Regression models for grouped survival data: Estimation and sensitivity analysis

In this study, regression models are evaluated for grouped survival data when the effect of censoring time is considered in the model and the regression structure is modeled through four link functions. The methodology for grouped survival data is based on life tables, and the times are grouped in k intervals so that ties are eliminated. Thus, the data modeling is performed by considering the discrete models of lifetime regression. The model parameters are estimated by using the maximum likelihood and jackknife methods. To detect influential observations in the proposed models, diagnostic measures based on case deletion, which are denominated global influence, and influence measures based on small perturbations in the data or in the model, referred to as local influence, are used. In addition to those measures, the local influence and the total influential estimate are also employed. Various simulation studies are performed and compared to the performance of the four link functions of the regression models for grouped survival data for different parameter settings, sample sizes and numbers of intervals. Finally, a data set is analyzed by using the proposed regression models. (C) 2010 Elsevier B.V. All rights reserved.

Molecular Identification and Phylogenetic Analysis of a Group 16SrI-B Phytoplasma Associated with Sugarcane Yellow Leaf Syndrome in Brazil

Yellow leaf syndrome was a serious problem in the beginning of the 1990s in Brazil, when yield losses were estimated to be around 50%. The disease is currently endemic, but it is considered potentially important. Previous studies have revealed only the presence of a luteovirus associated with the disease in Brazil. We report that a phytoplasma of 16SrI-B is also associated with this disease. This is the first demonstration of the presence of a group 16SrI-B phytoplasma in association with sugarcane yellow leaf in Brazil.

Cloning, expression, molecular modelling and docking analysis of glutathione transferase from Saccharum officinarum

Sugarcane yield and quality are affected by a number of biotic and abiotic stresses. In response to such stresses, plants may increase the activities of some enzymes such as glutathione transferase (GST), which are involved in the detoxification of xenobiotics. Thus, a sugarcane GST was modelled and molecular docked using the program LIGIN to investigate the contributions of the active site residues towards the binding of reduced glutathione (GSH) and 1-chloro-2,4-dinitrobenzene (CDNB). As a result, W13 and I119 were identified as key residues for the specificity of sugarcane GSTF1 (SoGSTF1) towards CDNB. To obtain a better understanding of the catalytic specificity of sugarcane GST (SoGSTF1), two mutants were designed, W13L and I119F. Tertiary structure models and the same docking procedure were performed to explain the interactions between sugarcane GSTs with GSH and CDNB. An electron-sharing network for GSH interaction was also proposed. The SoGSTF1 and the mutated gene constructions were cloned and expressed in Escherichia coli and the expressed protein purified. Kinetic analyses revealed different Km values not only for CDNB, but also for GSH. The Km values were 0.2, 1.3 and 0.3 mM for GSH, and 0.9, 1.2 and 0.5 mM for CDNB, for the wild type, W13L mutant and I119F mutant, respectively. The V(max) values were 297.6, 224.5 and 171.8 mu mol min(-1) mg(-1) protein for GSH, and 372.3, 170.6 and 160.4 mu mol min(-1) mg(-1) protein for CDNB.

Analysis of genomic and functional RFLP derived markers associated with sucrose content, fiber and yield QTLs in a sugarcane (Saccharum spp.) commercial cross

Expressed sequence tags derived markers have a great potential to be used in functional map construction and QTL tagging. In the present work, sugarcane genomic probes and expressed sequence tags having homology to genes, mostly involved in carbohydrate metabolism were used in RFLP assays to identify putative QTLs as well as their epistatic interactions for fiber content, cane yield, pol and tones of sugar per hectare, at two crop cycles in a progeny derived from a bi-parental cross of sugarcane elite materials. A hundred and twenty marker trait associations were found, of which 26 at both crop cycle and 32 only at first ratoon cane. A sucrose synthase derived marker was associated with a putative QTL having a high negative effect on cane yield and also with a QTL having a positive effect on Pol at both crop cycles. Fifty digenic epistatic marker interactions were identified for the four traits evaluated. Of these, only two were observed at both crop cycles.

