Genetic analysis of kernel oil content in tropical maize with design III and QTL mapping

Oil content and grain yield in maize are negatively correlated, and so far the development of high-oil high-yielding hybrids has not been accomplished. Then a fully understand of the inheritance of the kernel oil content is necessary to implement a breeding program to improve both traits simultaneously. Conventional and molecular marker analyses of the design III were carried out from a reference population developed from two tropical inbred lines divergent for kernel oil content. The results showed that additive variance was quite larger than the dominance variance, and the heritability coefficient was very high. Sixteen QTL were mapped, they were not evenly distributed along the chromosomes, and accounted for 30.91% of the genetic variance. The average level of dominance computed from both conventional and QTL analysis was partial dominance. The overall results indicated that the additive effects were more important than the dominance effects, the latter were not unidirectional and then heterosis could not be exploited in crosses. Most of the favorable alleles of the QTL were in the high-oil parental inbred, which could be transferred to other inbreds via marker-assisted backcross selection. Our results coupled with reported information indicated that the development of high-oil hybrids with acceptable yields could be accomplished by using marker-assisted selection involving oil content, grain yield and its components. Finally, to exploit the xenia effect to increase even more the oil content, these hybrids should be used in the Top Cross((TM)) procedure.

Molecular Characterization and Physical Mapping of Two Classes of 5S rDNA in the Genomes of Gymnotus sylvius and G. inaequilabiatus (Gymnotiformes, Gymnotidae)

The nucleotide sequences of the 5S rRNA multigene family and their distribution across the karyotypes in 2 species of Gymnotiformes, genus Gymnotus (G. sylvius and G. inaequilabiatus) were investigated by means of fluorescence in situ hybridization (FISH). The results showed the existence of 2 distinct classes of 5S rDNA sequences in both species: class I and class II. A high conservative pattern of the codifying region of the 5S rRNA gene was identified, contrasting with significant alterations detected in the nontranscribed spacer (NTS). The presence of TATA-like sequences along the NTS of both species was an expected occurrence, since such sequences have been associated with the regulation of the gene expression. FISH using 5S rDNA class I and class II probes revealed that both gene classes were collocated in the same chromosome pair in the genome of G. sylvius, while in that of G. inaequilabiatus, class II appeared more disperse than class I. Copyright (C) 2012 S. Karger AG, Basel

Characterization of multiple reflections and phase space properties for a periodically corrugated waveguide

Dynamical properties for a beam light inside a sinusoidally corrugated waveguide are discussed in this paper. The beam is confined inside two-mirrors: one is flat and the other one is sinusoidally corrugated. The evolution of the system is described by the use of a two-dimensional and nonlinear mapping. The phase space of the system is of mixed type therefore exhibiting a large chaotic sea, periodic islands and invariant KAM curves. A careful discussion of the numerical method to solve the transcendental equations of the mapping is given. We characterize the probability of observing successive reflections of the light by the corrugated mirror and show that it is scaling invariant with respect to the amplitude of the corrugation. Average properties of the chaotic sea are also described by the use of scaling arguments.

