Generalized discriminant analysis using a kernel approach

We present a new method that we call generalized discriminant analysis (GDA) to deal with nonlinear discriminant analysis using kernel function operator. The underlying theory is close to the support vector machines (SVM) insofar as the GDA method provides a mapping of the input vectors into high-dimensional feature space. In the transformed space, linear properties make it easy to extend and generalize the classical linear discriminant analysis (LDA) to nonlinear discriminant analysis. The formulation is expressed as an eigenvalue problem resolution. Using a different kernel, one can cover a wide class of nonlinearities. For both simulated data and alternate kernels, we give classification results, as well as the shape of the decision function. The results are confirmed using real data to perform seed classification.

Comprehensive genotyping of the USA national maize inbred seed bank

BACKGROUND

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.

RESULTS

The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits.

CONCLUSIONS

The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.

Comparative development of fiber in wild and cultivated cotton

One of the most striking examples of plant hairs is the single-celled epidermal seed trichome of cultivated cotton. The developmental morphology of these commercial "fibers" has been well-characterized in Gossypium hirsutum, but little is known about the pattern and tempo of fiber development in wild Gossypium species, all of which have short, agronomically inferior fiber. To identify developmental differences that account for variation in fiber length, and to place these differences in a phylogenetic context, we conducted SEM studies of ovules at and near the time of flowering, and generated growth curves for cultivated and wild diploid and tetraploid species. Trichome initiation was found to be similar in all taxa, with few notable differences in trichome density or early growth. Developmental profiles of the fibers of most wild species are similar, with fiber elongation terminating at about two weeks post-anthesis. In contrast, growth is extended to three weeks in the A- and F-genome diploids. This prolonged elongation period is diagnosed as a key evolutionary event in the origin of long fiber. A second evolutionary innovation is that absolute growth rate is higher in species with long fibers. Domestication of species is associated with a further prolongation of elongation at both the diploid and allopolyploid levels, suggesting the effects of parallel artificial selection. Comparative analysis of fiber growth curves lends developmental support to previous quantitative genetic suggestions that genes for fiber "improvement" in tetraploid cotton were contributed by the agronomically inferior D-genome diploid parent.

(13)C NMR-based metabolomics for the classification of green coffee beans according to variety and origin

(13)C NMR-based metabolomics was demonstrated as a useful tool for distinguishing the species and origins of green coffee bean samples of arabica and robusta from six different geographic regions. By the application of information on (13)C signal assignment, significantly different levels of 14 metabolites of green coffee beans were identified in the classifications, including sucrose, caffeine, chlorogenic acids, choline, amino acids, organic acids, and trigonelline, as captured by multivariate analytical models. These studies demonstrate that the species and geographical origin can be quickly discriminated by evaluating the major metabolites of green coffee beans quantitatively using (13)C NMR-based metabolite profiling.

Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation

Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species.

