A simplified procedure for lipid phosphorus analysis shows that digestion rates vary with phospholipid structure

A simplified procedure for lipid digestion, well suited for handling a large number of samples, was used to analyze a variety of common phospholipids. This procedure involves digestion of phospholipids in perchloric acid at 130 degrees C with minimal sample manipulation. For all lipids tested, complete destruction, needed for quantitation of phosphate, was achieved after a few hours of digestion under these conditions. Rates of phospholipid destruction, monitored by the spectrophotometric quantitation of released phosphate, varied with lipid structure. Phosphatidic acid (PA), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and phosphatidylinositol (PI) were found to release phosphate faster than phosphatidylserine (PS), phosphatidylethanolamine (PE) and phosphatidylcholine (PC). Although these differences may vary depending on the digestion conditions, they suggest that care should be exercised in lipid phosphate analyses to insure complete digestion.     

Molecular characterization of a plant FKBP12 that does not mediate action of FK506 and rapamycin

Immuonosuppressive drugs FK506 and rapamycin block a number of signal transduction pathways in eukaryotic systems. The 12 kDa FK506 binding protein (FKBP12) mediates the action of both FK506 and rapamycin against their functional targets. In this report, we cloned, sequenced and characterized a gene encoding FKBP12 in Vicia faba ( Vf FKBP12). While Vf FKBP12 is highly homologous to animal and yeast FKBP12, it does not mediate the action of FK506 and rapamycin. There are unique features in plant FKBP12 sequences that cause the variation in their function. One lies in the domain that is critical for interaction with calcineurin (CaN), the mammalian and yeast target of FKBP12-FK506 complex. Protein–protein interaction assays revealed a low-affinity and unstable Vf FKBP12-FK506-CaN ternary complex. In the genetic assay, Vf FKBP12 did not restore the sensitivity of yeast FKBP12 mutant to rapamycin or FK506, supporting that plant FKBP12-ligand complexes are unable to block the function of the drug target. Also unique to plant FKBP12 proteins, a pair of cysteines is spatially adjacent to potentially form disulfide linkage. Treatment of Vf FKBP12 with reductant dithiothreitol (DTT) abolished the formation of Vf FKBP12-FK506-CaN ternary complex. Site-directed mutagenesis to substitute one of the cysteines, Cys²⁶, with Ser produced a similar effect as DTT treatment. These results indicate that an intramolecular disulfide bond is a novel structural feature required for the low–affinity interaction between plant FKBP12 and CaN. In conclusion, plant FKBP12 proteins have evolved structural changes that modify their protein-protein interacting domains and cause loss of function against the drug targets.     

A C-reactive protein mutant that does not bind to phosphocholine and pneumococcal C-polysaccharide

C-reactive protein (CRP), the major human acute-phase plasma protein, binds to phosphocholine (PCh) residues present in pneumococcal C-polysaccharide (PnC) of Streptococcus pneumoniae and to PCh exposed on damaged and apoptotic cells. CRP also binds, in a PCh-inhibitable manner, to ligands that do not contain PCh, such as fibronectin (Fn). Crystallographic data on CRP-PCh complexes indicate that Phe(66) and Glu(81) contribute to the formation of the PCh binding site of CRP. We used site-directed mutagenesis to analyze the contribution of Phe(66) and Glu(81) to the binding of CRP to PCh, and to generate a CRP mutant that does not bind to PCh-containing ligands. Five CRP mutants, F66A, F66Y, E81A, E81K, and F66A/E81A, were constructed, expressed in COS cells, purified, and characterized for their binding to PnC, PCh-BSA, and Fn. Wild-type and F66Y CRP bound to PnC with similar avidities, while binding of E81A and E81K mutants to PnC was substantially reduced. The F66A and F66A/E81A mutants did not bind to PnC. Identical results were obtained with PCh-BSA. In contrast, all five CRP mutants bound to Fn as well as did wild-type CRP. We conclude that Phe(66) is the major determinant of CRP-PCh interaction and is critical for binding of CRP to PnC. The data also suggest that the binding sites for PCh and Fn on CRP are distinct. A CRP mutant incapable of binding to PCh provides a tool to assess PCh-inhibitable interactions of CRP with its other biologically significant ligands, and to further investigate the functions of CRP in host defense and inflammation.     

A Dictyostelium discoideum mitochondrial fluorescent tagging vector that does not affect respiratory function

Visualizing mitochondria in living Dictyostelium discoideum cells using fluorescent dyes is often problematic due to variability in staining, metabolism of the dyes, and unknown potential effects of the dyes on mitochondrial function. We show that fluorescent labelling of mitochondria, using an N-terminal mitochondrial localization sequence derived from the D. discoideum protein GcvH1 (glycine cleavage system H1) attached to a red fluorescent protein enables clear mitochondrial imaging. We also show that this labelling has no effect upon mitochondria load or respiratory function.     

