pine stands and 54 (+/- 16) species in cerradao. Of the total of 136 species recorded, 78 occurred in both habitats, eight were exclusive to the ""cerradao"" (shade tolerant and also occurring in forest ecosystems) and 18 were recorded only under pine stands (82% heliophytic, exclusive to the Cerrado biome). Among the functional attributes and abiotic variables analyzed, only light availability explained the floristic differences found. Since richness was higher under pine, we refuted the hypothesis that exotic species constrain the establishment of the native species richness in the understory. On the other hand, the dark environment under the closed-canopy of the ""cerradao"" acts as a filter inhibiting the establishment of typical Cerrado species. Since pine stands, if managed in long cycle, maintain a reasonable pool of Cerrado endemic species in the understory pine plantations may be a good starting point for savanna restoration. (C) 2011 Elsevier B.V. All rights reserved.

Relating MODIS vegetation index time-series with structure, light absorption and stem production of fast-growing Eucalyptus plantations

By allowing the estimation of forest structural and biophysical characteristics at different temporal and spatial scales, remote sensing may contribute to our understanding and monitoring of planted forests. Here, we studied 9-year time-series of the Normalized Difference Vegetation Index (NDVI) from the Moderate Resolution Imaging Spectroradiometer (MODIS) on a network of 16 stands in fast-growing Eucalyptus plantations in Sao Paulo State, Brazil. We aimed to examine the relationships between NDVI time-series spanning entire rotations and stand structural characteristics (volume, dominant height, mean annual increment) in these simple forest ecosystems. Our second objective was to examine spatial and temporal variations of light use efficiency for wood production, by comparing time-series of Absorbed Photosynthetically Active Radiation (APAR) with inventory data. Relationships were calibrated between the NDVI and the fractions of intercepted diffuse and direct radiation, using hemispherical photographs taken on the studied stands at two seasons. APAR was calculated from the NDVI time-series using these relationships. Stem volume and dominant height were strongly correlated with summed NDVI values between planting date and inventory date. Stand productivity was correlated with mean NDVI values. APAR during the first 2 years of growth was variable between stands and was well correlated with stem wood production (r(2) = 0.78). In contrast, APAR during the following years was less variable and not significantly correlated with stem biomass increments. Production of wood per unit of absorbed light varied with stand age and with site index. In our study, a better site index was accompanied both by increased APAR during the first 2 years of growth and by higher light use efficiency for stem wood production during the whole rotation. Implications for simple process-based modelling are discussed. (C) 2009 Elsevier B.V. All rights reserved.

3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents

Tuberculosis (TB) is the primary cause of mortality among infectious diseases. Mycobacterium tuberculosis monophosphate kinase (TMPKmt) is essential to DNA replication. Thus, this enzyme represents a promising target for developing new drugs against TB. In the present study, the receptor-independent, RI, 4D-QSAR method has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 81 thymidine analogues, and two corresponding subsets, reported as inhibitors of TMPKmt. The resulting optimized models are not only statistically significant with r (2) ranging from 0.83 to 0.92 and q (2) from 0.78 to 0.88, but also are robustly predictive based on test set predictions. The most and the least potent inhibitors in their respective postulated active conformations, derived from each of the models, were docked in the active site of the TMPKmt crystal structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. Moreover, the QSAR models provide insights regarding a probable mechanism of action of the analogues.

Rational Design and 3D-Pharmacophore Mapping of 5 `-Thiourea-Substituted alpha-Thymidine Analogues as Mycobacterial TMPK Inhibitors

