Estimation of Wheat Agronomic Parameters using New Spectral Indices

Crop agronomic parameters (leaf area index (LAI), nitrogen (N) uptake, total chlorophyll (Chl) content ) are very important for the prediction of crop growth. The objective of this experiment was to investigate whether the wheat LAI, N uptake, and total Chl content could be accurately predicted using spectral indices collected at different stages of wheat growth. Firstly, the product of the optimized soil-adjusted vegetation index and wheat biomass dry weight (OSAVI×BDW) were used to estimate LAI, N uptake, and total Chl content; secondly, BDW was replaced by spectral indices to establish new spectral indices (OSAVI×OSAVI, OSAVI×SIPI, OSAVI×CI_{red edge}, OSAVI×CI_{green mode} and OSAVI×EVI2); finally, we used the new spectral indices for estimating LAI, N uptake, and total Chl content. The results showed that the new spectral indices could be used to accurately estimate LAI, N uptake, and total Chl content. The highest R² and the lowest RMSEs were 0.711 and 0.78 (OSAVI×EVI2), 0.785 and 3.98 g/m² (OSAVI×CI_{red edge}) and 0.846 and 0.65 g/m² (OSAVI×CI_{red edge}) for LAI, nitrogen uptake and total Chl content, respectively. The new spectral indices performed better than the OSAVI alone, and the problems of a lack of sensitivity at earlier growth stages and saturation at later growth stages, which are typically associated with the OSAVI, were improved. The overall results indicated that this new spectral indices provided the best approximation for the estimation of agronomic indices for all growth stages of wheat.     

Bayesian Estimation of Concordance Among Gene Trees

Mol. Biol. Evol. 24:412-426. 2007 In Bayesian estimation of concordance among gene trees (Vol.24(2), 412–426)     

Definition and Distribution Analysis of Glycoprotein B Gene Alleles of Human Herpesvirus 7

As for other herpesviruses, glycoprotein B (gB) of human herpesvirus 7 (HHV-7) is believed to play a major role in virus infection and as a target of the host immunogenic response. Using nested PCR, we amplified the whole HHV-7 gB gene from 108 human peripheral blood mononuclear cell samples and studied its variability. By means of restriction fragment length polymorphism (RFLP) analysis, three distinct patterns, designated I, II, and III, were defined and detected at frequencies of 93, 5, and 2%, respectively. Determination of the nucleotide sequence allowed us to recognize five critical positions in the gB gene with six specific combinations of point changes at these positions. These combinations were gB alleles A, B, C, D, E, and F. Alleles D and E corresponded to RFLP patterns II and III, respectively, while the other four alleles corresponded to RFLP pattern I. Identical gB alleles were detected in serial samples as well as in paired samples of blood and saliva from the same individuals, except for one case. In contrast, the distribution of gB alleles differed according to the geographical origin of the human samples: C was the most frequent allele in both African and Caribbean samples, whereas F was the most frequent allele in European ones. Although none of the allele-specific nucleotide changes induced any modification at the protein level, the definition of gB alleles provided convenient viral markers for the study of both HHV-7 infections and human population genetics.     

Yule-Coefficients for Second- and Higher-Order Associations

The well-known Q coefficient of association defined by YULE (1900) for two attributes is generalized from first-order association Q to second-order association Q for three attributes and to higher-order Q's for more than three attributes (or binary variables). Q analysis of t binary variables is shown to be a suitable means for describing simple (quasi-parametric) or complex (multi-nonparametric) relationships in a t-dimensional contingency cube. A biometrical example is given using clinical data.     

Estimation of Fitness Components in DROSOPHILA MELANOGASTER . I. Heterozygote Viability Indices

We examine the assumption of "dominance" with regard to viability of the Cy and Pm marker chromosomes in D. melanogaster . This assumption is often invoked for the extraction of wild-type second chromosomes from natural populations and for the calculation of relative viability indices. Significant genotypic variances for viability are found among both Cy/+_j and Pm/+_i heterozygotes in California and Japanese populations. The magnitude of the Pm/+ _i genotypic variance is substantially less than that of the Cy/+_j heterozygotes (less than one half). Significant reciprocal effects are also found to influence Cy/+_j, Pm/+_i and +_i/+_j viabilities. We conclude that viability indices of heterozygotes based on the Curly method are biased. We suggest that viability indices in the future be expressed relative to the viability of the Cy/Pm genotype (Curly-Plum method) or possibly that of the Pm/+_i genotype (Plum method).     

