The complete set of genes encoding major intrinsic proteins in Arabidopsis provides a framework for a new nomenclature for major intrinsic proteins in plants

Major intrinsic proteins (MIPs) facilitate the passive transport of small polar molecules across membranes. MIPs constitute a very old family of proteins and different forms have been found in all kinds of living organisms, including bacteria, fungi, animals, and plants. In the genomic sequence of Arabidopsis, we have identified 35 different MIP-encoding genes. Based on sequence similarity, these 35 proteins are divided into four different subfamilies: plasma membrane intrinsic proteins, tonoplast intrinsic proteins, NOD26-like intrinsic proteins also called NOD26-like MIPs, and the recently discovered small basic intrinsic proteins. In Arabidopsis, there are 13 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, nine NOD26-like intrinsic proteins, and three small basic intrinsic proteins. The gene structure in general is conserved within each subfamily, although there is a tendency to lose introns. Based on phylogenetic comparisons of maize (Zea mays) and Arabidopsis MIPs (AtMIPs), it is argued that the general intron patterns in the subfamilies were formed before the split of monocotyledons and dicotyledons. Although the gene structure is unique for each subfamily, there is a common pattern in how transmembrane helices are encoded on the exons in three of the subfamilies. The nomenclature for plant MIPs varies widely between different species but also between subfamilies in the same species. Based on the phylogeny of all AtMIPs, a new and more consistent nomenclature is proposed. The complete set of AtMIPs, together with the new nomenclature, will facilitate the isolation, classification, and labeling of plant MIPs from other species.     

Simultaneous detection of IFN-gamma and IL-4 mRNAs using RT-PCR and time-resolved fluorometry

Time-resolved fluorometry was applied in the detection of RT-PCR amplified mRNAs for the Th1 and Th2 cell-derived cytokines interferon gamma (IFN-gamma) and interleukin (IL-)4, respectively. RNA stimulated cells was reverse transcribed and the cDNAs for the cytokine mRNAs and the constantly expressed beta-actin (beta-ACT) mRNA were simultaneously amplified in one multiplex PCR reaction. The PCR conditions were optimized to minimize mutual inhibition of individual amplifications. One of the PCR primers in each primer pair was biotinylated, and the PCR products were captured onto streptavidin-coated microtitre plates. The three PCR products were detected with three different lanthanide labelled target-specific probes in solution hybridization. IFN-gamma, IL-4 and beta-ACT were detected with europium (Eu), terbium (Tb) and samarium (Sm) labelled probes, respectively, using time-resolved fluorometry. Small cell numbers used in microtitre plate cultures were sufficient to detect cytokine messages after mitogen stimulation. This sequence-based method provides a sensitive, specific, fast and nonisotopic alternative to conventional blotting and hybridisation with radioactive probes. In addition, the multiplex fluorogenic dye detection facilitates relative quantification of target mRNAs.     

Evidence for cooperative binding of (-)Isoproterenol to rat brain beta1-adrenergic receptors

In the present study, the effects of the thiol oxidising agent diamide upon the properties of rat brain beta1-adrenergic and human platelet serotonin2A receptor recognition sites have been investigated using [3H](-)CGP-12177 (in the presence of ICI-118551) and [3H]LSD as ligands. (-)Isoprenaline inhibited [3H](-)CGP-12177 binding with nH values of 0.87, 0.67, and 0.56 for added Mg2+ concentrations of 0, 2.5, and 25 mM, respectively. Pretreatment with diamide increased the nH to above unity for the inhibition of the binding by (-)isoprenaline, without a concomitant effect on the inhibition of the binding by (-)propranolol. In contrast, diamide reduced the affinity of human platelet serotonin2A-receptors for antagonists, but did not consistently induce nH values above unity for the inhibition of antagonist binding by serotonin. These results suggest that cooperative interactions reported for cardiac muscarinic receptors may also occur for beta1-adrenergic receptors in the rat brain.     

A new dominant selection marker for transformation of Pichia pastoris to soraphen A resistance

Despite the considerable progress molecular genetics of filamentous fungi has made during the past decade, there is still an urgent need for efficiently working selectable markers for fungal transformation. Using Pichia pastoris as a host, we describe the development of a new dominant selectable marker of prokaryotic origin. This system, termed sor(R), is based upon the resistance of the bacterial enzyme acetyl-CoA carboxylase (ACCase) to the macrocyclic polyketide soraphen A, a potent inhibitor of fungal ACCase produced by the myxobacterium Sorangium cellulosum. In this study, we firstly demonstrate that the integration of a single sor(R) cassette into the P. pastoris genome confers resistance to elevated concentrations of soraphen A. Furthermore, it has been shown that the versatility of this marker can be considerably increased by splitting the sor(R) cassette, especially when successive transformations are performed on the same strain. As pronounced sensitivity to soraphen A is the rule among filamentous fungi, we expect the sor(R) marker to be a widely applicable tool for fungal transformation.     

