Global transcript analysis of rice leaf and seed using SAGE technology.

We have compiled two comprehensive gene expression profiles from mature leaf and immature seed tissue of rice (Oryza sativa ssp. japonica cultivar Nipponbare) using Serial Analysis of Gene Expression (SAGE) technology. Analysis revealed a total of 50 519 SAGE tags, corresponding to 15 131 unique transcripts. Of these, the large majority (approximately 70%) occur only once in both libraries. Unexpectedly, the most abundant transcript (approximately 3% of the total) in the leaf library was derived from a type 3 metallothionein gene. The overall frequency profiles of the abundant tag species from both tissues differ greatly and reveal seed tissue as exhibiting a non-typical pattern of gene expression characterized by an over abundance of a small number of transcripts coding for storage proteins. A high proportion ( approximately 80%) of the abundant tags (> or = 9) matched entries in our reference rice EST database, with many fewer matches for low abundant tags. Singleton transcripts that are common to both tissues were collated to generate a summary of low abundant transcripts that are expressed constitutively in rice tissues. Finally and most surprisingly, a significant number of tags were found to code for antisense transcripts, a finding that suggests a novel mechanism of gene regulation, and may have implications for the use of antisense constructs in transgenic technology.

Comparative analysis by protocol and key of seed storage behaviour of sixty Vietnamese tree species

Seed storage behaviour of 5 1 native and 9 introduced tree species in Vietnam was investigated using a brief protocol developed to aid biodiversity conservation in circumstances where little is known about the seeds. Of the 60 species, 34 appeared to show orthodox (Acacia auriculaeformis, Adenanthera pavonina, Afzelia xylocarpa, Bauhinia purpurea, Callistemon lanceolatus, Cananga odorata, Canarium nigrum, Cassia fistula, Cassia javanica, Cassia splendida, Chukrasia tabularis, Dalbergia bariaensis, Dialium cochinchinensis, Diospyros mollis, Diospyros mun, Dracuntomelon duperreanum, Erythrophleum fordii, Khaya senegalensis, Lagerstroemia speciosa, Leucaena leucocephala, Livistona cochinchinensis, Markhamia stipulata, Melaleuca cajuputi, Millettia ichthyotona, Peltophorum pterocarpum, Peltophorum tonkinensis, Pinus khasya, Pinus massoniana, Pinus merkusii, Pterocarpus macrocarpus, Sindora siamensis, Sophora tonkinense, Sterculia foetida, Swietenia macrophylla), 13 recalcitrant (Avicennia alba, Beilschmiedia roxburghiana, Caryota mitis, Dimocarpus sp., Diospyros malabarica, Dipterocarpus chartaceus, Dypsis pinnatifrons, Hopea odorata, Lithocarpus gigantophylla, Machilus odoratissimus, Melanorrhoea laccifera, Melanorrhea usitata, Syzygium cinereum) and 13 intermediate (Anisoptera cochinchinensis, Aphanamixis polystachya, Averrhoa carambola, Carissa carandas, Chrysopylum cainito, Cinnamomum camphora, Citrofortunella microcarpa, Citrus grandis var. grandis, Elaeis guineensis, Hydnocarpus anthelmintica, Madhuca floribunda, Manilkara achras, Mimusops elengi) seed storage behaviour. A double-criteria key to estimate likely seed storage behaviour showed good agreement with the above: the key can reduce the workload of seed storage behaviour identification considerably.

Gut microbial catabolism of grape seed flavan-3-ols by human faecal microbiota. Targetted analysis of precursor compounds, intermediate metabolites and end-products.

In vitro batch culture fermentations were conducted with grape seed polyphenols and human faecal microbiota, in order to monitor both changes in precursor flavan-3-ols and the formation of microbial-derived metabolites. By the application of UPLC-DAD-ESI-TQ MS, monomers, and dimeric and trimeric procyanidins were shown to be degraded during the first 10 h of fermentation, with notable inter-individual differences being observed between fermentations. This period (10 h) also coincided with the maximum formation of intermediate metabolites, such as 5-(3′,4′-dihydroxyphenyl)-γ-valerolactone and 4-hydroxy-5-(3′,4′-dihydroxyphenyl)-valeric acid, and of several phenolic acids, including 3-(3,4-dihydroxyphenyl)-propionic acid, 3,4-dihydroxyphenylacetic acid, 4-hydroxymandelic acid, and gallic acid (5–10 h maximum formation). Later phases of the incubations (10–48 h) were characterised by the appearance of mono- and non-hydroxylated forms of previous metabolites by dehydroxylation reactions. Of particular interest was the detection of γ-valerolactone, which was seen for the first time as a metabolite from the microbial catabolism of flavan-3-ols. Changes registered during fermentation were finally summarised by a principal component analysis (PCA). Results revealed that 5-(3′,4′-dihydroxyphenyl)-γ-valerolactone was a key metabolite in explaining inter-individual differences and delineating the rate and extent of the microbial catabolism of flavan-3-ols, which could finally affect absorption and bioactivity of these compounds.

