Seed Number, Seed Size and Seed Diversity in Washington Lupin (Lupinus polyphyllus Lindl.)

Over 20 000 seeds of the Washington lupin (Lupinus polyphyllusLindl.) were examined and measured in an experiment carriedout over a 10 year period (1989–1999). Four differentgroups of Washington lupin seeds were found: dark, patterned,grey and light seeds. During the 10 year experiment, the totalaverage number of seeds per plant decreased from 2654 (1990)to 1220 (1999), there was a slight decrease in seed weight perplant and an increase in the average weight per seed. Therewas a clear seed size/number trade-off at the intraspecificlevel. The relative proportions of each seed group also changedwith patterned seeds becoming dominant (50% at the beginningand 90% at the end of the experiment), grey seeds remained constant(constituting 10% of the total seeds) and the proportion ofboth dark (33% at the beginning and 5% at the end) and light(10% at the beginning and 5% at the end of the experiment) seedsdecreased. Six hundred and sixty nine seeds were found to havea different testa ornamentation; they were distributed amongthe different groups as follows: 48% patterned seeds, 29% darkseeds, 12% grey seeds and 11% light seeds. There were no significantdifferences in the physical dimensions of the ornamented seedscompared with all other seeds. The results suggest that theWashington lupin is a mixture of different species and botanicalforms; this is discussed in relation to possible selection pressuresto produce both smaller and larger seeds. The possibility thatchanges in testa ornamentation are influenced by genes controllingthe synthesis of the seed coat pigment is discussed. Copyright2001 Annals of Botany Company Lupinus polyphyllus Lindl., lupine, plant biotechnology, plant parameters, selection pressure, seed size/number trade-off, testa ornamentation     

Notch-dependent Fizzy-related/Hec1/Cdh1 expression is required for the mitotic-to-endocycle transition in Drosophila follicle cells

During Drosophila oogenesis, Notch function regulates the transition from mitotic cell cycle to endocycle in follicle cells at stage 6. Loss of either Notch function or its ligand Delta (Dl) disrupts the normal transition; this disruption causes mitotic cycling to continue and leads to an overproliferation phenotype. In this context, the only known cell cycle component that responds to the Notch pathway is String/Cdc25 (Stg), a G2/M cell cycle regulator. We found that prolonged expression of string is not sufficient to keep cells efficiently in mitotic cell cycle past stage 6, suggesting that Notch also regulates other cell cycle components in the transition. By using an expression screen, we found such a component: Fizzy-related/Hec1/Cdh1 (Fzr), a WD40 repeat protein. Fzr regulates the anaphase-promoting complex/cyclosome (APC/C) and is expressed at the mitotic-to-endocycle transition in a Notch-dependent manner. Mutant clones of Fzr revealed that Fzr is dispensable for mitosis but essential for endocycles. Unlike in Notch clones, in Fzr mutant cells mitotic markers are absent past stage 6. Only a combined reduction of Fzr and ectopic Stg expression prolongs mitotic cycles in follicle cells, suggesting that these two cell cycle regulators, Fzr and Stg, are important mediators of the Notch pathway in the mitotic-to-endocycle transition.     

Culture-independent microbial community analysis reveals that inulin in the diet primarily affects previously unknown bacteria in the mouse cecum

Inulin is a well-known fructose-based prebiotic which has been shown to stimulate the growth of bifidobacteria, a bacterial group generally considered beneficial for intestinal health. In the present study, we analyzed inulin-associated shifts in the total bacterial community of wild-type mice and mice carrying a genetically inactivated adenomatous polyposis coli tumor suppressor gene by using DNA-based approaches independent of bacterial culturability. Mice were fed a high-fat, nonfiber diet with or without inulin inclusion at a 10% (wt/wt) concentration. Cecal contents were analyzed after 0, 3, and 9 weeks on the experimental diets. Inulin inclusion significantly affected the total bacterial community structure of the cecum as determined by both a nonselective percent-guanine-plus-cytosine-based profiling analysis and a more specific 16S ribosomal DNA sequence analysis. The shifts included stimulation of bifidobacteria and suppression of clostridia, but sequence comparison revealed that the major shifts were within previously unknown bacterial taxa. Concomitantly, significantly higher bacterial densities, determined by flow cytometry, were observed with the inulin-amended diet, and the metabolism of the cecal bacterial community was altered, as indicated by higher levels of residual short-chain fatty acids, particularly lactic acid. With regard to all of the microbiological parameters measured, the wild-type mice and mice carrying a genetically inactivated adenomatous polyposis coli tumor suppressor gene were essentially identical. Studies of the implications of pre- and probiotics may need to be expanded to include careful analysis of their effects on the entire microbial community, rather than just a few well-known species. Further studies are needed to increase our understanding of the possible roles of currently unknown gastrointestinal bacteria in health and disease.     