Phytochemical profiles and antioxidant activity of adlay varieties

Consumption of whole grains has been associated with reduced risk of developing major chronic diseases. These health benefits have been attributed in part to their unique phytochemicals. Little is known about the complete profiles of phytochemicals and antioxidant activities of different adlay varieties. The objectives of this study were to determine the phytochemicals profiles of the three adlay varieties, including both free and bound of total phenolics and total flavonoids, and to determine the total antioxidant activity of adlay. The free, bound, and total phenolic contents of adlay samples ranged from 31.23 to 45.19 mg of gallic acid equiv/100 g of sample, from 28.07 to 30.86 mg of gallic acid equiv/100 g of sample, and from 59.30 to 76.04 mg of gallic acid equiv/100 g of sample, respectively. On average, the bound phenolics contributed 45.3% of total phenolic content of the adlay varieties analyzed. The free, bound, and total flavonoid contents of adlay samples ranged from 6.21 to 18.24 mg of catechin equiv/100 g, from 18.68 to 35.27 mg of catechin equiv/100 g, and from 24.88 to 52.86 mg of catechin equiv/100 g, respectively. The average values of bound flavonoids contributed 71.1% of total flavonoids of the adlay varieties analyzed. The percentage contribution of flavonoid content to phenolic content of free, bound, and total ranged from 11.6 to 35.2%, from 50.5 to 66.8%, and from 24.6 to 50.5%. The free, bound, and total oxygen radical absorbance capacity (ORAC) values of adlay samples ranged from 231.9 to 316.6 mg of Trolox equiv/100 g, from 209.0 to 351.4 mg of Trolox equiv/100 g, and from 440.9 to 668.0 mg of Trolox equiv/100 g, respectively. The average ORAC values of bound phytochemicals contributed 48.1% of total antioxidant activity of the adlay varieties analyzed. The content of total polyphenol and the antioxidant capacity are obviously different among different species. Liaoning 5 adlay and Longyi 1 adlay are significantly better than Guizhou heigu adlay. The adlay extracts have obvious proliferate inhibition on human liver cancer cells, and substantially in the experimental concentration range, the adlay sample itself has no cytotoxicity. Knowing the phytochemical profiles and antioxidant activity of adlay gives insights to its potential application to promote health.

Seed dispersal by neotropical seed predators

From a plant's perspective, the difference between a seed predator and a seed disperser should be straightforward: attract animals that will disperse seeds and defend seeds from potential predators. Unlike pulp-eating frugivores, seed predators regularly encounter diverse plant protective mechanisms. The purpose of this paper is to examine feeding constraints, morphological adaptations, and the mechanical process of seed predation. While there is evidence that some seed predators cause severe losses to seed crops, there is also evidence that seed predators enhance seed dispersal and germination. We also examine four methods by which neotropical seed predators may contribute to dispersal. 1) Seed predators examined here ingested fruit when seeds were full-sized, but not yet mature (i.e., seeds of mature fruit may be avoided by seed predators and available for dispersal by other frugivores). 2) Sympatric seed predators may ingest seeds from different plants thus reducing overall predator load on any individual plant. 3) Seed predators that manipulate seeds (e.g., remove pericarp and seed coat) may enhance germination if the prepared seeds are dropped, discarded, or buried and not ingested. 4) Small seeds may miss mastication and swallowed intact with a food bolus. The last mechanism is the most likely to contribute to seed dispersal by the widest array of vertebrate seed predators, but primate seed predators may facilitate seed dispersal using all four mechanisms. Therefore, the traditional dichotomy of seed predator vs. seed disperser oversimplifies the interactions between seed predators and plants.

Comparison of the effectiveness of fatty acids, chlorogenic acids, and elements for the chemometric discrimination of coffee (Coffea arabica L.) varieties and growing origins

The objective of this work was to compare the effectiveness of three chemical families, namely, chlorogenic acids, fatty acids, and elements, for the discrimination of Arabica varieties (traditional versus modern introgressed lines) and potential terroirs within a given coffee-growing area. The experimental design included three Colombian locations in full combination with five (one traditional and four introgressed) Arabica varieties and two field replications. Chlorogenic acids, fatty acids, and elements were analyzed in coffee bean samples by HPLC, GC, and ICP-AES, respectively. Principal component analysis and discriminant analysis were carried out to compare the three methods. Although elements provided an excellent classification of the three locations studied, this chemical class was useless for Arabica variety discrimination. Chlorogenic acids gave satisfactory results, but fatty acids clearly offered the best results for the determination of both varieties and environments, with very high percentages of correct classification (79 and 90%, respectively).