Quantitative Surface-Enhanced Raman for Gene Expression Estimation

We demonstrate for the first time, to our knowledge, a unique gene expression assay by surface-enhanced Raman scattering (SERS) using nonfluorescent Raman labels to quantify gene expression at the resolution of alternative splicing using RNA extracted from cancer cells without any amplification steps. Our approach capitalizes on the inherent plasmon-phonon mode of SERS substrates as a self-referencing standard for the detection and quantification of genetic materials. A strategy integrating S1 nuclease digestion with SERS detection was developed to quantify the expression levels of splice junction Δ(9,10), a segment of the breast cancer susceptibility gene 1 (BRCA1) from MCF-7 and MDA-MB-231 cells. Quantification results were cross-validated using two Raman tags and qualitatively confirmed by RT-PCR. Our methodology based on SERS technology provides reliable gene expression data with high sensitivity, bypassing the intricacies involved in fabricating a consistent SERS substrate.     

Analysis of Gene Coexpression by B-Spline Based CoD Estimation

The gene coexpression study has emerged as a novel holistic approach for microarray data analysis. Different indices have been used in exploring coexpression relationship, but each is associated with certain pitfalls. The Pearson's correlation coefficient, for example, is not capable of uncovering nonlinear pattern and directionality of coexpression. Mutual information can detect nonlinearity but fails to show directionality. The coefficient of determination (CoD) is unique in exploring different patterns of gene coexpression, but so far only applied to discrete data and the conversion of continuous microarray data to the discrete format could lead to information loss. Here, we proposed an effective algorithm, CoexPro, for gene coexpression analysis. The new algorithm is based on B-spline approximation of coexpression between a pair of genes, followed by CoD estimation. The algorithm was justified by simulation studies and by functional semantic similarity analysis. The proposed algorithm is capable of uncovering both linear and a specific class of nonlinear relationships from continuous microarray data. It can also provide suggestions for possible directionality of coexpression to the researchers. The new algorithm presents a novel model for gene coexpression and will be a valuable tool for a variety of gene expression and network studies. The application of the algorithm was demonstrated by an analysis on ligand-receptor coexpression in cancerous and noncancerous cells. The software implementing the algorithm is available upon request to the authors.     

Biological N2 Fixation in wetland rice fields: Estimation and contribution to nitrogen balance

This paper 1) reviews improvements and new approaches in methodologies for estimating biological N₂ fixation (BNF) in wetland soils, 2) summarizes earlier quantitative estimates and recent data, and 3) discusses the contribution of BNF to N balance in wetland-rice culture.Measuring acetylene reducing activity (ARA) is still the most popular method for assessing BNF in rice fields. Recent studies confirm that ARA measurements present a number of problems that may render quantitative extrapolations questionable. On the other hand, few comparative measures show ARA's potential as a quantitative estimate. Methods for measuring photodependent and associative ARA in field studies have been standardized, and major progress has been made in sampling procedures. Standardized ARA measurements have shown significant differences in associative N₂ fixation among rice varieties.The ¹⁵N dilution method is suitable for measuring the percentage of N derived from the atmosphere (% Ndfa) in legumes and rice. In particular, the ¹⁵N dilution technique, using available soil N as control, appears to be a promising method for screening rice varieties for ability to utilize biologically fixed N. Attempts to adapt the ¹⁵N dilution method to aquatic N₂ fixers (Azolla and blue-green algae [BGA]) encountered difficulties due to the rapid change in ¹⁵N enrichment of the water.Differences in natural ¹⁵N abundance have been used to show differences among plant organs and species or varieties in rice and Azolla, and to estimate Ndfa by Azolla, but the method appears to be semi-quantitative.Recent pot experiments using stabilized ¹⁵N-labelled soil or balances in pots covered with black cloth indicate a contribution of 10–30 kg N ha^-1 crop^-1 by heterotrophic BNF in flooded planted soil with no or little N fertilizer used.Associative BNF extrapolated from ARA and ¹⁵N incorporation range from 1 to 7 kg N ha^-1 crop^-1. Straw application increases heterotrophic and photodependent BNF. Pot experiments show N gains of 2–4 mg N g^-1 straw added at 10 tons ha^-1.N₂ fixation by BGA has been almost exclusively estimated by ARA and biomass measurements. Estimates by ARA range from a few to 80 kg N ha^-1 crop^-1 (average 27 kg). Recent extensive measurements show extrapolated values of about 20 kg N ha^-1 crop^-1 in no-N plots, 8 kg in plots with broadcast urea, and 12 kg in plots with deep-placed urea.Most information on N₂ fixed by Azolla and legume green manure comes from N accumulation measurements and determination of % Ndfa. Recent trials in an international network show standing crops of Azolla averaging 30–40 kg N ha^-1 and the accumulation of 50–90 kg N ha^-1 for two crops of Azolla grown before and after transplanting rice. Estimates of % Ndfa in Azolla by ¹⁵N dilution and delta ¹⁵N methods range from 51 to 99%. Assuming 50–80% Ndfa in legume green manures, one crop can provide 50–100 kg N ha^-1 in 50 days. Few balance studies in microplots or pots report extrapolated N gains of 150–250 kg N ha^-1 crop^-1.N balances in long-term fertility experiments range from 19 to 98 kg N ha^-1 crop^-1 (average 50 kg N) in fields with no N fertilizer applied. The problems encountered with ARA and ¹⁵N methods have revived interest in N balance studies in pots. Balances are usually highest in flooded planted pots exposed to light and receiving no N fertilizer; extrapolated values range from 16 to 70 kg N ha^-1 crop^-1 (average 38 kg N). A compilation of balance experiments with rice soil shows an average balance of about 30 kg N ha^-1 crop^-1 in soils where no inorganic fertilizer N was applied.Biological N₂ fixation by individual systems can be estimated more or less accurately, but total BNF in a rice field has not yet been estimated by measuring simultaneously the activities of the various components in situ. As a result, it is not clear if the activities of the different N₂-fixing systems are independent or related. A method to estimate in situ the contribution of N₂ fixed to rice nutrition is still not available. Dynamics of BNF during the crop cycle is known for indigenous agents but the pattern of fixed N availability to rice is known only for a few green manure crops.     