The ECVAM international validation study on in vitro embryotoxicity tests: results of the definitive phase and evaluation of prediction models. European Centre for the Validation of Alternative Methods

From 1996 to 2000, ZEBET (Centre for Documentation and Evaluation of Alternative Methods to Animal Experiments at the BgVV, Berlin, Germany) coordinated the European Centre for the Validation of Alternative Methods (ECVAM) prevalidation and validation study on three embryotoxicity tests: a) a test employing embryonic stem cell lines (EST); b) the micromass (MM) test; and c) the postimplantation rat whole-embryo culture assay (WEC test). The main objectives of the study were to assess the performance of these three in vitro tests in discriminating between non- embryotoxic, weakly embryotoxic and strongly embryotoxic compounds. Phase I of the study (1997) was designed as a prevalidation phase, for test protocol optimisation, and for the establishment of a comprehensive database of in vivo and in vitro data on embryotoxic compounds. Phase II (1998-2000) involved a formal validation trial, conducted under blind conditions on 20 test compounds selected from the database, which were coded and distributed to the participating laboratories. In the preliminary phase of the validation study, six chemicals out of the 20, which showed embryotoxic potential, were tested. These results were used to define new biostatistically based prediction models (PMs) for the MM and WEC tests, and to evaluate those developed previously for the EST. As a next step, the PMs were evaluated by using the results for the remaining 14 chemicals of the definitive phase of the validation study. The three in vitro embryotoxicity tests proved to be applicable to testing a diverse group of chemicals with different embryotoxic potentials (non-embryotoxic, weakly embryotoxic, and strongly embryotoxic). The reproducibility of the three in vitro embryotoxicity tests were acceptable according to the acceptance criteria defined by the Management Team. The concordances between the embryotoxic potentials derived from the in vitro data and from the in vivo data were good for the EST and the WEC (PM2) test, and sufficient for the MM test and the WEC (PM1) tests according to the performance criteria defined by the Management Team before the formal validation study. When applying the PM of the EST to the in vitro data obtained in the definitive phase of the formal validation study, chemicals were classified correctly in 78% of the experiments. For the MM and the WEC tests, the PMs provided 70% and 80% (PM2) correct classifications, respectively. And, very importantly, an excellent predictivity (100%, except for PM1 of the WEC test, with 79%, considered as good) was obtained with strong embryotoxic chemicals in each of the three in vitro tests.     

Arabidopsis RADICAL-INDUCED CELL DEATH1 belongs to the WWE protein-protein interaction domain protein family and modulates abscisic acid, ethylene, and methyl jasmonate responses

Experiments with several Arabidopsis thaliana mutants have revealed a web of interactions between hormonal signaling. Here, we show that the Arabidopsis mutant radical-induced cell death1 (rcd1), although hypersensitive to apoplastic superoxide and ozone, is more resistant to chloroplastic superoxide formation, exhibits reduced sensitivity to abscisic acid, ethylene, and methyl jasmonate, and has altered expression of several hormonally regulated genes. Furthermore, rcd1 has higher stomatal conductance than the wild type. The rcd1-1 mutation was mapped to the gene At1g32230 where it disrupts an intron splice site resulting in a truncated protein. RCD1 belongs to the (ADP-ribosyl)transferase domain-containing subfamily of the WWE protein-protein interaction domain protein family. The results suggest that RCD1 could act as an integrative node in hormonal signaling and in the regulation of several stress-responsive genes.     

