MIAME/Plant - adding value to plant microarrray experiments.

Appropriate biological interpretation of microarray data calls for relevant experimental annotation. The widely accepted MIAME guidelines provide a generic, organism-independant standard for minimal information about microarray experiments. In its overall structure, MIAME is very general and specifications cover mostly technical aspects, while relevant organism-specific information useful to understand the underlying experiments is largely missing.

MSI1-like proteins: an escort service for chromatin assembly and remodeling complexes.

MSI1-like WD40 repeat proteins are subunits of many protein complexes controlling chromatin dynamics. These proteins do not have any catalytic activity, but several recent studies using loss-of-function mutants established specific functions during development. Here, we review the current knowledge of MSI1-like proteins, including their phylogenetic history, expression patterns, biochemical interactions and mutant phenotypes.

GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.

High-throughput gene expression analysis has become a frequent and powerful research tool in biology. At present, however, few software applications have been developed for biologists to query large microarray gene expression databases using a Web-browser interface. We present GENEVESTIGATOR, a database and Web-browser data mining interface for Affymetrix GeneChip data.

Transcriptional programs of early reproductive stages in Arabidopsis.

The life cycle of flowering plants alternates between a diploid sporophytic and a haploid gametophytic generation. After fertilization of each the egg and central cells by one male gamete, the development of both fertilization products occurs coordinated with the maternally derived seed coat and carpel tissues forming the fruit. The reproduction program is likely to involve the concerted activity of many genes.

Protein farnesylation in plants--conserved mechanisms but different targets.

Protein farnesylation has an important role in the regulation of plant development and signal transduction, but the exact function of this modification is not well understood. The identification of protein farnesyltransferase substrates, together with the genetic analysis of mutants that are deficient in protein farnesylation, should significantly increase our knowledge of this form of protein modification in plants.

The Arabidopsis SRR1 gene mediates phyB signaling and is required for normal circadian clock function.

Plants possess several photoreceptors to sense the light environment. In Arabidopsis cryptochromes and phytochromes play roles in photomorphogenesis and in the light input pathways that synchronize the circadian clock with the external world. We have identified SRR1 (sensitivity to red light reduced), a gene that plays an important role in phytochrome B (phyB)-mediated light signaling.

Kinetics and mechanism of long-chain fatty acid transport into phosphatidylcholine vesicles from various donor systems.

The kinetics of long-chain fatty acid (FA) transfer from three different donor systems to unilamellar egg phosphatidylcholine (EPC) vesicles containing the pH-sensitive fluorophore pyranine in the vesicle cavity were determined. The transfer of long-chain FA from three FA donors, FA vesicles, unilamellar EPC vesicles containing FA, and bovine serum albumin-FA complexes to pyranine-containing EPC vesicles is a true first-order process, indicating that the FA transfer proceeds through the aqueous phase and not through collisional contacts between the donor and acceptor. A collisional mechanism would be at least bimolecular, giving rise to second-order kinetics.

Acute sensory responses of nonsmokers at very low environmental tobacco smoke concentrations in controlled laboratory settings.

The objective of this study was to provide a basis for effectively protecting nonsmokers from acute sensory impacts and for preventing deterioration of indoor air quality caused by environmental tobacco smoke (ETS) emissions. With an olfactory experiment we determined odor detection thresholds (OT) of sidestream ETS (sETS), and with a full-body exposure experiment we investigated sensory symptoms at very low sETS exposure concentrations. OT concentrations for sETS are three and more orders of magnitude lower than ETS concentrations measured in field settings and correspond to a fresh air dilution volume of > 19,000 m(3) per cigarette, over 100 times more than had previously been suggested for acceptable indoor air conditions.

Role of scavenger receptors SR-BI and CD36 in selective sterol uptake in the small intestine.

The serum lipoprotein high-density lipoprotein (HDL), which is a ligand of scavenger receptors such as scavenger receptor class B type I (SR-BI) and cluster determinant 36 (CD36), can act as a donor particle for intestinal lipid uptake into the brush border membrane (BBM). Both cholesterol and phospholipids are taken up by the plasma membrane of BBM vesicles (BBMV) and Caco-2 cells in a facilitated (protein-mediated) process. The protein-mediated transfer of cholesterol from reconstituted HDL to BBMV depends on the lipid composition of the HDL.

Structure elucidation of beta-mannanase: from the electron-density map to the DNA sequence.

The crystal structure of affinity-purified Thermomonospora fusca beta-mannanase has been solved despite the lack of the major part of the amino-acid sequence. A high-quality electron-density map allowed the identification of a stretch of eight amino acids close to the C-terminus which was used to design a degenerate downstream PCR primer. Together with a specific primer previously derived from the N-terminus, 95.

Intestinal sterol absorption mediated by scavenger receptors is competitively inhibited by amphipathic peptides and proteins.