Covalent binding of the 13C-labeled skin sensitizers 5-chloro-2-methylisothiazol-3-one (MCI) and 2-methylisothiazol-3-one (MI) to a model peptide and glutathione

The reactivity of 4-[13C]- and 5-[13C]-5-chloro-2-methylisothiazol-3-one (MCI) and 2-methylisothiazol-3-one (MI) towards a model peptide and glutathione was followed by 13C and 1H[13C] NMR spectroscopy. Both molecules were found to react with GSH but in addition MCI was found to react with histidine and lysine to form adducts of a different nature. Reaction with histidine led to stable substitution adducts through an addition-elimination reaction at position 5 while reaction with lysine led to the formation of open adducts of the thioamide or amide type.     

Postreplicative recruitment of cohesin to double-strand breaks is required for DNA repair

Chromosome stability depends on accurate chromosome segregation and efficient DNA double-strand break (DSB) repair. Sister chromatid cohesion, established during S phase by the protein complex cohesin, is central to both processes. In the absence of cohesion, chromosomes missegregate and G2-phase DSB repair fails. Here, we demonstrate that G2-phase repair also requires the presence of cohesin at the damage site. Cohesin components are shown to be recruited to extended chromosome regions surrounding DNA breaks induced during G2. We find that in the absence of functional cohesin-loading proteins (Scc2/Scc4), the accumulation of cohesin at DSBs is abolished and repair is defective, even though sister chromatids are connected by S phase generated cohesion. Evidence is also provided that DSB induction elicits establishment of sister chromatid cohesion in G2, implicating that damage-recruited cohesin facilitates DNA repair by tethering chromatids.     

A comparison of scoring functions for protein sequence profile alignment

MOTIVATION: In recent years, several methods have been proposed for aligning two protein sequence profiles, with reported improvements in alignment accuracy and homolog discrimination versus sequence-sequence methods (e.g. BLAST) and profile-sequence methods (e.g. PSI-BLAST). Profile-profile alignment is also the iterated step in progressive multiple sequence alignment algorithms such as CLUSTALW. However, little is known about the relative performance of different profile-profile scoring functions. In this work, we evaluate the alignment accuracy of 23 different profile-profile scoring functions by comparing alignments of 488 pairs of sequences with identity < or =30% against structural alignments. We optimize parameters for all scoring functions on the same training set and use profiles of alignments from both PSI-BLAST and SAM-T99. Structural alignments are constructed from a consensus between the FSSP database and CE structural aligner. We compare the results with sequence-sequence and sequence-profile methods, including BLAST and PSI-BLAST. RESULTS: We find that profile-profile alignment gives an average improvement over our test set of typically 2-3% over profile-sequence alignment and approximately 40% over sequence-sequence alignment. No statistically significant difference is seen in the relative performance of most of the scoring functions tested. Significantly better results are obtained with profiles constructed from SAM-T99 alignments than from PSI-BLAST alignments. AVAILABILITY: Source code, reference alignments and more detailed results are freely available at http://phylogenomics.berkeley.edu/profilealignment/     

Analysis of kavalactones from Piper methysticum (kava-kava)

The chemical analysis and quality control of both Piper methysticum G. Forster (kava-kava) and extracts obtained by aqueous acetone or aqueous methanol as well as supercritical fluid extraction are reviewed. In the last two decades various procedures concerning the separation and detection of kavalactones have been routinely carried out by gas chromatography (without previous derivatization of kavalactones) and high performance liquid chromatography but most of them are not validated or only partially validated. Recently, analyses by supercritical fluid chromatography and micellar electrokinetic chromatography have also been reported. Both gas chromatography and high performance liquid chromatography can be used for the analysis of kavalactones with some advantages and disadvantages for each method. Using gas chromatography analysis, methysticin and yangonin, which are two of the major components, are generally not separated. In addition, the high temperature of the injection port caused the decomposition of methysticin. Concerning high performance liquid chromatography analyses, the reversed-phase is generally better because highly reproducible with a very low detection limit for all compounds even if the quantitative analysis of the kavalactones by liquid chromatography needs to be carried out in the absence of light to prevent the cis/trans isomerisation of yangonin.     

Mesenchymal stem/progenitor cells developed in cultures from UC blood

Background Whether umbilical cord blood (UCB) serves as a source of mesenchymal stem/progenitor cells (MSPC) is controversial. MSPC are the best candidates for cellular therapy of orthopedic skeletal tissues. In order to explore the possibility of UCB as a useful source of MSPC, we identified, expanded in culture, and characterized MSPC from UCB harvests on a large scale. Methods Mononuclear cells isolated from UCB harvests (n=411) were cultured in media supplemented with 10% FBS. MSPC-like cells cultured from each UCB harvest were expanded ex vivo by successive subcultivation. UCB harvests with a more than 1000-fold expanding capacity (n=9) were examined for surface Ag phenotypes and in vitro differentiation potentials into osteogenic, chondrogenic and adipogenic lineages. Results Ninety-five out of a total of 411 UCB units (23.1%) generated MSPC-like cells during cultivation. Nine UCB units (2.2%) yielded MSPC with more than 1000-fold expansion capacity. These cells positively expressed MSPC-related Ag, but did not express myeloid, histocompatibility or endothelial Ag. These cells also possessed multiple capacities for osteogenic, chondrogenic and adipogenic differentiation. Discussion Although the incidence of UCB harvests producing MSPC in culture was low, some of them showed a more than 1000-fold expanding capacity, which is enough in cell numbers to be an allogeneic source for cellular therapy. Our results may encourage the use of UCB as an attractive target for allogeneic cellular therapeutic options in tissue engineering.