Patterns of pollen and seed dispersal in a small, fragmented population of the wind-pollinated tree Araucaria angustifolia in southern Brazil

Paternity analysis based on eight microsatellite loci was used to investigate pollen and seed dispersal patterns of the dioecious wind- pollinated tree, Araucaria angustifolia. The study sites were a 5.4 ha isolated forest fragment and a small tree group situated 1.7 km away, located in Paran alpha State, Brazil. In the forest fragment, 121 males, 99 females, 66 seedlings and 92 juveniles were mapped and genotyped, together with 210 seeds. In the tree group, nine male and two female adults were mapped and genotyped, together with 20 seeds. Paternity analysis within the forest fragment indicated that at least 4% of the seeds, 3% of the seedlings and 7% of the juveniles were fertilized by pollen from trees in the adjacent group, and 6% of the seeds were fertilized by pollen from trees outside these stands. The average pollination distance within the forest fragment was 83 m; when the tree group was included the pollination distance was 2006m. The average number of effective pollen donors was estimated as 12.6. Mother- trees within the fragment could be assigned to all seedlings and juveniles, suggesting an absence of seed immigration. The distance of seedlings and juveniles from their assigned mother- trees ranged from 0.35 to 291m ( with an average of 83m). Significant spatial genetic structure among adult trees, seedlings, and juveniles was detected up to 50m, indicating seed dispersal over a short distance. The effective pollination neighborhood ranged from 0.4 to 3.3 ha. The results suggest that seed dispersal is restricted but that there is longdistance pollen dispersal between the forest fragment and the tree group; thus, the two stands of trees are not isolated.

Barley oxalate oxidase is a hexameric protein related to seed storage proteins: evidence from X-ray crystallography

The oxalate oxidase enzyme expressed in barley roots is a thermostable, protease-resistant enzyme that generates H2O2. It has great medical importance because of its use to assay plasma and urinary oxalate, and it has also been used to generate transgenic, pathogen-resistant crops. This protein has now been purified and three types of crystals grown. X-ray analysis shows that the symmetry present in these crystals is consistent with a hexameric arrangement of subunits, probably a trimer of dimers. This structure may be similar to that found in the related seed storage proteins.

Sequence analysis of the cupin gene family in Synechocystis PCC6803

The recently described cupin superfamily of proteins includes the germin and germinlike proteins, of which the cereal oxalate oxidase is the best characterized. This superfamily also includes seed storage proteins, in addition to several microbial enzymes and proteins with unknown function. All these proteins are characterized by the conservation of two central motifs, usually containing two or three histidine residues presumed to be involved with metal binding in the catalytic active site. The present study on the coding regions of Synechocystis PCC6803 identifies a previously unknown group of 12 related cupins, each containing the characteristic two-motif signature. This group comprises 11 single-domain proteins, ranging in length from 104 to 289 residues, and includes two phosphomannose isomerases and two epimerases involved in cell wall synthesis, a member of the pirin group of nuclear proteins, a possible transcriptional regulator, and a close relative-of a cytochrome c551 from Rhodococcus. Additionally, there is a duplicated, two-domain protein that has close similarity to an oxalate decarboxylase from the fungus Collybia velutipes and that is a putative progenitor of the storage proteins of land plants.

Microbial relatives of seed storage proteins: conservation of motifs in a functionally diverse superfamily of enzymes

Plant storage proteins comprise a major part of the human diet. Sequence analysis has revealed that these proteins probably share a common ancestor with a fungal oxalate decarboxylase and/or related bacterial genes. Additionally, all these proteins share a central core sequence with several other functionally diverse enzymes and binding proteins, many of which are associated with synthesis of the extracellular matrix during sporulation/encystment. A possible prokaryotic relative of this sequence is a bacterial protein (SASP) known to bind to DNA and thereby protect spores from extreme environmental conditions. This ability to maintain cell viability during periods of dehydration in spores and seeds may relate to absolute conservation of residues involved in structure determination.

