Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index.

MOTIVATION: Matching both the retention index (RI) and the mass spectrum of an unknown compound against a mass spectral reference library provides strong evidence for a correct identification of that compound. Data on retention indices are, however, available for only a small fraction of the compounds in such libraries. We propose a quantitative structure-RI model that enables the ranking and filtering of putative identifications of compounds for which the predicted RI falls outside a predefined window. RESULTS: We constructed multiple linear regression and support vector regression (SVR) models using a set of descriptors obtained with a genetic algorithm as variable selection method. The SVR model is a significant improvement over previous models built for structurally diverse compounds as it covers a large range (360-4100) of RI values and gives better prediction of isomer compounds. The hit list reduction varied from 41% to 60% and depended on the size of the original hit list. Large hit lists were reduced to a greater extend compared with small hit lists. AVAILABILITY: http://appliedbioinformatics.wur.nl/GC-MS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Evoked potentials: three-dimensional display.

Procedures are described for displaying large numbers of evoked potentials. A photographic superposition of average evoked responses, with the concurrent modulation of the brightness of each trace, yields a display having the appearance of a three-dimensional surface formed from hundreds of average responses.

High level fructan accumulation in a transgenic sugar beet.

We have transformed sugar beet into a crop that produces fructans. The gene encoding 1-sucrose:sucrose fructosyl transferase (1-SST), which was isolated from Helianthus tuberosus, was introduced into sugar beet. In H. tuberosus, 1-SST mediates the first steps in fructan synthesis through the conversion of sucrose (GF) into low molecular weight fructans GF2, GF3, and GF4. In the taproot of sugar beet transformed with the 1-sst gene, the stored sucrose is almost totally converted into low molecular weight fructans. In contrast, 1-sst expression in the leaves resulted in only low levels of fructans. Despite the storage carbohydrate having been altered, the expression of the 1-sst gene did not have any visible effect on phenotype and did not affect the growth rate of the taproot as observed under greenhouse conditions.

A high efficiency technique for the generation of transgenic sugar beets from stomatal guard cells.

An optimized protocol has been developed for the efficient and rapid genetic modification of sugar beet (Beta vulgaris L.). A polyethylene glycol-mediated DNA transformation technique could be applied to protoplast populations enriched specifically for a single totipotent cell type derived from stomatal guard cells, to achieve high transformation frequencies. Bialaphos resistance, conferred by the pat gene, produced a highly efficient selection system. The majority of plants were obtained within 8 to 9 weeks and were appropriate for plant breeding purposes. All were resistant to glufosinate-ammonium-based herbicides. Detailed genomic characterization has verified transgene integration, and progeny analysis showed Mendelian inheritance.

Inconsistencies between human genetic cytolocations and those derived using genomic sequence.

One result of the publishing of the human genome sequence is the ability to define objects through their position on the consensus sequence. While this has simplified the process of creating order maps for genes on a chromosome, it has created discrepancies between the published cytolocations of human genes, as presented through genetic references, and those locations derived computationally from the genomic sequence. For the 6,830 records with HUGO gene symbols shared between the online version of Mendelian Inheritance in Man and Ensembl, 18% of the records have a discrepancy of at least one cytogenetic band between the datasets. Discordance between data sets at this frequency would have a significant impact on the utility of datasets created by the amalgamation of numerous biological databases.

Metabolomics meets functional assays: coupling LC-MS and microfluidic cell-based receptor-ligand analyses.

INTRODUCTION: Metabolomics has become a valuable tool in many research areas. However, generating metabolomics-based biochemical profiles without any related bioactivity is only of indirect value in understanding a biological process. Therefore, metabolomics research could greatly benefit from tools that directly determine the bioactivity of the detected compounds. OBJECTIVE: We aimed to combine LC-MS metabolomics with a cell based receptor assay. This combination could increase the understanding of biological processes and may provide novel opportunities for functional metabolomics. METHODS: We developed a flow through biosensor with human cells expressing both the TRPV1, a calcium ion channel which responds to capsaicin, and the fluorescent intracellular calcium ion reporter, YC3.6. We have analysed three contrasting Capsicum varieties. Two were selected with contrasting degrees of spiciness for characterization by HPLC coupled to high mass resolution MS. Subsequently, the biosensor was then used to link individual pepper compounds with TRPV1 activity. RESULTS: Among the compounds in the crude pepper fruit extracts, we confirmed capsaicin and also identified both nordihydrocapsaicin and dihydrocapsaicin as true agonists of the TRPV1 receptor. Furthermore, the biosensor was able to detect receptor activity in extracts of both Capsicum fruits as well as a commercial product. Sensitivity of the biosensor to this commercial product was similar to the sensory threshold of a human sensory panel. CONCLUSION: Our results demonstrate that the TRPV1 biosensor is suitable for detecting bioactive metabolites. Novel opportunities may lie in the development of a continuous functional assay, where the biosensor is directly coupled to the LC-MS.

Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics.

The quality of rice in terms not only of its nutritional value but also in terms of its aroma and flavour is becoming increasingly important in modern rice breeding where global targets are focused on both yield stability and grain quality. In the present paper we have exploited advanced, multi-platform metabolomics approaches to determine the biochemical differences in 31 rice varieties from a diverse range of genetic backgrounds and origin. All were grown under the specific local conditions for which they have been bred and all aspects of varietal identification and sample purity have been guaranteed by local experts from each country. Metabolomics analyses using 6 platforms have revealed the extent of biochemical differences (and similarities) between the chosen rice genotypes. Comparison of fragrant rice varieties showed a difference in the metabolic profiles of jasmine and basmati varieties. However with no consistent separation of the germplasm class. Storage of grains had a significant effect on the metabolome of both basmati and jasmine rice varieties but changes were different for the two rice types. This shows how metabolic changes may help prove a causal relationship with developing good quality in basmati rice or incurring quality loss in jasmine rice in aged grains. Such metabolomics approaches are leading to hypotheses on the potential links between grain quality attributes, biochemical composition and genotype in the context of breeding for improvement. With this knowledge we shall establish a stronger, evidence-based foundation upon which to build targeted strategies to support breeders in their quest for improved rice varieties.

Superoxide, hydrogen peroxide and singlet oxygen in hematoporphyrin derivative-cysteine, -NADH and -light systems.

Hematoporphyrin derivative and light in the presence of cysteine or glutathione were found to convert oxygen to superoxide and hydrogen peroxide at pH less than approx. 6.5, while at pH greater than 6.5 no superoxide or hydrogen peroxide production was observed. However, at pH values greater than 6.5 the rate of oxygen consumption increased. This rate paralleled the acid dissociation curve of the cysteine thiol group and is consistent with the chemical quenching of 1O2 by cysteine. The superoxide and hydrogen peroxide formation observed below pH 6.5 appeared not to be related to the singlet oxygen production of hematoporphyrin derivative. In addition, superoxide and hydrogen peroxide production was observed with hematoporphyrin derivative and light in the presence of NADH, both above and below pH 6.5. Direct detection of singlet oxygen luminescence at 1268 nm in the hematoporphyrin derivative-light system (2H2O as solvent) revealed an apparent linear increase in the singlet oxygen emission intensity as the p2H was raised from 7.0 to 10.0. Azide efficiently quenched this observed emission. In addition, at p2H 7.4, 1 mM cysteine resulted in a 40% reduction of the singlet oxygen luminescence, while at p2H 9.4 the signal was quenched by over 95% (under the experimental conditions employed). In total, we interpret these results as consistent with the chemical quenching of 1O2 by the ionized thiol group of cysteine.

Activation of nonspecific lipase (EC 3.1.1.-) by bile salts.

The enzyme nonspecific lipase (EC 3.1.1.-) from rat pancreas has been isolated and its amino acid composition determined. The amino acid composition confirms more indirect evidence that nonspecific lipase is not the same enzyme as cholesteryl ester hydrolase. Activation of the enzymatic activity by bile salts has been studied by equilibrium dialysis, gel filtration, light scattering, circular dichroism and fluorescence polarization. The binding of bile salt by the enzyme is saturable and is associated with a conformational change. Upon binding cholate, the protein experiences a decrease in beta-structure with no significant change in alpha-helix content, an increase in apparent Stokes radius, a decrease in light scattering properties, and a slight decrease in polarization of the intrinsic tryptophan fluorescence. Attachment of bile salt is associated with decreased reactivity of essential sulfhydryl groups, but no detectable change in reactivity of amino groups. A change to a more nearly spherical shape upon binding bile salt would be consistent with the experimental observations, but the exact sites of binding remain uncertain.

The Neurospora crassa genome: cosmid libraries sorted by chromosome.