Radiative transfer analyses of Titan's tropical atmosphere

Titan's optical and near-IR spectra result primarily from the scattering of sunlight by haze and its absorption by methane. With a column abundance of 92 km amagat (11 times that of Earth), Titan's atmosphere is optically thick and only similar to 10% of the incident solar radiation reaches the surface, compared to 57% on Earth. Such a formidable atmosphere obstructs investigations of the moon's lower troposphere and surface, which are highly sensitive to the radiative transfer treatment of methane absorption and haze scattering. The absorption and scattering characteristics of Titan's atmosphere have been constrained by the Huygens Probe Descent Imager/Spectral Radiometer (DISR) experiment for conditions at the probe landing site (Tomasko, M.G., Bezard, B., Doose, L., Engel, S., Karkoschka, E. 120084 Planet. Space Sci. 56, 624-247: Tomasko, M.G. et al. [2008b] Planet. Space Sci. 56, 669-707). Cassini's Visual and Infrared Mapping Spectrometer (VIMS) data indicate that the rest of the atmosphere (except for the polar regions) can be understood with small perturbations in the high haze structure determined at the landing site (Penteado, P.F., Griffith, CA., Tomasko, M.G., Engel, S., See, C., Doose, L, Baines, K.H., Brown, R.H., Buratti, B.J., Clark, R., Nicholson, P., Sotin, C. [2010]. Icarus 206, 352-365). However the in situ measurements were analyzed with a doubling and adding radiative transfer calculation that differs considerably from the discrete ordinates codes used to interpret remote data from Cassini and ground-based measurements. In addition, the calibration of the VIMS data with respect to the DISR data has not yet been tested. Here, VIMS data of the probe landing site are analyzed with the DISR radiative transfer method and the faster discrete ordinates radiative transfer calculation; both models are consistent (to within 0.3%) and reproduce the scattering and absorption characteristics derived from in situ measurements. Constraints on the atmospheric opacity at wavelengths outside those measured by DISR, that is from 1.6 to 5.0 mu m, are derived using clouds as diffuse reflectors in order to derive Titan's surface albedo to within a few percent error and cloud altitudes to within 5 km error. VIMS spectra of Titan at 2.6-3.2 mu m indicate not only spectral features due to CH4 and CH3D (Rannou, P., Cours, T., Le Mouelic, S., Rodriguez, S., Sotin, C., Drossart, P., Brown, R. [2010]. Icarus 208, 850-867), but also a fairly uniform absorption of unknown source, equivalent to the effects of a darkening of the haze to a single scattering albedo of 0.63 +/- 0.05. Titan's 4.8 mu m spectrum point to a haze optical depth of 0.2 at that wavelength. Cloud spectra at 2 mu m indicate that the far wings of the Voigt profile extend 460 cm(-1) from methane line centers. This paper releases the doubling and adding radiative transfer code developed by the DISR team, so that future studies of Titan's atmosphere and surface are consistent with the findings by the Huygens Probe. We derive the surface albedo at eight spectral regions of the 8 x 12 km(2) area surrounding the Huygens landing site. Within the 0.4-1.6 mu m spectral region our surface albedos match DISR measurements, indicating that DISR and VIMS measurements are consistently calibrated. These values together with albedos at longer 1.9-5.0 mu m wavelengths, not sampled by DISR, resemble a dark version of the spectrum of Ganymede's icy leading hemisphere. The eight surface albedos of the landing site are consistent with, but not deterministic of, exposed water ice with dark impurities. (C) 2011 Elsevier Inc. All rights reserved.

Mapeamento de solos e da produtividade de plantações de Eucalyptus grandis, com uso de sistema de informação geográfica

Detailed environmental land characterization is essential for technical and financial planning, for both the scientific point of view and technological application. This work aimed at the physiographic and pedological characterization and eucalyptus productivity mapping at Itatinga Forest Sciences Experimental Station (southeastern Brazil), using geographic information systems in order to identify possible cause-effect relationships between forest productivity and soil attributes. The digital cartographic dataset was structured as follows: as primary source of data, aerial photograph and field survey were used and, as a secondary source, topographical, geological and land use occupation maps were used. For mapping wood productivity at age six (MAI6, Mean Annual Increment), inventory data of permanent plots (same species, provenance and age) were used, which were obtained from Eucalyptus grandis plantations. Using simple linear correlation and backward stepwise multiple regression analysis, the dependent variable (MAI) was related with physical and chemical characteristics of the soils. Two standards of contour curves were identified, one with close curves, narrow and surrounding the drainage network, in the steeper and lower altitude areas; the other, with spaced contour lines, in the areas of higher altitude and with plane relief. Six types of soils were characterized as being highly related to the physiographic patterns of the area: loamy sandy to sandy clayey Typic Hapludox (LVAd, 47.5%), clayey Rhodic Hapludox (LVd1, 33.4%), sandy clay Rhodic Hapludox (LVd2, 6%), clayey Rhodic Hapludox (LVdf, 9.1%), Entisols (G, 3.4%) and Fluvents soil (RY, 0.6%). There were large variations in wood productivity in the Eucalyptus grandis plantations, characterized in six classes, ranging from 26 to 52 m(3) ha(-1) yr(-1). These productivity changes were strictly related to soil mapping units. Through multiple regression analysis, we found that clay and organic matter contents were the attributes which most strongly explained the productivity differences.