Exchangeable serum apolipoproteins and amphipathic alpha-helical peptides are effective inhibitors of sterol (free and esterified cholesterol) uptake at the small-intestinal brush border membrane. The minimal structural requirement of an inhibitor is an amphipathic alpha-helix of 18 amino acids. The inhibition is competitive, indicating that the inhibitor binds to scavenger receptor class B type I (SR-BI) present in the brush border membrane and responsible for sterol uptake.

The Atger3 promoter confers circadian clock-regulated transcription with peak expression at the beginning of the night.

In Arabidopsis thaliana, steady-state abundance of the Atger3 transcript encoding a germin-like cell wall protein follows a circadian rhythm, reaching its highest level at the beginning of the night. As a first step towards dissecting the molecular mechanisms underlying these transcript oscillations, the Atger3 genomic locus was characterised. Transcriptional fusions of 1.

Circadian clock-regulated expression of an RNA-binding protein in Arabidopsis: characterisation of a minimal promoter element.

The Atgrp7 transcript encodes a clock-regulated, glycine-rich, RNA-binding protein in Arabidopsis thaliana and shows a circadian variation in steady-state abundance. Constitutive overexpression of its product, AtGRP7, in transgenic Arabidopsis plants depresses the oscillations of the endogenous Atgrp7 transcript, indicating that both the transcript and the protein are part of a clock-regulated negative feedback circuit. Here we characterise the upstream region of the Atgrp7 gene in order to begin to dissect the molecular basis of this oscillating autoregulatory feedback loop.

The circadian system of Arabidopsis thaliana: forward and reverse genetic approaches.

It is now widely accepted that autoregulatory circuits involving transcription/translation of clock genes form the molecular basis of the endogenous circadian clock in different organisms. In Arabidopsis thaliana, the RNA-binding protein AtGRP7 (Arabidopsis thaliana glycine-rich protein) has been identified as part of a negative-feedback loop through which AtGRP7 regulates the circadian oscillations of its own transcript. Experimental evidence indicates that this feedback loop also is influenced by another oscillator.

Relevance of Na,K-ATPase to local extracellular potassium homeostasis and modulation of synaptic transmission.

The ion gradients generated by the Na,K-ATPase are essential for Na+-coupled transport systems, osmoregulation and restoration of ion concentrations in excitable tissues. Indirectly, the sodium pump controls intracellular Ca2+ concentration through the Na/Ca exchanger. In the nervous system various neurotransmitters can modulate Na,K-ATPase activity.

The extracellular domain of the sodium pump beta isoforms determines complex stability with alpha 1.

Both subunits of the Na,K-ATPase are encoded by several genes giving rise to at least six isozymes. To examine whether beta isoforms assemble with alpha 1 in a selective manner, we have overexpressed wild-type and chimeric beta subunits in L929 cells and examined assembly as a function of resistance towards detergent-mediated dissociation. In the presence of digitonin all beta chimeras coimmunoprecipitate the endogenous alpha 1 subunit.

A vector for the synthesis of cRNAs encoding Myc epitope-tagged proteins in Xenopus laevis oocytes.

We describe a plasmid, pNKS2-myc, designed for convenient in-frame fusion of an antibody-specific epitope sequence to the N terminus of a desired cDNA and subsequent synthesis of transcripts that direct the synthesis of the tagged polypeptide in Xenopus laevis (Xl) oocytes. pNKS2-myc contains an SP6 promoter, followed by the translation initiation sequence of the Na,K-pump beta 3 subunit of Xl and the sequence encoding an epitope derived from the human c-myc proto-oncogene product. Appropriate restriction sites allow one to insert virtually any desired cDNA fragment directly behind the epitope-specific sequence and before a long poly(A) tail.

Differentiation of embryonic chick brain cells in monolayer and reaggregate cultures: A potential model in vitro for neurotoxicity.

In order to develop a model for potential neurotoxicity and teratogenicity, chick brain cells (embryonic day 7) were mechanically dissociated and cultured for up to several months. Differentiation of nerve and glial cells (monolayers in petri dishes and reaggregates in suspension cultures) were monitored with monoclonal antibodies against 68 kDa neurofilament protein (anti-NF) and glial fibrillary acidic protein (anti-GFAP). Anti-NF stains neurons in vitro as they differentiate morphologically; at day 1 many nerve processes already are feebly stained.

Do we find relevant parameters for in vitro cytotoxicity testing?

The current strategy for the design of cytotoxicity tests is briefly reviewed in light of goals that need to be reached, and in the capacity of in vitro tests to fulfill the high public expectations for alternative methods to animal testing. Various cytotoxicity tests and parameters used for the assessment of topical toxicity and of neurotoxicity are chosen as examples and their relevance is discussed. Past experience with in vitro and short-term tests for mutagenicity shows not to look for one single supertest.