Cytogenetic Definition and Morphogenetic Analysis of Delta, a Gene Affecting Neurogenesis in Drosophila Melanogaster

We have conducted a genetic analysis of a small interval of the third chromosome known to include Delta (Dl), a locus that affects the segregation of the ectoderm into neural and epidermal lineages during embryogenesis and the morphogenesis of some ectodermally derived structures, in Drosophila melanogaster. This analysis has led to the definition of seven independent complementation groups, one of which is Delta, within the interval extending from 91F6-13 to 92A2. Among the extant mutations in these seven loci, only mutations in Dl lead to the so-called neurogenic phenotype: hypertrophy of the nervous system and reduction of the epidermis. Combined cytogenetic and genetic analyses allow us to define absolute proximal (91F5-92A1) and distal (92A2) cytogenetic limits for the Dl locus. We have isolated hypomorphic and amorphic alleles of Dl and find that, for any given allele, there is an inverse correlation between neural hypertrophy and epidermal reduction in embryos and a direct correlation between the severity of embryonic phenotypes in mutant homozygotes and hemizygotes and the imaginal phenotype in heterozygous adults.     

Soil TPH Concentration Estimation Using Vegetation Indices in an Oil Polluted Area of Eastern China

Assessing oil pollution using traditional field-based methods over large areas is difficult and expensive. Remote sensing technologies with good spatial and temporal coverage might provide an alternative for monitoring oil pollution by recording the spectral signals of plants growing in polluted soils. Total petroleum hydrocarbon concentrations of soils and the hyperspectral canopy reflectance were measured in wetlands dominated by reeds (Phragmites australis) around oil wells that have been producing oil for approximately 10 years in the Yellow River Delta, eastern China to evaluate the potential of vegetation indices and red edge parameters to estimate soil oil pollution. The detrimental effect of oil pollution on reed communities was confirmed by the evidence that the aboveground biomass decreased from 1076.5 g m⁻² to 5.3 g m⁻² with increasing total petroleum hydrocarbon concentrations ranging from 9.45 mg kg⁻¹ to 652 mg kg⁻¹. The modified chlorophyll absorption ratio index (MCARI) best estimated soil TPH concentration among 20 vegetation indices. The linear model involving MCARI had the highest coefficient of determination (R ² = 0.73) and accuracy of prediction (RMSE = 104.2 mg kg⁻¹). For other vegetation indices and red edge parameters, the R² and RMSE values ranged from 0.64 to 0.71 and from 120.2 mg kg⁻¹ to 106.8 mg kg⁻¹ respectively. The traditional broadband normalized difference vegetation index (NDVI), one of the broadband multispectral vegetation indices (BMVIs), produced a prediction (R ² = 0.70 and RMSE = 110.1 mg kg⁻¹) similar to that of MCARI. These results corroborated the potential of remote sensing for assessing soil oil pollution in large areas. Traditional BMVIs are still of great value in monitoring soil oil pollution when hyperspectral data are unavailable.     

Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes

The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log₁₀-transformed protein-coding gene number (Y′) versus log₁₀-transformed genome size (X′, genome size in kbp) were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y′ = ln(-46.200+22.678X′, whereas non-eukaryotes a linear model, Y′ = 0.045+0.977X′, both with high significance (p<0.001, R²>0.91). Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%–1%) compared to higher and relatively stable percentages in prokaryotes and viruses (97%–47%). The eukaryotic regression models project that the smallest dinoflagellate genome (3×10⁶ kbp) contains 38,188 protein-coding (40,086 total) genes and the largest (245×10⁶ kbp) 87,688 protein-coding (92,013 total) genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.     

Estimation of Levels of Gene Flow from DNA Sequence Data

We compare the utility of two methods for estimating the average levels of gene flow from DNA sequence data. One method is based on estimating FST from frequencies at polymorphic sites, treating each site as a separate locus. The other method is based on computing the minimum number of migration events consistent with the gene tree inferred from their sequences. We compared the performance of these two methods on data that were generated by a computer simulation program that assumed the infinite sites model of mutation and that assumed an island model of migration. We found that in general when there is no recombination, the cladistic method performed better than FST while the reverse was true for rates of recombination similar to those found in eukaryotic nuclear genes, although FST performed better for all recombination rates for very low levels of migration (Nm = 0.1).     

Higher-Order Spike Triggered Analysis of Neural Oscillators

For the purpose of elucidating the neural coding process based on the neural excitability mechanism, researchers have recently investigated the relationship between neural dynamics and the spike triggered stimulus ensemble (STE). Ermentrout et al. analytically derived the relational equation between the phase response curve (PRC) and the spike triggered average (STA). The STA is the first cumulant of the STE. However, in order to understand the neural function as the encoder more explicitly, it is necessary to elucidate the relationship between the PRC and higher-order cumulants of the STE. In this paper, we give a general formulation to relate the PRC and the nth moment of the STE. By using this formulation, we derive a relational equation between the PRC and the spike triggered covariance (STC), which is the covariance of the STE. We show the effectiveness of the relational equation through numerical simulations and use the equation to identify the feature space of the rat hippocampal CA1 pyramidal neurons from their PRCs. Our result suggests that the hippocampal CA1 pyramidal neurons oscillating in the theta frequency range are commonly sensitive to inputs composed of theta and gamma frequency components.     

Relevance of Higher-Order Epistasis in Drug Resistance

We studied five chemically distinct but related 1,3,5-triazine antifolates with regard to their effects on growth of a set of mutants in dihydrofolate reductase. The mutants comprise a combinatorially complete data set of all 16 possible combinations of four amino acid replacements associated with resistance to pyrimethamine in the malaria parasite Plasmodium falciparum. Pyrimethamine was a mainstay medication for malaria for many years, and it is still in use in intermittent treatment during pregnancy or as a partner drug in artemisinin combination therapy. Our goal was to investigate the extent to which the alleles yield similar adaptive topographies and patterns of epistasis across chemically related drugs. We find that the adaptive topographies are indeed similar with the same or closely related alleles being fixed in computer simulations of stepwise evolution. For all but one of the drugs the topography features at least one suboptimal fitness peak. Our data are consistent with earlier results indicating that third order and higher epistatic interactions appear to contribute only modestly to the overall adaptive topography, and they are largely conserved. In regard to drug development, our data suggest that higher-order interactions are likely to be of little value as an advisory tool in the choice of lead compounds.     

Genetic Differentiation and Estimation of Gene Flow from F-Statistics under Isolation by Distance

I reexamine the use of isolation by distance models as a basis for the estimation of demographic parameters from measures of population subdivision. To that aim, I first provide results for values of F-statistics in one-dimensional models and coalescence times in two-dimensional models, and make more precise earlier results for F-statistics in two-dimensional models and coalescence times in one-dimensional models. Based on these results, I propose a method of data analysis involving the regression of F(ST)/(1 - F(ST)) estimates for pairs of subpopulations on geographic distance for populations along linear habitats or logarithm of distance for populations in two-dimensional habitats. This regression provides in principle an estimate of the product of population density and second moment of parental axial distance. In two cases where comparison to direct estimates is possible, the method proposed here is more satisfactory than previous indirect methods.