A Desulfitobacterium strain isolated from human feces that does not dechlorinate chloroethenes or chlorophenols

An anaerobic bacterium, strain DP7, was isolated from human feces in mineral medium with formate and 0.02% yeast extract as energy and carbon source. This rod-shaped motile bacterium used pyruvate, lactate, formate, hydrogen, butyrate, and ethanol as electron donor for sulfite reduction. Other electron acceptors such as thiosulfate, nitrate and fumarate stimulated growth in the presence of 0.02% yeast extract and formate. Acetate was the only product during fermentative growth on pyruvate. Six mol of pyruvate were fermented to 7 mol of acetate. 13C-NMR labeling experiments showed homoacetogenic 13C-CO2 incorporation into acetate. The pH and temperature optimum of fermentative growth on pyruvate was 7.4 and 37 degrees C, respectively. The growth rate under these conditions was approximately 0.10 h(-1). Strain DP7 was identified as a new strain of Desulfitobacterium frappieri on the basis of 16S rRNA sequence analysis (99% similarity) and DNA-DNA hybridization (reassociation value of 83%) with Desulfitobacterium frappieri TCE1. In contrast to described Desulfitobacterium strains, the newly isolated strain has not been isolated from a polluted environment and did not use chloroethenes or chlorophenols as electron acceptor.     

A divergent testis-specific alpha-tubulin isotype that does not contain a coded C-terminal tyrosine.

On the basis of analysis of cDNA clones of alpha-tubulin RNAs expressed during spermiogenesis in chickens, we report the identification of a novel alpha-tubulin which is expressed exclusively in chicken testes. Comparison of its sequence with those previously determined not only demonstrates that the encoded polypeptide is significantly divergent from other alpha-tubulins but also supports the hypothesis that alpha-tubulin isotypes are distinguished by a carboxy-terminal variable region sequence and, to a lesser extent, by a domain near the amino terminus. Since essentially all previously known alpha-tubulins undergo a unique cycle of removal and posttranslational readdition of a tyrosine residue at the extreme carboxy terminus, the presence in this testes alpha-tubulin of a very divergent carboxy terminus that does not contain an encoded tyrosine raises the possibility that this polypeptide does not participate in the usual cycle of tyrosination/detyrosination.     

Carboxylate composition of root exudates does not relate consistently to a crop species' ability to use phosphorus from aluminium, iron or calcium phosphate sources

* The relationship between carboxylate release from roots and the ability of the species to utilize phosphorus from sparingly soluble forms was studied by comparing Triticum aestivum, Brassica napus, Cicer arietinum, Pisum sativum, Lupinus albus, Lupinus angustifolius and Lupinus cosentinii. * Plants were grown in sand and supplied with 40 mg P kg(-1) in the sparingly soluble forms AlPO(4), FePO(4) or Ca(5)OH(PO(4))(3), or as soluble KH(2)PO(4); control plants received no P. * The ability to utilize sparingly soluble forms of P differed between forms of P supplied and species. Pisum sativum and C. arietinum did not access AlPO(4) or FePO(4) despite releasing carboxylates into the rhizosphere. * Species accessed different forms of sparingly soluble P, but no species was superior in accessing all forms. We conclude that a single trait cannot explain access to different forms of sparingly soluble P, and hypothesize that in addition to carboxylates, rhizosphere pH and root morphology are key factors.     

A genomic survey shows that the haloarchaeal type tyrosyl tRNA synthetase is not a synapomorphy of opisthokonts

The haloarchaeal-type tyrosyl tRNA synthetase (tyrRS) have previously been proposed to be a molecular synapomorphy of the opisthokonts. To re-evaluate this we have performed a taxon-wide genomic survey of tyrRS in eukaryotes and prokaryotes. Our phylogenetic trees group eukaryotes with archaea, with all opisthokonts sharing the haloarchaeal-type tyrRS. However, this type of tyrRS is not exclusive to opisthokonts, since it also encoded by two amoebozoans. Whether this is a consequence of lateral gene transfer or lineage sorting remains unsolved, but in any case haloarchaeal-type tyrRS is not a synapomorphy of opisthokonts. This demonstrates that molecular markers should be re-evaluated once a better taxon sampling becomes available.     

35Cl nuclear magnetic resonance line broadening shows that eosin-5-maleimide does not block the external anion access channel of band 3.