Oxidation of biogenic and water-soluble compounds in aqueous and organic aerosol droplets by ozone: a kinetic and product analysis approach using laser Raman tweezers

The results of an experimental study into the oxidative degradation of proxies for atmospheric aerosol are presented. We demonstrate that the laser Raman tweezers method can be used successfully to obtain uptake coeffcients for gaseous oxidants on individual aqueous and organic droplets, whilst the size and composition of the droplets is simultaneously followed. A laser tweezers system was used to trap individual droplets containing an unsaturated organic compound in either an aqueous or organic ( alkane) solvent. The droplet was exposed to gas- phase ozone and the reaction kinetics and products followed using Raman spectroscopy. The reactions of three different organic compounds with ozone were studied: fumarate anions, benzoate anions and alpha pinene. The fumarate and benzoate anions in aqueous solution were used to represent components of humic- like substances, HULIS; a alpha- pinene in an alkane solvent was studied as a proxy for biogenic aerosol. The kinetic analysis shows that for these systems the diffusive transport and mass accommodation of ozone is relatively fast, and that liquid- phase di. ffusion and reaction are the rate determining steps. Uptake coe. ffcients, g, were found to be ( 1.1 +/- 0.7) x 10(-5), ( 1.5 +/- 0.7) x 10 (-5) and ( 3.0 - 7.5) x 10 (-3) for the reactions of ozone with the fumarate, benzoate and a- pinene containing droplets, respectively. Liquid- phase bimolecular rate coe. cients for reactions of dissolved ozone molecules with fumarate, benzoate and a- pinene were also obtained: k(fumarate) = ( 2.7 +/- 2) x 10 (5), k(benzoate) = ( 3.5 +/- 3) x 10 (5) and k(alpha-pinene) = ( 1-3) x 10(7) dm(3) mol (-1) s (- 1). The droplet size was found to remain stable over the course of the oxidation process for the HULIS- proxies and for the oxidation of a- pinene in pentadecane. The study of the alpha- pinene/ ozone system is the first using organic seed particles to show that the hygroscopicity of the particle does not increase dramatically over the course of the oxidation. No products were detected by Raman spectroscopy for the reaction of benzoate ions with ozone. One product peak, consistent with aqueous carbonate anions, was observed when following the oxidation of fumarate ions by ozone. Product peaks observed in the reaction of ozone with alpha- pinene suggest the formation of new species containing carbonyl groups.

Survival analysis of cereal crop variety innovations in the UK

This paper explores the changing survival patterns of cereal crop variety innovations in the UK since the introduction of plant breeders’ rights in the mid-1960s. Using non-parametric, semi-parametric and parametric approaches, we examine the determinants of the survival of wheat variety innovations, focusing on the impacts of changes to Plant Variety Protection (PVP) regime over the last four decades. We find that the period since the introduction of the PVP regime has been characterised by the accelerated development of new varieties and increased private sector participation in the breeding of cereal crop varieties. However, the increased flow of varieties has been accompanied by a sharp decline in the longevity of innovations. These trends may have contributed to a reduction in the returns appropriated by plant breeders from protected variety innovations and may explain the decline of conventional plant breeding in the UK. It may also explain the persistent demand from the seed industry for stronger protection. The strengthening of the PVP regime in conformity with the UPOV Convention of 1991, the introduction of EU-wide protection through the Community Plant Variety Office and the introduction of royalties on farm-saved seed have had a positive effect on the longevity of protected variety innovations, but have not been adequate to offset the long term decline in survival durations.