A Neurospora crassa cosmid library of 12,000 clones (at least nine genome equivalents) has been created using an improved cosmid vector pLorist6Xh, which contains a bacteriophage lambda origin of replication for low-copy-number replication in bacteria and the hygromycin phosphotransferase marker for direct selection in fungi. The electrophoretic karyotype of the seven chromosomes comprising the 42.9-Mb N. crassa genome was resolved using two translocation strains. Using gel-purified chromosomal DNAs as probes against the new cosmid library and the commonly used medium-copy-number pMOcosX N. crassa cosmid library in two independent screenings, the cosmids were assigned to chromosomes. Assignments of cosmids to linkage groups on the basis of the genetic map vs. the electrophoretic karyotype are 93 +/- 3% concordant. The size of each chromosome-specific subcollection of cosmids was found to be linearly proportional to the size of the particular chromosome. Sequencing of an entire cosmid containing the qa gene cluster indicated a gene density of 1 gene per 4 kbp; by extrapolation, 11,000 genes would be expected to be present in the N. crassa genome. By hybridizing 79 nonoverlapping cosmids with an average insert size of 34 kbp against cDNA arrays, the density of previously characterized expressed sequence tags (ESTs) was found to be slightly <1 per cosmid (i.e., 1 per 40 kbp), and most cosmids, on average, contained an identified N. crassa gene sequence as a starting point for gene identification.

Computer-Assisted Identification of Protoplasts Responsible for Rare Division Events Reveals Guard-Cell Totipotency.

With the use of a computer-controlled microscope system to assist in the positioning and rapid relocation of large numbers of cultured cells, we were able to identify those protoplasts with the capacity to divide within a highly recalcitrant culture in which only a tiny fraction of the total population proceeds to produce viable microcalli. In the cultures used, comprising Beta vulgaris L. (sugar beet) leaf protoplasts, it was confirmed that these cells can be recognized solely on the basis of morphological characters. Therefore, a direct link exists between competence for cell division in vitro and cell type. Divergent callus morphologies and totipotent potential could also be ascribed to distinct protoplast types and hence to cells with a specific origin. The progenitors of the totipotent protoplasts in these cultures have been confirmed as being stomatal guard cells. Consequently, in plants even the most highly adapted living cells clearly retain and can reactivate all of the functional genetic information necessary to recreate the whole organism; an extreme degree of cytodifferentiation is, therefore, no hindrance to expressing totipotent potential. In addition to the considerable practical value of these findings, their implications concerning our understanding of both the control of gene expression and plant cell differentiation and its reversibility are of fundamental significance.

Stomatal Guard Cells Are Totipotent.

It has been successfully demonstrated, using epidermis explants of sugar beet (Beta vulgaris L.), that stomatal guard cells retain full totipotent capacity. Despite having one of the highest degrees of morphological adaptation and a unique physiological specialization, it is possible to induce a re-expression of full (embryogenic) genetic potential in these cells in situ by reversing their highly differentiated nature to produce regenerated plants via a callus stage. The importance of these findings both to stomatal research and to our understanding of cytodifferentiation in plants is discussed.

Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees.

The effects of conventional industrial processing steps on global phytochemical composition of broccoli, tomato and carrot purees were investigated by using a range of complementary targeted and untargeted metabolomics approaches including LC-PDA for vitamins, (1)H NMR for polar metabolites, accurate mass LC-QTOF MS for semi-polar metabolites, LC-MRM for oxylipins, and headspace GC-MS for volatile compounds. An initial exploratory experiment indicated that the order of blending and thermal treatments had the highest impact on the phytochemicals in the purees. This blending-heating order effect was investigated in more depth by performing alternate blending-heating sequences in triplicate on the same batches of broccoli, tomato and carrot. For each vegetable and particularly in broccoli, a large proportion of the metabolites detected in the purees was significantly influenced by the blending-heating order, amongst which were potential health-related phytochemicals and flavour compounds like vitamins C and E, carotenoids, flavonoids, glucosinolates and oxylipins. Our metabolomics data indicates that during processing the activity of a series of endogenous plant enzymes, such as lipoxygenases, peroxidases and glycosidases, including myrosinase in broccoli, is key to the final metabolite composition and related quality of the purees.

Singlet oxygen intermediacy in the photodynamic action of membrane-bound hematoporphyrin derivative.

The cell-damaging photochemistry of hematoporphyrin derivative (HPD) has been investigated using isolated erythrocyte membranes as a test system. Irradiation of membranes in the presence of the tumor-localizing fraction of HPD resulted in formation of singlet molecular oxygen (1O2) as measured by the phosphorescence at 1268 nm. The authentic product of 1O2 attack on cholesterol, 3 beta-hydroxy-5 alpha-cholest-6-ene-5-hydroperoxide, was identified in this system. Relatively insignificant amounts of free radical-derived hydroperoxides were detected. These results suggest that 1O2 plays a major role in the HPD-sensitized photokilling of tumor cells in vivo.

Plant cell culture initiation. Practical tips.