Genetic structure and mating system of Euterpe edulis Mart. populations: A comparative analysis using microsatellite and allozyme markers

A comparative study between microsatellite and allozyme markers was conducted on the genetic structure and mating system in natural populations of Euterpe edulis Mart. Three cohorts, including seedlings, saplings, and adults, were examined in 4 populations using 10 allozyme loci and 10 microsatellite loci. As expected, microsatellite markers had a much higher degree of polymorphism than allozymes, but estimates of multilocus outcrossing rate ((t) over cap (m) = 1.00), as well as estimates of genetic structure (F(IS), G(ST)), were similar for the 2 sets of markers. Estimates of R(ST), for microsatellites, were higher than those of GST, but results of both statistics revealed a close agreement for the genetic structure of the species. This study provides support for the important conclusion that allozymes are still useful and reliable markers to estimate population genetic parameters. Effects of sample size on estimates from hypervariable loci are also discussed in this paper.

In silico analysis of candidate genes involved in light sensing and signal transduction pathways in soybean

Several aspects of photoperception and light signal transduction have been elucidated by studies with model plants. However, the information available for economically important crops, such as Fabaceae species, is scarce. In order to incorporate the existing genomic tools into a strategy to advance soybean research, we have investigated publicly available expressed sequence tag ( EST) sequence databases in order to identify Glycine max sequences related to genes involved in light-regulated developmental control in model plants. Approximately 38,000 sequences from open-access databases were investigated, and all bona fide and putative photoreceptor gene families were found in soybean sequence databases. We have identified G. max orthologs for several families of transcriptional regulators and cytoplasmic proteins mediating photoreceptor-induced responses, although some important Arabidopsis phytochrome-signaling components are absent. Moreover, soybean and Arabidopsis gene-family homologs appear to have undergone a distinct expansion process in some cases. We propose a working model of light perception, signal transduction and response-eliciting in G. max, based on the identified key components from Arabidopsis. These results demonstrate the power of comparative genomics between model systems and crop species to elucidate several aspects of plant physiology and metabolism.

Canonical discriminant analysis applied to broiler chicken performance

The mechanisms involved in the control of growth in chickens are too complex to be explained only under univariate analysis because all related traits are biologically correlated. Therefore, we evaluated broiler chicken performance under a multivariate approach, using the canonical discriminant analysis. A total of 1920 chicks from eight treatments, defined as the combination of four broiler chicken strains (Arbor Acres, AgRoss 308, Cobb 500 and RX) from both sexes, were housed in 48 pens. Average feed intake, average live weight, feed conversion and carcass, breast and leg weights were obtained for days 1 to 42. Canonical discriminant analysis was implemented by SAS((R)) CANDISC procedure and differences between treatments were obtained by the F-test (P < 0.05) over the squared Mahalanobis` distances. Multivariate performance from all treatments could be easily visualised because one graph was obtained from two first canonical variables, which explained 96.49% of total variation, using a SAS((R)) CONELIP macro. A clear distinction between sexes was found, where males were better than females. Also between strains, Arbor Acres, AgRoss 308 and Cobb 500 (commercial) were better than RX (experimental), Evaluation of broiler chicken performance was facilitated by the fact that the six original traits were reduced to only two canonical variables. Average live weight and carcass weight (first canonical variable) were the most important traits to discriminate treatments. The contrast between average feed intake and average live weight plus feed conversion (second canonical variable) were used to classify them. We suggest analysing performance data sets using canonical discriminant analysis.

Inheritance of growth habit detected by genetic linkage analysis using microsatellites in the common bean (Phaseolus vulgaris L.)

The genetic linkage map for the common bean (Phaseolus vulgaris L.) is a valuable tool for breeding programs. Breeders provide new cultivars that meet the requirements of farmers and consumers, such as seed color, seed size, maturity, and growth habit. A genetic study was conducted to examine the genetics behind certain qualitative traits. Growth habit is usually described as a recessive trait inherited by a single gene, and there is no consensus about the position of the locus. The aim of this study was to develop a new genetic linkage map using genic and genomic microsatellite markers and three morphological traits: growth habit, flower color, and pod tip shape. A mapping population consisting of 380 recombinant F10 lines was generated from IAC-UNA x CAL143. A total of 871 microsatellites were screened for polymorphisms among the parents, and a linkage map was obtained with 198 mapped microsatellites. The total map length was 1865.9 cM, and the average distance between markers was 9.4 cM. Flower color and pod tip shape were mapped and segregated at Mendelian ratios, as expected. The segregation ratio and linkage data analyses indicated that the determinacy growth habit was inherited as two independent and dominant genes, and a genetic model is proposed for this trait.