Mapping of risk and susceptibility of shallow-landslide in the city of Sao Paulo, Brazil

In the city of Sao Paulo, where about 11 million people live, landslides and flooding occur frequently, especially during the summer. These landslides cause the destruction of houses and urban equipment, economic damage, and the loss of lives. The number of areas threatened by landslides has been increasing each year. The objective of this article is to analyze the probability of risk and susceptibility to shallow landslides in the Limoeiro River basin, which is located at the head of the Aricanduva River basin, one of the main hydrographic basins in the city of Sao Paulo. To map areas of risk, we created a cadastral survey form to evaluate landslide risk in the field. Risk was categorized into four levels based on natural and anthropogenic factors: R1 (low risk), R2 (average risk), R3 (high risk), and R4 (very high risk). To analyze susceptibility to shallow landslides, we used the SHALSTAB (Shallow Landsliding Stability) mathematical model and calculated the Distribution Frequency (DF) of the susceptibility classes for the entire basin. Finally, we performed a joint analysis of the average Risk Concentration (RC) and Risk Potential (RP). We mapped 14 risk sectors containing approximately 685 at-risk homes, more than half of which presented a high (R3) or very high (R4) probability of risk to the population. In the susceptibility map, 41% of the area was classified as stable and 20% as unconditionally unstable. Although the latter category accounted a smaller proportion of the total area, it contained a concentration (RC) of 41% of the mapped risk areas with a risk potential (RP) of 12%. We found that the locations of areas predicted to be unstable by the model coincided with the risk areas mapped in the field. This combination of methods can be applied to evaluate the risk of shallow landslides in densely populated areas and can assist public managers in defining areas that are unstable and inappropriate for occupation. (C) 2012 Elsevier B.V. All rights reserved.

Mapping and Quantification of the Cotton Chain in Brazil

The CHAINPlan method developed by Neves (2007) is a practical tool which can be used to construct strategic plans for production chains. A preliminary step in this process includes mapping and quantifying the production chain. We present the results of applying the method to one of the most important agribusiness chains in Brazil-the cotton sector. The Gross Domestic Product for the cotton sector in the 2010-2011 crop year was estimated at nearly $19.2 billion. We show the interconnections between the links in the chain and its ability to generate revenues, taxes and jobs.

MAPPING, ORGANIC MATTER MASS AND WATER VOLUME OF A PEATLAND IN SERRA DO ESPINHACO MERIDIONAL

Peatlands form in areas where net primary of organic matter production exceeds losses due to the decomposition, leaching or disturbance. Due to their chemical and physical characteristics, bogs can influence water dynamics because they can store large volumes of water in the rainy season and gradually release this water during the other months of the year. In Diamantina, Minas Gerais, Brazil, a peatland in the environmental protection area of Pau-de-Fruta ensures the water supply of 40,000 inhabitants. The hypothesis of this study is that the peat bogs in Pau-de-Fruta act as an environment for carbon storage and a regulator of water flow in the Corrego das Pedras basin. The objective of this study was to estimate the water volume and organic matter mass in this peatland and to study the influence of this environment on the water flow in the Corrego das Pedras basin. The peatland was mapped using 57 transects, at intervals of 100 m. Along all transects, the depth of the peat bog, the Universal Transverse Mercator (UTM) coordinates and altitude were recorded every 20 m and used to calculate the area and volume of the peatland. The water volume was estimated, using a method developed in this study, and the mass of organic matter based on samples from 106 profiles. The peatland covered 81.7 hectares (ha), and stored 497,767 m(3) of water, representing 83.7 % of the total volume of the peat bog. The total amount of organic matter (OM) was 45,148 t, corresponding to 552 t ha(-1) of OM. The peat bog occupies 11.9 % of the area covered by the Corrego das Pedras basin and stores 77.6 % of the annual water surplus, thus controlling the water flow in the basin and consequently regulating the water course.

Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity

The time is ripe for a comprehensive mission to explore and document Earth's species. This calls for a campaign to educate and inspire the next generation of professional and citizen species explorers, investments in cyber-infrastructure and collections to meet the unique needs of the producers and consumers of taxonomic information, and the formation and coordination of a multi-institutional, international, transdisciplinary community of researchers, scholars and engineers with the shared objective of creating a comprehensive inventory of species and detailed map of the biosphere. We conclude that an ambitious goal to describe 10 million species in less than 50 years is attainable based on the strength of 250 years of progress, worldwide collections, existing experts, technological innovation and collaborative teamwork. Existing digitization projects are overcoming obstacles of the past, facilitating collaboration and mobilizing literature, data, images and specimens through cyber technologies. Charting the biosphere is enormously complex, yet necessary expertise can be found through partnerships with engineers, information scientists, sociologists, ecologists, climate scientists, conservation biologists, industrial project managers and taxon specialists, from agrostologists to zoophytologists. Benefits to society of the proposed mission would be profound, immediate and enduring, from detection of early responses of flora and fauna to climate change to opening access to evolutionary designs for solutions to countless practical problems. The impacts on the biodiversity, environmental and evolutionary sciences would be transformative, from ecosystem models calibrated in detail to comprehensive understanding of the origin and evolution of life over its 3.8 billion year history. The resultant cyber-enabled taxonomy, or cybertaxonomy, would open access to biodiversity data to developing nations, assure access to reliable data about species, and change how scientists and citizens alike access, use and think about biological diversity information.

In-plane mapping of buried InGaAs quantum rings and hybridization effects on the electronic structure

This work reports the investigation on the structural differences between InAs quantum rings and their precursor quantum dots species as well as on the presence of piezoelectric fields and asymmetries in these nanostructures. The experimental results show significant reduction in the ring dimensions when the sizes of capped and uncapped ring and dot samples are compared. The iso-lattice parameter mapped by grazing-incidence x-ray diffraction has revealed the lateral extent of strained regions in the buried rings. A comparison between strain and composition of dot and ring structures allows inferring on how the ring formation and its final configuration may affect optical response parameters. Based on the experimental observations, a discussion has been introduced on the effective potential profile to emulate theoretically the ring-shape confinement. The effects of confinement and strain field modulation on electron and hole band structures are simulated by a multiband k.p calculation. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4733964]

Global and Regional Ventricular Repolarization Study by Body Surface Potential Mapping in Patients with Left Bundle-Branch Block and Heart Failure Undergoing Cardiac Resynchronization Therapy

Background: The controversial effects promoted by cardiac resynchronization therapy (CRT) on the ventricular repolarization (VR) have motivated VR evaluation by body surface potential mapping (BSPM) in CRT patients. Methods: Fifty-two CRT patients, mean age 58.8 +/- 12.3 years, 31 male, LVEF 27.5 +/- 9.2, NYHA III-IV heart failure with QRS181.5 +/- 14.2 ms, underwent 87-lead BSPM in sinus rhythm (BASELINE) and biventricular pacing (BIV). Measurements of mean and corrected QT intervals and dispersion, mean and corrected T peak end intervals and their dispersion, and JT intervals characterized global and regional (RV, Intermediate, and LV regions) ventricular repolarization response. Results: Global QTm (P < 0.001) and QTcm (P < 0.05) were decreased in BIV; QTm was similar across regions in both modes (P = ns); QTcm values were lower in RV/LV than in Intermediate region in BASELINE and BIV (P < 0.001); only RV/Septum showed a significant difference (P < 0.01) in the BIV mode. QTD values both of BASELINE (P < 0.01) and BIV (P < 0.001) were greater in the Intermediate than in the LV region. CRT effect significantly reduced global/regional QTm and QTcm values. QTD was globally decreased in RV/LV (Intermediate: P = ns). BIV mode significantly reduced global T peak end mean and corrected intervals and their dispersion. JT values were not significant. Conclusions: Ventricular repolarization parameters QTm, QTcm, and QTD global/regional values, as assessed by BSPM, were reduced in patients under CRT with severe HF and LBBB. Greater recovery impairment in the Intermediate region was detected by the smaller variation of its dispersion.

Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription

Abstract Background RNAs transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression. However, the complement of human genes in which introns are transcribed, and the number of intronic transcriptional units and their tissue expression patterns are not known. Results A survey of mRNA and EST public databases revealed more than 55,000 totally intronic noncoding (TIN) RNAs transcribed from the introns of 74% of all unique RefSeq genes. Guided by this information, we designed an oligoarray platform containing sense and antisense probes for each of 7,135 randomly selected TIN transcripts plus the corresponding protein-coding genes. We identified exonic and intronic tissue-specific expression signatures for human liver, prostate and kidney. The most highly expressed antisense TIN RNAs were transcribed from introns of protein-coding genes significantly enriched (p = 0.002 to 0.022) in the 'Regulation of transcription' Gene Ontology category. RNA polymerase II inhibition resulted in increased expression of a fraction of intronic RNAs in cell cultures, suggesting that other RNA polymerases may be involved in their biosynthesis. Members of a subset of intronic and protein-coding signatures transcribed from the same genomic loci have correlated expression patterns, suggesting that intronic RNAs regulate the abundance or the pattern of exon usage in protein-coding messages. Conclusion We have identified diverse intronic RNA expression patterns, pointing to distinct regulatory roles. This gene-oriented approach, using a combined intron-exon oligoarray, should permit further comparative analysis of intronic transcription under various physiological and pathological conditions, thus advancing current knowledge about the biological functions of these noncoding RNAs.

Ultra-structural mapping of sugarcane bagasse after oxalic acid fiber expansion (OAFEX) and ethanol production by Candida shehatae and Saccharomyces cerevisiae

Background Diminishing supplies of fossil fuels and oil spills are rousing to explore the alternative sources of energy that can be produced from non-food/feed-based substrates. Due to its abundance, sugarcane bagasse (SB) could be a model substrate for the second-generation biofuel cellulosic ethanol. However, the efficient bioconversion of SB remains a challenge for the commercial production of cellulosic ethanol. We hypothesized that oxalic-acid-mediated thermochemical pretreatment (OAFEX) would overcome the native recalcitrance of SB by enhancing the cellulase amenability toward the embedded cellulosic microfibrils. Results OAFEX treatment revealed the solubilization of hemicellulose releasing sugars (12.56 g/l xylose and 1.85 g/l glucose), leaving cellulignin in an accessible form for enzymatic hydrolysis. The highest hydrolytic efficiency (66.51%) of cellulignin was achieved by enzymatic hydrolysis (Celluclast 1.5 L and Novozym 188). The ultrastructure characterization of SB using scanning electron microscopy (SEM), atomic force microscopy (AFM), Raman spectroscopy, Fourier transform–near infrared spectroscopy (FT-NIR), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD) revealed structural differences before and after OAFEX treatment with enzymatic hydrolysis. Furthermore, fermentation mediated by C. shehatae UFMG HM52.2 and S. cerevisiae 174 showed fuel ethanol production from detoxified acid (3.2 g/l, yield 0.353 g/g; 0.52 g/l, yield, 0.246 g/g) and enzymatic hydrolysates (4.83 g/l, yield, 0.28 g/g; 6.6 g/l, yield 0.46 g/g). Conclusions OAFEX treatment revealed marked hemicellulose degradation, improving the cellulases’ ability to access the cellulignin and release fermentable sugars from the pretreated substrate. The ultrastructure of SB after OAFEX and enzymatic hydrolysis of cellulignin established thorough insights at the molecular level.