Spatio-ecological niche segregation of two sympatric species of<Emphasis Type="Italic">Clidemia (Melastomataceae)</Emphasis> in Western Amazonian non-flooded rainforests

The frequent occurrence of sympatric series of closely related plant species in tropical rainforests has evoked claims for and against the application of the competitive exclusion principle in these ecosystems. Narrow niche limits defined by biotic as well as abiotic specialization have been reported for sympatric species of the same genus or family. In Amazonian lowland rainforests this question deserves renewed attention because: (1) the existence of edaphically defined community types has recently been well established, and (2) spatio-ecological niche segregation of congeneric species may help explain not only the maintenance of the high Amazonian alpha-diversity, but also its origin through sympatric ecological speciation. In this study, the morphology, ecology, and distribution patterns of two species,Clidemia epiphytica andC. longifolia (Melastomataceae), from western Amazonia, were analyzed. The aims were to find out whether they really are two distinct taxonomic species and if so, whether they also can be considered biological species; if the species are sympatric; and if they are ecologically specialized. The results showed that the morphological variation of the species seems continuous, but that they exhibit opposite morphological responses to variation in soil cation concentration, which suggests that they also are separate biological species. Furthermore, the species occur sympatrically but in different habitats. It is suggested that a part of the enigma of sympatric congeners in rainforests may be explainable by spatial segregation stemming from ecological specialization in relation to subtle environmental variation. It is hypothesized that the studied species are a good candidate case of sympatric speciation driven by ecological specialization.     

GRIM REAPER peptide binds to receptor kinase PRK5 to trigger cell death in Arabidopsis

Recognition of extracellular peptides by plasma membrane-localized receptor proteins is commonly used in signal transduction. In plants, very little is known about how extracellular peptides are processed and activated in order to allow recognition by receptors. Here, we show that induction of cell death in planta by a secreted plant protein GRIM REAPER (GRI) is dependent on the activity of the type II metacaspase METACASPASE-9. GRI is cleaved by METACASPASE-9 in vitro resulting in the release of an 11 amino acid peptide. This peptide bound in vivo to the extracellular domain of the plasma membrane-localized, atypical leucine-rich repeat receptor-like kinase POLLEN-SPECIFIC RECEPTOR-LIKE KINASE 5 (PRK5) and was sufficient to induce oxidative stress/ROS-dependent cell death. This shows a signaling pathway in plants from processing and activation of an extracellular protein to recognition by its receptor.     

The effect of cocoa and polydextrose on bacterial fermentation in gastrointestinal tract simulations

Effects of cocoa mass and supplemented dietary fiber (polydextrose) on microbial fermentation were studied by combining digestion simulations of stomach and small intestine with multi-staged colon simulations. During the four phases of digestion, concentrations of available soluble proteins and reducing sugars reflected in vivo absorption of nutrients in small intestine. In colon simulation vessels, addition of polydextrose to digested cocoa mass significantly increased concentrations of total short-chain fatty acids and butyric acid, from 103 to 468 mM (P<0.01) and from 12 to 22 mM (P<0.01), respectively. Long-chain fatty acid concentrations (decreasing from 1,222 to 240 mM) were mainly affected by the presence of digested cocoa mass. Cocoa mass with or without polydextrose addition significantly decreased production of cadaverine (P<0.02) and branched-chain fatty acids compared to control during colon simulations. Results indicate beneficial effects on metabolism of colonic microbiota after digestion of cocoa mass, and even more so with polydextrose addition.     

Exploring the lipoprotein composition using Bayesian regression on serum lipidomic profiles

MOTIVATION: Serum lipids have been traditionally studied in the context of lipoprotein particles. Today's emerging lipidomics technologies afford sensitive detection of individual lipid molecular species, i.e. to a much greater detail than the scale of lipoproteins. However, such global serum lipidomic profiles do not inherently contain any information on where the detected lipid species are coming from. Since it is too laborious and time consuming to routinely perform serum fractionation and lipidomics analysis on each lipoprotein fraction separately, this presents a challenge for the interpretation of lipidomic profile data. An exciting and medically important new bioinformatics challenge today is therefore how to build on extensive knowledge of lipid metabolism at lipoprotein levels in order to develop better models and bioinformatics tools based on high-dimensional lipidomic data becoming available today. RESULTS: We developed a hierarchical Bayesian regression model to study lipidomic profiles in serum and in different lipoprotein classes. As a background data for the model building, we utilized lipidomic data for each of the lipoprotein fractions from 5 subjects with metabolic syndrome and 12 healthy controls. We clustered the lipid profiles and applied a regression model within each cluster separately. We found that the amount of a lipid in serum can be adequately described by the amounts of lipids in the lipoprotein classes. In addition to improved ability to interpret lipidomic data, we expect that our approach will also facilitate dynamic modelling of lipid metabolism at the individual molecular species level.