Does using stepwise variable selection to build sequential path analysis models make sense?

Causal inference methods - mainly path analysis and structural equation modeling - offer plant physiologists information about cause-and-effect relationships among plant traits. Recently, an unusual approach to causal inference through stepwise variable selection has been proposed and used in various works on plant physiology. The approach should not be considered correct from a biological point of view. Here, it is explained why stepwise variable selection should not be used for causal inference, and shown what strange conclusions can be drawn based upon the former analysis when one aims to interpret cause-and-effect relationships among plant traits.

Immunological responses and cytokine gene expression analysis to Cooperia punctata infections in resistant and susceptible Nelore cattle

Cellular and humoral immune response, as well as cytokine gene expression, was assessed in Nelore cattle with different degrees of resistance to Cooperia punctata natural infection. One hundred cattle (male, weaned, 11-12 months old), kept together on pasture, were evaluated. Faecal and blood samples were collected for parasitological and immunological assays. Based on nematode faecal egg counts (FEC) and worm burden, the seven most resistant and the eight most susceptible animals were selected. Tissue samples of the small intestine were collected for histological quantification of inflammatory cells and analysis of cytokine gene expression (IL-2, IL-4, IL-8, IL-1 2p35, IL-13, TNF-alpha, IFN-gamma, MCP-1, MCP-2, and MUC- 1) using real-time RT-PCR. Mucus samples were also collected for IgA levels determination. Serum IgG1 mean levels against C. punctata antigens were higher in the resistant group, but significant differences between groups were only observed 14 days after the beginning of the experiment against infective larvae (1-3) and 14 and 84 days against adult antigens. The resistant group also presented higher IgA levels against C. punctata (L3 and adult) antigens with significant difference 14 days after the beginning of the trial (P < 0.05). In the small-intestine mucosa, levels of IgA anti-L3 and anti-adult C. punctata were higher in the resistant group, compared with the susceptible group (P < 0.05). Gene expression of both T(H)2 cytokines (IL-4 and IL-13) in the resistant group and T(H)1 cytokines (IL-2, IL-1 2p35, IFN-gamma and MCP-1) in the susceptible group was up-regulated. Such results suggested that immune response to C. punctata was probably mediated by TH2 cytokines in the resistant group and by T(H)1 cytokines in the susceptible group. (C) 2008 Elsevier B.V. All rights reserved.

LC-MSn analysis of the cis isomers of chlorogenic acids

The behaviour of cis isomers of selected mono- and di-acyl chlorogenic acids produced by UV-irradiation has been investigated by LC-MSn. cis Isomers fragment identically to the more common trans isomers. cis-5-Acyl chlorogenic acids are more hydrophobic and elute later than their mono- or di-trans counterparts whereas the reverse is true for cis-3-acyl and cis-4-acyl chlorogenic acids. The cis isomers of 1,3-dicaffeoylquinic acid, the only I-acyl chlorogenic acid investigated, are also more hydrophobic than the di-trans isomer. Coffee leaves had a proportionately greater content of cis isomers relative to trans isomers compared with coffee beans suggesting that UV-irradiation in vivo may also cause geometric isomerisation. (c) 2007 Elsevier Ltd. All rights reserved.