Thymidine monophosphate kinase (TMPK) has emerged as an attractive target for developing inhibitors of Mycobacterium tuberculosis growth. In this study the receptor-independent (RI) 4D-QSAR formalism has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 5`-thiourea-substituted alpha-thymidine inhibitors. Models were developed for the entire training set and for a subset of the training set consisting of the most potent inhibitors. The optimized (RI) 4D-QSAR models are statistically significant (r(2) = 0.90, q(2) = 0.83 entire set, r(2) = 0.86, q(2) = 0.80 high potency subset) and also possess good predictivity based on test set predictions. The most and least potent inhibitors, in their respective postulated active conformations derived from the models, were docked in the active site of the TMPK crystallographic structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. This model identifies new regions of the inhibitors that contain pharmacophore sites, such as the sugar-pyrimidine ring structure and the region of the 5`-arylthiourea moiety. These new regions of the ligands can be further explored and possibly exploited to identify new, novel, and, perhaps, better antituberculosis inhibitors of TMPKmt. Furthermore, the 3D-pharmacophores defined by these models can be used as a starting point for future receptor-dependent antituberculosis drug design as well as to elucidate candidate sites for substituent addition to optimize ADMET properties of analog inhibitors.

The emergence of the determiner system in Mauritian Creole: a syntax semantics mapping

This paper describes the emergence of new functional items in the Mauritian Creole noun phrase, following the collapse of the French determiner system when superstrate and substrate came into contact. The aim of the paper is to show how the new language strived to express the universal semantic contrasts of (in)definiteness and singular vs. plural. The process of grammaticalization of new functional items in the determiner system was accompanied by changes in the syntax from French to creole. An analysis within Chomsky’s Minimalist framework (1995, 2000, 2001) suggests that these changes were driven by the need to map semantic features onto the syntax.

Remotely sensed estimates of vegetation structural characteristics in restored wetlands, Southern California

Traditional field sampling approaches for ecological studies of restored habitat can only cover small areas in detail, con be time consuming, and are often invasive and destructive. Spatially extensive and non-invasive remotely sensed data can make field sampling more focused and efficient. The objective of this work was to investigate the feasibility and accuracy of hand-held and airborne remotely sensed data to estimate vegetation structural parameters for an indicator plant species in a restored wetland. High spatial resolution, digital, multispectral camera images were captured from an aircraft over Sweetwater Marsh (San Diego County, California) during each growing season between 1992-1996. Field data were collected concurrently, which included plant heights, proportional ground cover and canopy architecture type, and spectral radiometer measurements. Spartina foliosa (Pacific cordgrass) is the indicator species for the restoration monitoring. A conceptual model summarizing the controls on the spectral reflectance properties of Pacific cordgrass was established. Empirical models were developed relating the stem length, density, and canopy architecture of cordgrass to normalized-difference-vegetation-index values. The most promising results were obtained from empirical estimates of total ground cover using image data that had been stratified into high, middle, and low marsh zones. As part of on-going restoration monitoring activities, this model is being used to provide maps of estimated vegetation cover.

A framework to monitor sustainability in the grains industry

Community awareness of the sustainable use of land, water and vegetation resources is increasing. The sustainable use of these resources is pivotal to sustainable farming systems. However, techniques for monitoring the sustainable management of these resources are poorly understood and untested. We propose a framework to benchmark and monitor resources in the grains industry. Eight steps are listed below to achieve these objectives: (i) define industry issues; (ii) identify the issues through growers, stakeholder and community consultation; (iii) identify indicators (measurable attributes, properties or characteristics) of sustainability through consultation with growers, stakeholders, experts and community members, relating to: crop productivity; resource maintenance/enhancement; biodiversity; economic viability; community viability; and institutional structure; (iv) develop and use selection criteria to select indicators that consider: responsiveness to change; ease of capture; community acceptance and involvement; interpretation; measurement error; stability, frequency and cost of measurement; spatial scale issues; and mapping capability in space and through time. The appropriateness of indicators can be evaluated using a decision making system such as a multiobjective decision support system (MO-DSS, a method to assist in decision making from multiple and conflicting objectives); (v) involve stakeholders and the community in the definition of goals and setting benchmarking and monitoring targets for sustainable farming; (vi) take preventive and corrective/remedial action; (vii) evaluate effectiveness of actions taken; and (viii) revise indicators as part of a continual improvement principle designed to achieve best management practice for sustainable farming systems. The major recommendations are to: (i) implement the framework for resources (land, water and vegetation, economic, community and institution) benchmarking and monitoring, and integrate this process with current activities so that awareness, implementation and evolution of sustainable resource management practices become normal practice in the grains industry; (ii) empower the grains industry to take the lead by using relevant sustainability indicators to benchmark and monitor resources; (iii) adopt a collaborative approach by involving various industry, community, catchment management and government agency groups to minimise implementation time. Monitoring programs such as Waterwatch, Soilcheck, Grasscheck and Topcrop should be utilised; (iv) encourage the adoption of a decision making system by growers and industry representatives as a participatory decision and evaluation process. Widespread use of sustainability indicators would assist in validating and refining these indicators and evaluating sustainable farming systems. The indicators could also assist in evaluating best management practices for the grains industry.