Mapping the lignin distribution in pretreated sugarcane bagasse by confocal and fluorescence lifetime imaging microscopy

Abstract Background Delignification pretreatments of biomass and methods to assess their efficacy are crucial for biomass-to-biofuels research and technology. Here, we applied confocal and fluorescence lifetime imaging microscopy (FLIM) using one- and two-photon excitation to map the lignin distribution within bagasse fibers pretreated with acid and alkali. The evaluated spectra and decay times are correlated with previously calculated lignin fractions. We have also investigated the influence of the pretreatment on the lignin distribution in the cell wall by analyzing the changes in the fluorescence characteristics using two-photon excitation. Eucalyptus fibers were also analyzed for comparison. Results Fluorescence spectra and variations of the decay time correlate well with the delignification yield and the lignin distribution. The decay dependences are considered two-exponential, one with a rapid (τ1) and the other with a slow (τ2) decay time. The fastest decay is associated to concentrated lignin in the bagasse and has a low sensitivity to the treatment. The fluorescence decay time became longer with the increase of the alkali concentration used in the treatment, which corresponds to lignin emission in a less concentrated environment. In addition, the two-photon fluorescence spectrum is very sensitive to lignin content and accumulation in the cell wall, broadening with the acid pretreatment and narrowing with the alkali one. Heterogeneity of the pretreated cell wall was observed. Conclusions Our results reveal lignin domains with different concentration levels. The acid pretreatment caused a disorder in the arrangement of lignin and its accumulation in the external border of the cell wall. The alkali pretreatment efficiently removed lignin from the middle of the bagasse fibers, but was less effective in its removal from their surfaces. Our results evidenced a strong correlation between the decay times of the lignin fluorescence and its distribution within the cell wall. A new variety of lignin fluorescence states were accessed by two-photon excitation, which allowed an even broader, but complementary, optical characterization of lignocellulosic materials. These results suggest that the lignin arrangement in untreated bagasse fiber is based on a well-organized nanoenvironment that favors a very low level of interaction between the molecules.

Functional markers for gene mapping and genetic diversity studies in sugarcane

Abstract Background The database of sugarcane expressed sequence tags (EST) offers a great opportunity for developing molecular markers that are directly associated with important agronomic traits. The development of new EST-SSR markers represents an important tool for genetic analysis. In sugarcane breeding programs, functional markers can be used to accelerate the process and select important agronomic traits, especially in the mapping of quantitative traits loci (QTL) and plant resistant pathogens or qualitative resistance loci (QRL). The aim of this work was to develop new simple sequence repeat (SSR) markers in sugarcane using the sugarcane expressed sequence tag (SUCEST database). Findings A total of 365 EST-SSR molecular markers with trinucleotide motifs were developed and evaluated in a collection of 18 genotypes of sugarcane (15 varieties and 3 species). In total, 287 of the EST-SSRs markers amplified fragments of the expected size and were polymorphic in the analyzed sugarcane varieties. The number of alleles ranged from 2-18, with an average of 6 alleles per locus, while polymorphism information content values ranged from 0.21-0.92, with an average of 0.69. The discrimination power was high for the majority of the EST-SSRs, with an average value of 0.80. Among the markers characterized in this study some have particular interest, those that are related to bacterial defense responses, generation of precursor metabolites and energy and those involved in carbohydrate metabolic process. Conclusions These EST-SSR markers presented in this work can be efficiently used for genetic mapping studies of segregating sugarcane populations. The high Polymorphism Information Content (PIC) and Discriminant Power (DP) presented facilitate the QTL identification and marker-assisted selection due the association with functional regions of the genome became an important tool for the sugarcane breeding program.