Spatial patterns of soil attributes and components in a mangrove system in Southeast Brazil (Sao Paulo)

Purpose Among environmental factors governing innumerous processes that are active in estuarine environments, those of edaphic character have received special attention in recent studies. With the objectives of determining the spatial patterns of soil attributes and components across different mangrove forest landscapes and obtaining additional information on the cause-effect relationships between these variables and position within the estuary, we analyzed several soil attributes in 31 mangrove soil profiles from the state of So Paulo (Guaruja, Brazil). Materials and methods Soil samples were collected at low tide along two transects within the CrumahA(0) mangrove forest. Samples were analyzed to determine pH, Eh, salinity, and the percentages of sand, silt, clay, total organic carbon (TOC), and total S. Mineralogy of the clay fraction (< 2 mm) was also studied by X-ray diffraction analysis, and partitioning of solid-phase Fe was performed by sequential extraction. Results and discussion The results obtained indicate important differences in soil composition at different depths and landscape positions, causing variations in physicochemical parameters, clay mineralogy, TOC contents, and iron geochemistry. The results also indicate that physicochemical conditions may vary in terms of different local microtopographies. Soil salinity was determined by relative position in relation to flood tide and transition areas with highlands. The proportions of TOC and total S are conditioned by the sedimentation of organic matter derived from vegetation and by the prevailing redox conditions, which clearly favored intense sulfate reduction in the soils (similar to 80% of the total Fe is Fe-pyrite). Particle-size distribution is conditioned by erosive/deposition processes (present and past) and probably by the positioning of ancient and reworked sandy ridges. The existing physicochemical conditions appear to contribute to the synthesis (smectite) and transformation (kaolinite) of clay minerals. Conclusions The results demonstrate that the position of soils in the estuary greatly affects soil attributes. Differences occur even at small scales (meters), indicating that both edaphic (soil classification, soil mineralogy, and soil genesis) and environmental (contamination and carbon stock) studies should take such variability into account.

A split-pot experiment with sorghum to test a root water uptake partitioning model

Correct modeling of root water uptake partitioning over depth is an important issue in hydrological and crop growth models. Recently a physically based model to describe root water uptake was developed at single root scale and upscaled to the root system scale considering a homogeneous distribution of roots per soil layer. Root water uptake partitioning is calculated over soil layers or compartments as a function of respective soil hydraulic conditions, specifically the soil matric flux potential, root characteristics and a root system efficiency factor to compensate for within-layer root system heterogeneities. The performance of this model was tested in an experiment performed in two-compartment split-pot lysimeters with sorghum plants. The compartments were submitted to different irrigation cycles resulting in contrasting water contents over time. The root system efficiency factor was determined to be about 0.05. Release of water from roots to soil was predicted and observed on several occasions during the experiment; however, model predictions suggested root water release to occur more often and at a higher rate than observed. This may be due to not considering internal root system resistances, thus overestimating the ease with which roots can act as conductors of water. Excluding these erroneous predictions from the dataset, statistical indices show model performance to be of good quality.

Evaluation of the genetic variability of orchid fleck virus by single-strand conformational polymorphism analysis and nucleotide sequencing of a fragment from the nucleocapsid gene

The variability of a fragment of the nucleocapsid gene of orchid fleck virus (OFV) was investigated by single-strand conformational polymorphism (SSCP) analysis and nucleotide sequencing. Forty-eight samples of 18 genera of orchids were collected from Brazil, Costa Rica and Australia. The SSCP analysis yielded six different band patterns, and phylogenetic analysis based on the nucleotide fragment sequence obtained in this work and six available in GenBank showed two different groups, one with isolates 023Germany and So-Japan, and other with the rest of the isolates. None of the analyses showed geographic correlation among the Brazilian strains. The data obtained in this study showed a low genetic variation in this region of the genome; the d(N)/d(S) ratio of 0.251-0.405 demonstrated a negative selective pressure that maintains the stability of the analyzed fragments.

Thermal analysis of vitamin PP Niacin and niacinamide

Vitamin PP includes two vitamers, niacin and niacinamide which are essential for energy production. Vitamins are sensitive and losses can occur during shelf life and heating processes. Thermal analysis can provide information about thermal behavior of each vitamer relating them with time and/or temperature exposure. The vitamers thermal behavior were studied by TG/DTG and DSC under air and nitrogen atmosphere and the results showed that niacin is more stable than the niacinamide and the decomposition happens by volatilization at 238 A degrees C while niacinamide melts at 129 A degrees C and volatilize at 254 A degrees C when there is the total mass loss in the TG/DTG curves.