The use of cultured plant cells in either organized or unorganized form has increased vey considerably in the last 10-15 yr. Many new technologies have been developed and applications in both fundamental and applied research have led to the development of some powerful tools for improving our knowledge of botanical systems and for gaining external influence over some of the key processes involved in inter- and intracellular organization. This is particularly the case when cell culture techniques are combined with those for the genetic modification of plant cells. Being able to regenerate whole plants that have gained or lost the expression of one or more specific genes has revolutionized the way in which we approach scientific questions and has opened up many additional possibilities for the molecular dissection of plants. The success or fall of all plant cell culture technologies lies with culture initiation. The choice of plant material, its physiologival state and cultivation history, the media used, and their means of preparation are just some of the factors that can greatly influence whether the desired end result will be achieved. In this article are described some of the practical aspects involved in successful plant cell culture initiation and the choices that have to be made. Attention is given to some of the pitfalls that can occur and how to avoid them. A good start is half the work.

The biphotonic photoionization of chlorpromazine during conventional flash photolysis: spin trapping results with 5,5-dimethyl-1-pyrroline-N-oxide.

A novel combination of conventional flash photolysis and electron spin resonance (ESR) spin-trapping has been used to demonstrate that photoionization of chlorpromazine (CPZ), and the concomitant production of hydrated electron, occurs through a stepwise biphotonic mechanism during conventional flash photolysis at wavelengths above 290 nm. The production of hydrated electron in the flash photolysis experiment has been monitored and quantified through the use of the spin trapping agent, 5,5-dimethyl-1-pyrroline-N-oxide (DMPO). The effects of nitrous oxide, varying concentrations of CPZ and DMPO, and a range of flash intensities on the ESR spectra of the observed spin adducts of DMPO are discussed. The use of ESR spin trapping to monitor hydrated electron yields in flash photolysis experiments has the potential to permit the use of a much wider range of flash intensities than is typically possible with conventional optical experiments. Thus, there is a greater possibility of distinguishing between monophotonic and biphotonic processes.

Spectroscopic studies of cutaneous photosensitizing agents--XV. Anthralin and its oxidation product 1,8-dihydroxyanthraquinone.

The photochemistry (Type I and II) of anthralin and its photo-oxidation product 1,8-dihydroxyanthraquinone (1,8-DHAQ) has been studied in ethanol, acetonitrile and dimethylsulfoxide using spin-trapping and direct detection of singlet oxygen (1O2) luminescence techniques. In ethanol, where it exists in its neutral form (AN), anthralin does not undergo either Type I or II reactions upon UV-irradiation. In contrast, irradiation of anthralin in acetonitrile, a solvent in which anthralin is partially converted to its corresponding mono-anion (AN-), generates both superoxide and singlet oxygen. Irradiation of anthralin in dimethylsulfoxide, where the AN- form is present in substantial quantity, generates superoxide and solvent derived radicals but no detectable singlet oxygen. UV-irradiation of 1,8-DHAQ in ethanol and acetonitrile produces both superoxide and singlet oxygen in significant yields. In dimethylsulfoxide, on the other hand, only superoxide and solvent derived radicals are observed. The 1O2 quantum yield for AN- and 1,8-DHAQ in acetonitrile were determined to be 0.14 and 0.88 relative to rose bengal in the same solvent. These findings suggest that the AN photosensitization occurs via Type I and II pathways, is solvent dependent and involves AN- as well as its oxidation product 1,8-DHAQ, which is a more potent generator of both singlet oxygen and superoxide.

The stepwise biphotonic photoionization of chlorpromazine as seen by laser flash photolysis.

It is generally accepted that both promazine (PZ) and chlorpromazine (CPZ) photionize monophotonically to their respective cation radicals and the corresponding hydrated electrons. It is also supposed that this photoinization has a role in the phototoxic effects of these drugs. However, using laser flash photolysis, we have observed that photoionization of CPZ during S1 excitation (lambda greater than 300 nm) is a stepwise biphotonic process. In the case of PZ our flash photolysis results are less clearcut, but are consistent with stepwise biphotonic photoionization for S1 excitation. We demonstrate, using computer simulation of the intramolecular kinetics, that the estimated triplet state lifetime of CPZ is sufficiently long (23 ns at room temperature) to account for the apparent monophotonic photoionization that has been observed by others at high light intensities and short pulse times. Our laser flash photolysis results also suggest that the photo-ionization mechanism of PZ and CPZ is wavelength-dependent. Both drugs exhibit apparent monophotonic photoionization when they are excited at 266 nm under conditions of laser pulse width and intensity similar to those at 355 nm. We suggest that photoionization is not an important mechanism in the observed phototoxic and photoallergic effects of PZ and CPZ in sunlight.