Seed dispersal by long-tailed macaques

We review here the methods by which long-tailed macaques (Macaca fascicularis fascicularis) process seeds in Bukit Timah Nature Reserve, Singapore, and the factors that influence this. Feeding observations have revealed that these macaques either destroy seeds in their mouth with their teeth, spit them out whole from the mouth after removing much of the flesh, or else clean the flesh off them at the front of the mouth and then drop them. Absence of these observed behaviors is associated with the presence of intact seeds in the feces, indicating that macaques swallow some seeds whole. All these options were exhibited by one group of macaques and were not random alternatives; evidence links their frequency to the type of fruit (fleshy vs. dry) and the size of the seed(s). Adaptations of the mouth of long-tailed macaques, such as gape and the presence of well-innervated cheek pouches and relatively large incisor and postcanine teeth, are predicted to influence these thresholds strongly. In a faunally depleted reserve like Bukit Timah, this dispersal is effective, but we see no evidence in this of coevolution between macaques and fruits. Many seeds in the macaque diet are probably dispersed more effectively by other vertebrates, such as birds, bats, gibbons, and civets, when these are present. However, in sites where large vertebrates have been eliminated, macaques may become important for dispersing large, large-seeded fruits.

Morphological and molecular phylogenetic context of the angiosperms: contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers

Recent attempts to address the long-debated 'origin' of the angiosperms depend on a phylogenetic framework derived from a matrix of taxa versus characters; most assume that empirical rigour is proportional to the size of the matrix. Sequence-based genotypic approaches increase the number of characters (nucleotides and indels) in the matrix but are confined to the highly restricted spectrum of extant species, whereas morphology-based approaches increase the number of phylogenetically informative taxa (including fossils) at the expense of accessing only a restricted spectrum of phenotypic characters. The two approaches are currently delivering strongly contrasting hypotheses of relationship. Most molecular studies indicate that all extant gymnosperms form a natural group, suggesting surprisingly early divergence of the lineage that led to angiosperms, whereas morphology-only phylogenies indicate that a succession of (mostly extinct) gymnosperms preceded a later angiosperm origin. Causes of this conflict include: (i) the vast phenotypic and genotypic lacuna, largely reflecting pre-Cenozoic extinctions, that separates early-divergent living angiosperms from their closest relatives among the living gymnosperms; (ii) profound uncertainty regarding which (a) extant and (b) extinct angiosperms are most closely related to gymnosperms; and (iii) profound uncertainty regarding which (a) extant and (b) extinct gymnosperms are most closely related to angiosperms, and thus best serve as 'outgroups' dictating the perceived evolutionary polarity of character transitions among the early-divergent angiosperms. These factors still permit a remarkable range of contrasting, yet credible, hypotheses regarding the order of acquisition of the many phenotypic characters, reproductive and vegetative, that distinguish 'classic' angiospermy from 'classic' gymnospermy. The flower remains ill-defined and its mode (or modes) of origin remains hotly disputed; some definitions and hypotheses of evolutionary relationships preclude a role for the flower in delimiting the angiosperms. We advocate maintenance of parallel, reciprocally illuminating programmes of morphological and molecular phylogeny reconstruction, respectively supported by homology testing through additional taxa (especially fossils) and evolutionary-developmental genetic studies that explore genes potentially responsible for major phenotypic transitions.

Differential accumulation of phenolic compounds and expression of related genes in black- and yellow-seeded Brassica napus

Developing yellow-seeded Brassica napus (rapeseed) with improved qualities is a major breeding goal. The intermediate and final metabolites of the phenylpropanoid and flavonoid pathways affect not only oil quality but also seed coat colour of B. napus. Here, the accumulation of phenolic compounds was analysed in the seed coats of black-seeded (ZY821) and yellow-seeded (GH06) B. napus. Using toluidine blue O staining and liquid chromatography-mass spectrometry, histochemical and biochemical differences were identified in the accumulation of phenolic compounds between ZY821 and GH06. Two and 13 unique flavonol derivatives were detected in ZY821 and GH06, respectively. Quantitative real-time PCR analysis revealed significant differences between ZY821 and GH06 in the expression of common phenylpropanoid biosynthetic genes (BnPAL and BnC4H), common flavonoid biosynthetic genes (BnTT4 and BnTT6), anthocyanin- and proanthocyandin-specific genes (BnTT3 and BnTT18), proanthocyandin-specific genes (BnTT12, BnTT10, and BnUGT2) and three transcription factor genes (BnTTG1, BnTTG2, and BnTT8) that function in the flavonoid biosynthetic pathway. These data provide insight into pigment accumulation in B. napus, and serve as a useful resource for researchers analysing the formation of seed coat colour and the underlying regulatory mechanisms in B. napus.