In vitro fermentation of grape seed flavan-3-ol fractions by human faecal microbiota: changes in microbial groups and phenolic metabolites

With the aim of investigating the potential of flavan-3-ols to influence the growth of intestinal bacterial groups, we have carried out the in vitro fermentation, with human faecal microbiota, of two purified fractions from grape seed extract (GSE): GSE-M (70% monomers and 28% procyanidins) and GSE-O (21% monomers and 78 % procyanidins). Samples were collected at 0, 5, 10, 24, 30 and 48 h of fermentation for bacterial enumeration by fluorescent in situ hybridization and for analysis of phenolic metabolites. Both GSE-M and GSE-O fractions promoted growth of Lactobacillus/Enterococcus and decrease in the Clostridium histolyticum group during fermentation, although the effects were only statistically significant with GSE-M for Lactobacillus/Enterococcus (at 5 and 10 h of fermentation) and GSE-O for C. histolyticum (at 10 h of fermentation). Main changes in polyphenol catabolism also occurred during the first 10 h of fermentation, however no significant correlation coefficients (P>0.05) were found between changes in microbial populations and precursor flavan-3-ols or microbial metabolites. Together these data suggest that the flavan-3-ol profile of a particular food source could affect the microbiota composition and its catabolic activity, inducing changes that could in turn affect the bioavailability and potential bioactivity of these compounds.

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.

Heterozygosity and diversity analysis using mapped single nucelotide polymorphisms in a faba bean inbreeding programme

The aim of this study was to convert existing faba bean (Vicia faba L.) single nucleotide polymorphism (SNP) markers from cleaved amplification polymorphic sequences and SNaPshot® formats, which are expensive and time-consuming, to the more convenient KBiosciences competitive allele‐specific PCR (KASP) assay format. Out of 80 assays designed, 75 were validated, though a core set of 67 of the most robust markers is recommended for further use. The 67 best KASP SNP assays were used across two generations of single seed descent to detect unintended outcrossing and to track and quantify loss of heterozygosity, a capability that will significantly increase the efficiency and performance of pure line production and maintenance. This same set of assays was also used to examine genetic relationships between the 67 members of the partly inbred panel, and should prove useful for line identification and diversity studies in the future.

High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes

Background: Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. Results: We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. Conclusions: Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service.

Promoter analysis and immunolocalisation show that puroindoline genes are exclusively expressed in starchy endosperm cells of wheat grain

The purolindolines are small cysteine-rich proteins which are present in the grain of wheat. They have a major impact on the utilisation of the grain as they are the major determinants of grain texture, which affects both milling and baking properties. Bread and durum wheats were transformed with constructs comprising the promoter regions of the Puroindoline a (Pina) and Puroindoline b (Pinb) genes fused to the uidA (GUS) reporter gene. Nine lines showing 3:1 segregation for the transgene and comprising all transgene/species combinations were selected for detailed analysis of transgene expression during grain development. This showed that transgene expression occurred only in the starchy endosperm cells and was not observed in any other seed or vegetative tissues. The location of the puroindoline proteins in these cells was confirmed by tissue printing of developing grain, using a highly specific monoclonal antibody for detection and an antibody to the aleurone-localised 8S globulin as a control. This provides clear evidence that puroindolines are only synthesised and accumulated in the starchy endosperm cells of the wheat grain.

Analysis of tyrosine phosphorylation and phosphotyrosine-binding proteins in germinating seeds from Scots pine

Protein tyrosine phosphorylation in angiosperms has been implicated in various physiological processes, including seed development and germination. In conifers, the role of tyrosine phosphorylation and the mechanisms of its regulation are yet to be investigated. In this study, we examined the profile of protein tyrosine phosphorylation in Scots pine seeds at different stages of germination. We detected extensive protein tyrosine phosphorylation in extracts from Scots pine (Pinus sylvestris L.) dormant seeds. In addition, the pattern of tyrosine phosphorylation was found to change significantly during seed germination, especially at earlier stages of post-imbibition which coincides with the initiation of cell division, and during the period of intensive elongation of hypocotyls. To better understand the molecular mechanisms of phosphotyrosine signaling, we employed affinity purification and mass spectrometry for the identification of pTyr-binding proteins from the extracts of Scots pine seedlings. Using this approach, we purified two proteins of 10 and 43 kDa, which interacted specifically with pTyr-Sepharose and were identified by mass spectrometry as P. sylvestris defensin 1 (PsDef1) and aldose 1-epimerase (EC:5.1.3.3), respectively. Additionally, we demonstrated that both endogenous and recombinant PsDef1 specifically interact with pTyr-Sepharose, but not Tyr-beads. As the affinity purification approach did not reveal the presence of proteins with known pTyr binding domains (SH2, PTB and C2), we suggest that plants may have evolved a different mode of pTyr recognition, which yet remains to be uncovered.