Molecular cloning and chromosomal mapping of the human homologue of MYB binding protein (P160) 1A (MYBBP1A) to 17p13.3

We have previously isolated and characterized murine MYB binding protein (p160) 1a, a protein that specifically interacts with the leucine zipper motif within the negative regulatory domain of the c-Myb proto-oncoprotein, We now describe the molecular cloning of the human MYBBP1A cDNA and chromosomal localization to 17p13.3 by fluorescence in situ hybridization analysis, Given the likely presence of a tumor suppressor gene (or genes) within this region of chromosome 17, the position of MYBBP1A was further mapped by radiation hybrid analysis and was found to lie between markers D17S1828 and D17S938. A P1 artificial chromosome clone containing the 5' region of MYBBP1A was isolated and indicates a physical linkage between MYBBP1A and the 15-lipoxygenase gene (ALOX15), A novel, polymorphic (CA)(25) dinucleotide repeat was also isolated from this PAC and may serve as a useful marker for MYBBP1A and this region of chromosome 17. (C) 1999 Academic Press.

Determining forest structural attributes using an inverted geometric-optical model in mixed eucalypt forests, Southeast Queensland, Australia

The Montreal Process indicators are intended to provide a common framework for assessing and reviewing progress toward sustainable forest management. The potential of a combined geometrical-optical/spectral mixture analysis model was assessed for mapping the Montreal Process age class and successional age indicators at a regional scale using Landsat Thematic data. The project location is an area of eucalyptus forest in Emu Creek State Forest, Southeast Queensland, Australia. A quantitative model relating the spectral reflectance of a forest to the illumination geometry, slope, and aspect of the terrain surface and the size, shape, and density, and canopy size. Inversion of this model necessitated the use of spectral mixture analysis to recover subpixel information on the fractional extent of ground scene elements (such as sunlit canopy, shaded canopy, sunlit background, and shaded background). Results obtained fron a sensitivity analysis allowed improved allocation of resources to maximize the predictive accuracy of the model. It was found that modeled estimates of crown cover projection, canopy size, and tree densities had significant agreement with field and air photo-interpreted estimates. However, the accuracy of the successional stage classification was limited. The results obtained highlight the potential for future integration of high and moderate spatial resolution-imaging sensors for monitoring forest structure and condition. (C) Elsevier Science Inc., 2000.

Ecological interface design for pasteurizer II: A process description of semantic mapping

Ecological interface design (EID) is proving to be a promising approach to the design of interfaces for complex dynamic systems. Although the principles of EID and examples of its effective use are widely available, few readily available examples exist of how the individual displays that constitute an ecological interface are developed. This paper presents the semantic mapping process within EID in the context of prior theoretical work in this area. The semantic mapping process that was used in developing an ecological interface for the Pasteurizer II microworld is outlined, and the results of an evaluation of the ecological interface against a more conventional interface are briefly presented. Subjective reports indicate features of the ecological interface that made it particularly valuable for participants. Finally, we outline the steps of an analytic process for using EID. The findings presented here can be applied in the design of ecological interfaces or of configural displays for dynamic processes.