Low-field (1)H NMR spectroscopy for distinguishing between arabica and robusta ground roast coffees

This work reports a new screening protocol for addressing issues of coffee authenticity using low-field (60MHz) bench-top (1)H NMR spectroscopy. Using a simple chloroform-based extraction, useful spectra were obtained from the lipophilic fraction of ground roast coffees. It was found that 16-O-methylcafestol (16-OMC, a recognized marker compound for robusta beans) gives rise to an isolated peak in the 60MHz spectrum, which can be used as an indicator of the presence of robusta beans in the sample. A total of 81 extracts from authenticated coffees and mixtures were analysed, from which the detection limit of robusta in arabica was estimated to be between 10% and 20% w/w. Using the established protocol, a surveillance exercise was conducted of 27 retail samples of ground roast coffees which were labelled as "100% arabica". None were found to contain undeclared robusta content above the estimated detection limit.

Seed handling by three prosimian primates in southeastern Madagascar: implications for seed dispersal

In this paper, we studied three species of prosimian primate (Propithecus diadema edwardsi, Eulemur fulvus rufus, and Eulemur rubriventer) from June-July 1995 at the Ranomafana National Park to answer three questions: 1) how they handle and process seeds, 2) how the physical properties of seeds influence seed handling and seed fate, and 3) whether handling and processing patterns influence seed dispersal. Seeds from five plant species were collected from feces and examined for external damage (punctures and scrapes), weighed, measured, and checked daily for germination. P. d. edwardsi masticated seeds into two or more pieces while feeding. Seed fragments were either dropped under the parent tree or chewed and swallowed; seeds never emerged as recognizable units in feces. In contrast, both Eulemur species either dropped or swallowed seeds whole while feeding. E. rubriventer passed seeds that were longer, wider, and heavier than seeds passed by E.f. rufus. Although seeds emerged as separate units when passed by both Eulemur species, 65 Protorhus sp. seeds were scraped and/or punctured prior to being swallowed. Based on physical property tests, Protorhus seeds were more susceptible to mastication than undamaged seeds from Eugenia sp., Cissus sp., and Chrysophyllum madagascariensis. H. madagascariensis seeds also were undamaged but had physical properties comparable to Protorhus and may avoid being masticated due to their small size (2-3 mm). All damaged seeds were moldy or rotten within 6 days, and only 15% of the undamaged seeds passed by E. rubriventer germinated. None of the seeds passed by E.f. rufus germinated. Eulemur species also rested in the same tree after feeding and defecated prior to a new feeding bout or before moving, so seeds were most likely to be dispersed under the parent tree. Consequently, we concluded that these primate species do not appear to serve as effective seed dispersers for these plant species at this time of year.

Economic use of plants is key to their naturalization success

Humans cultivate thousands of economic plants (i.e. plants with economic value) outside their native ranges. To analyze how this contributes to naturalization success, we combine global databases on economic uses and naturalization success of the world's seed plants. Here we show that naturalization likelihood is 18 times higher for economic than non-economic plants. Naturalization success is highest for plants grown as animal food or for environmental uses (e.g. ornamentals), and increases with number of uses. Taxa from the Northern Hemisphere are disproportionately over-represented among economic plants, and economic plants from Asia have the greatest naturalization success. In regional naturalized floras, the percentage of economic plants exceeds the global percentage and increases towards the equator. Phylogenetic patterns in the naturalized flora partly result from phylogenetic patterns in the plants we cultivate. Our study illustrates that accounting for the intentional introduction of economic plants is key to unravelling drivers of plant naturalization.

Open field trial of genetically modified parthenocarpic tomato: seedlessness and fruit quality

Background

Parthenocarpic tomato lines transgenic for the DefH9-RI-iaaM gene have been cultivated under open field conditions to address some aspects of the equivalence of genetically modified (GM) fruit in comparison to controls (non-GM).

Results

Under open field cultivation conditions, two tomato lines (UC 82) transgenic for the DefH9-RI-iaaM gene produced parthenocarpic fruits. DefH9-RI-iaaM fruits were either seedless or contained very few seeds. GM fruit quality, with the exception of a higher β-carotene level, did not show any difference, neither technological (colour, firmness, dry matter, °Brix, pH) nor chemical (titratable acidity, organic acids, lycopene, tomatine, total polyphenols and antioxidant capacity – TEAC), when compared to that of fruits from control line. Highly significant differences in quality traits exist between the tomato F1 commercial hybrid Allflesh and the three UC 82 genotypes tested, regardless of whether or not they are GM. Total yield per plant did not differ between GM and parental line UC 82. Fruit number was increased in GM lines, and GM fruit weight was decreased.

Conclusion

The use in the diet of fruits from a new line or variety introduces much greater changes than the consumption of GM fruits in comparison to its genetic background. Parthenocarpic fruits, produced under open field conditions, contained 10-fold less seeds than control fruits. Thus parthenocarpy caused by DefH9-RI-iaaM gene represents also a tool for mitigating GM seeds dispersal in the environment.

Identification of rice seed varieties using neural network

A digital image analysis algorithm based color and morphological features was developed to identify the six varieties (ey7954, syz3, xs11, xy5968, xy9308, z903) rice seeds which are widely planted in Zhejiang Province. Seven color and fourteen morphological features were used for discriminant analysis. Two hundred and forty kernels used as the training data set and sixty kernels as the test data set in the neural network used to identify rice seed varieties. When the model was tested on the test data set, the identification accuracies were 90.00%, 88.00%, 95.00%, 82.00%, 74.00%, 80.00% for ey7954, syz3, xs11, xy5968, xy9308, z903 respectively.

Changes of tocopherols, tocotrienols, γ-oryzanol, and γ-aminobutyric acid levels in the germinated brown rice of pigmented and nonpigmented cultivars

This study examined the changes of tocopherols (Toc), tocotrienols (T3), γ-oryzanol (GO), and γ-aminobutyric acid (GABA) contents in germinated brown rice (GBR) of pigmented and nonpigmented cultivars under different germination conditions. Results showed that the Toc and T3 contents in GBR were significantly different between treatments in both rice cultivars. The pigmented GBR possessed higher total vitamin E, total Toc, total T3, and GO contents than the nonpigmented GBR; however, its level of GABA was lower. The order of the three highest vitamin E homologues in pigmented and nonpigmented GBR was γ-T3 > γ-Toc > α-Toc and α-Toc > γ-T3 > α-T3, respectively; β-Toc, β-T3, δ-Toc, and δ-T3 were present in only small amounts (≤1.0 mg/kg) in GBR of both cultivars. Although both cultivars showed an increase in GABA contents with increasing germination time, the GABA content in nonpigmented GBR was higher.

Lowland gorillas and seed dispersal: the importance of nest sites

Lowland gorillas eat the fruit and disperse the seeds of many tree species in the Lopé Reserve, Gabon. This study aimed to show whether deposition of seeds at gorilla ground nest sites conferred any advantage for germination and seedling establishment as compared to the fate of seeds deposited in gorilla dung on trails or under parents. Four tree species were chosen for study, which had a range of fruit types and fruiting patterns but which were all important foods for gorillas. Data showed that gorillas removed significant quantities of seeds from all four species and deposited them in dung at nest sites or on trail. Nest sites were not always favorable for germination, but the most favorable sites permitted the best survival and growth of any of the seedlings, including those deposited in dung on trail or scatter-dispersed under or away from parent canopies. Initial performance in the first few weeks after deposition was not always indicative of long-term survival and growth, so data collection over 1-2 years was absolutely essential. The main factors affecting seedling fate at nest sites appeared to be vegetation cover and desiccation. It is suggested that the nesting habits of gorillas are an additional factor encouraging the successful establishment of seedlings over and above the obvious advantages of large body size, gut capacity, and extended day ranges.

Comprehensive Chemical Fingerprinting of High-Quality Cocoa at Early Stages of Processing: Effectiveness of Combined Untargeted and Targeted Approaches for Classification and Discrimination

This study investigates chemical information of volatile fractions of high-quality cocoa (Theobroma cacao L. Malvaceae) from different origins (Mexico, Ecuador, Venezuela, Columbia, Java, Trinidad, and Sao Tomè) produced for fine chocolate. This study explores the evolution of the entire pattern of volatiles in relation to cocoa processing (raw, roasted, steamed, and ground beans). Advanced chemical fingerprinting (e.g., combined untargeted and targeted fingerprinting) with comprehensive two-dimensional gas chromatography coupled with mass spectrometry allows advanced pattern recognition for classification, discrimination, and sensory-quality characterization. The entire data set is analyzed for 595 reliable two-dimensional peak regions, including 130 known analytes and 13 potent odorants. Multivariate analysis with unsupervised exploration (principal component analysis) and simple supervised discrimination methods (Fisher ratios and linear regression trees) reveal informative patterns of similarities and differences and identify characteristic compounds related to sample origin and manufacturing step.

Regional and racial specificities in sorghum germplasm assessed with DNA markers

Three different molecular marker technologies were used to determine the relatedness of 84 different lines of sorghum. Both racial characterization and geographical origin were found to be correlated with relatedness. In some cases, the region of origin was the more significant factor, where samples of different races from the same locality were more closely related than were samples of the same race from different localities. Wild sorghums were shown to have few novel alleles, suggesting that they would be poor sources of germplasm diversity. The results also indicated that Chinese sorghums are a narrow and distinctive group that is most closely related to race bicolor.

Identification and quantification of phytochemical composition and anti-inflammatory, cellular antioxidant, and radical scavenging activities of 12 Plantago species

Twenty-eight seed samples of 12 Plantago species were investigated for their chemical compositions and anti-inflammatory, cellular antioxidant, and radical scavenging properties. A new UPLC-UV procedure was developed and applied to quantify acteoside and geniposidic acid, the characteristic constituents of the genus Plantago. The amounts of acteoside and geniposidic acid ranged from 0.07 to 15.96 mg/g and from 0.05 to 10.04 mg/g in the tested samples, respectively. Furthermore, 26 compounds were tentatively identified by UPLC/Q-TOF-MS analysis. The Plantago samples significantly differed in their phytochemical compositions. The extracts of Plantago seeds also showed inhibitory effects on LPS-induced IL-1β, IL-6, and COX-2 mRNA expression in RAW 264.7 mouse macrophage cells. Additionally, significant variations were observed among different samples on cellular antioxidant activities in HepG2 cells, as well as DPPH and hydroxyl radical scavenging capacities. The results from this study may be used to promote the use of the genus Plantago in improving human health.

Identification and Quantification of Avenanthramides and Free and Bound Phenolic Acids in Eight Cultivars of Husked Oat ( Avena sativa L) from Finland

Finland is the second largest oat producer in Europe. Despite the existing knowledge of phenolics in oat, there is little information on the phenolic composition of oats from Finland. The aim of the study was to investigate the concentrations of free and bound phenolic acids, as well as avenanthramides in eight Finnish cultivars of husked oat ( Avena sativa L.). Seven phenolic acids and one phenolic aldehyde were identified, including, in decreasing order of abundance: p-coumaric, ferulic, cinnamic, syringic, vanillic, 2,4-dihydroxybenzoic, and o-coumaric acids and syringaldehyde. Phenolic acids were mostly found as bound compounds. Significant varietal differences ( p < 0.05) were observed in the cumulative content of phenolic acids, with the lowest level found in cv. 'Viviana' (1202 ± 52.9 mg kg^-1) and the highest in cv. 'Akseli' (1687 ± 80.2 mg kg^-1). Avenanthramides (AVNs) 2a, 2p, and 2f were the most abundant. Total AVNs levels ranged from 26.7 ± 1.44 to 185 ± 12.5 mg kg^-1 in cv. 'Avetron' and 'Viviana', respectively.

Isotopes as tracers of the Hawaiian coffee-producing regions

Green coffee bean isotopes have been used to trace the effects of different climatic and geological characteristics associated with the Hawaii islands. Isotope ratio mass spectrometry (IRMS) and inductively coupled plasma mass spectrometry ((MC)-ICP-SFMS and ICP-QMS) were applied to determine the isotopic composition of carbon (δ13C), nitrogen (δ15N), sulfur (δ34S), and oxygen (δ18O), the isotope abundance of strontium (87Sr/86Sr), and the concentrations of 30 different elements in 47 green coffees. The coffees were produced in five Hawaii regions: Hawaii, Kauai, Maui, Molokai, and Oahu. Results indicate that coffee plant seed isotopes reflect interactions between the coffee plant and the local environment. Accordingly, the obtained analytical fingerprinting could be used to discriminate between the different Hawaii regions studied.

Discrimination of green arabica and Robusta coffee beans by Raman spectroscopy

This paper presents an approach that may be applied as an accurate and rapid tool for classifying coffee beans on the basis of the specific kahweol content. Using Fourier-transform Raman spectroscopy with 1064 nm excitation it is possible to monitor the characteristic Raman bands of kahweol in green coffee beans without chemical and physical processing of the beans. The procedure was optimized on the basis of 83 and 125 measurements of whole and ground beans, respectively, using coffee samples of two different species, Coffea arabica L. and Coffea canephora L. (var. Robusta), and different origins (Asia, Africa, and South America). The relative contribution of the kahweol in individual beans can be determined quantitatively by means of a component analysis of the spectra, yielding a spectral kahweol index (σka) that is proportional to the relative content of kahweol in a coffee bean. The reproducibility of the spectroscopic measurement and analysis was found to be 3.5%. Individual beans of the same type and origin reveal a scattering of the σka values. Nevertheless, an unambiguous distinction between Arabica and Robusta samples is possible on the basis of single-bean measurements as the σka values are greater than and less than 10 for Arabica and Robusta coffees, respectively. Measurements of whole and ground beans afforded very similar results, despite the heterogeneous distribution of kahweol within a bean. Unlike conventional analytical techniques, the single-bean sensitivity of the present approach may also allow for a rapid detection of unwanted admixtures of low-value Robusta coffee to high-quality and more expensive Arabica coffee.

The soil seed bank during Atlantic Forest regeneration in Southeast Brazil

A survey was conducted to determine the density and species composition of viable seeds buried in four stands of a tropical montane forest at Parque Estadual Intervales, Brazil. The objective was to understand: (1) how numbers and composition of the soil seed bank change as the forest regrows, and (2) how such changes affect the species available for regeneration if forests of different ages are cut down. In each forest stand (5, 18, 27-yr-old and a mature forest), 57 soil samples were collected (0-2.5 and 2.5-5 cm deep). Viable seed density of herbaceous species ranged between 11,003 seeds. m-2 (5-yr-old vegetation) and 482 (mature forest), and between 25 (5-yr-old vegetation) and 389 seeds. m-2 (mature forest) for woody plant species in the 0-5 cm soil layer, suggesting a decrease in seed stocks in the course of forest regeneration. Seeds buried in the 0-2.5 cm soil layer represented between 56.9% and 67.4% of all viable seeds. Most of the viable seeds belonged to weeds of Asteraceae, Poaceae, Malvaceae and Solanaceae. The results provide evidence that, in forests of different ages, the soil does not store seeds of the same key ecological groups involved in the regeneration of Atlantic forest. Allochthonous seeds from remaining patches of forest, as well as their vertebrate dispersers, are needed for forest regeneration since the soil seed bank does not store large seeds of shade-tolerant species.