It has been suggested that Lys-430 of band 3, with which eosin-5-maleimide (EM) reacts, is located in the external channel through which anions gain access to the external transport site, and that EM inhibits anion exchange by blocking this channel. To test this, we have used 35Cl nuclear magnetic resonance (NMR) to measure Cl- binding to the external transport site in control and EM-treated human red blood cells. Intact cells were used rather than ghosts, because in this case all line broadening (LB) results from binding to external sites. In an NMR spectrometer with a 9.4-T magnetic field, red blood cells at 50% concentration (v/v) in 150 mM Cl- medium at 3 degrees C caused 19.0 +/- 1.2 Hz LB. Of this, 7.9 +/- 0.7 Hz was due to Cl- binding to the high affinity band 3 transport sites, because it was prevented by an apparently competitive inhibitor of anion exchange, 4,4'-dinitrostilbene-2,2'-disulfonate (DNDS). The LB was not due to hemoglobin released from the cells, as little LB remained in the supernatant after cells were removed by centrifugation. Saturable Cl- binding remained in EM-treated cells, although the binding was no longer DNDS-sensitive, because EM prevents binding of DNDS. The lower limit for the rate at which Cl- goes from the binding site to the external medium is 2.15 x 10(5) s-1 for control cells and 1.10 x 10(5) s-1 for EM-treated cells, far higher than the Cl- translocation rate at 3 degrees C (about 400 s-1). Thus, EM does not inhibit Cl- exchange by blocking the external access channel. EM may therefore be useful for fixing band 3 in one conformation for studies of Cl- binding to the external transport site.     

A natural ErbB4 isoform that does not activate phosphoinositide 3-kinase mediates proliferation but not survival or chemotaxis

ErbB4 is a member of the epidermal growth factor receptor (ErbB) family that mediates cellular responses activated by neuregulins (NRG) and other epidermal growth factor-like growth factors. Two naturally occurring ErbB4 isoforms, ErbB4 CYT-1 and ErbB4 CYT-2, have previously been identified. Unlike ErbB4 CYT-1, ErbB4 CYT-2 lacks a phosphoinositide 3-kinase (PI3-K)-binding site and is incapable of activating PI3-K. We have now examined the consequences of the inability of this isoform to activate PI3-K on cell proliferation, survival, and chemotaxis in response to NRG-1beta: (i) NRG-1beta stimulated proliferation of cells expressing either ErbB4 CYT-1 or ErbB4 CYT-2. Consistent with the mitogenic responsiveness, analysis of downstream signaling showed that Shc and MAPK were phosphorylated after stimulating either isoform with NRG-1beta. (ii) NRG-1beta protected cells expressing ErbB4 CYT-1 but not cells expressing ErbB4 CYT-2 from starvation-induced apoptosis as measured by effects on cell number and 4', 6-diamidino-2-phenylindole staining. Furthermore, in cells expressing ErbB4 CYT-2, Akt, a protein kinase that mediates cell survival, was not phosphorylated. (iii) NRG-1beta stimulated chemotaxis and membrane ruffling in cells expressing ErbB4 CYT-1 but not in cells expressing ErbB4 CYT-2. In summary, ErbB4 CYT-2 can mediate proliferation but not chemotaxis or survival. These results suggest a novel mechanism by which cellular responses such as chemotaxis and survival may be regulated by the expression of alternative receptor-tyrosine kinase isoforms that differ in their coupling to PI3-K signaling.     

A monoclonal antibody reactive with 5-bromo-2-deoxyuridine that does not require DNA denaturation

We describe a mouse monoclonal antibody (BU-1) reactive with 5-bromo-2-deoxyuridine (BrdUrd). The antibody is different from previously described BrdUrd monoclonal antibodies in that BU-1 does not require pretreatment of cells with strong DNA denaturants in order for the antibody to react with BrdUrd incorporated in the DNA. The antibody can be used in immunocytochemical and indirect immunofluorescent assays and can be used to identify cells that have incorporated BrdUrd. Double staining with BU-1 antibody and propidium iodide has been used to confirm S-phase measurements with the BU-1 antibody. Immunocytochemical stains using the BU-1 antibody do not destroy cell morphology and allow cell identification to be performed simultaneously with S-phase measurements. Flow cytometer two-color fluorescence analysis allows the simultaneous identification of cell surface or cytoplasmic markers and S-phase quantitation. The BU-1 antibody should broaden the application of cell kinetic measurements to individual elements of cell populations that are heterogeneous with respect to morphology, surface marker, and other biological features.     

A new Sendai virus vector deficient in the matrix gene does not form virus particles and shows extensive cell-to-cell spreading

A new recombinant Sendai virus vector (SeV/DeltaM), in which the gene encoding matrix (M) protein was deleted, was recovered from cDNA and propagated in a packaging cell line expressing M protein by using a Cre/loxP induction system. The titer of SeV/DeltaM carrying the enhanced green fluorescent protein gene in place of the M gene was 7 x 10(7) cell infectious units/ml or more. The new vector showed high levels of infectivity and gene expression, similar to those of wild-type SeV vector, in vitro and in vivo. Virus maturation into a particle was almost completely abolished in cells infected with SeV/DeltaM. Instead, SeV/DeltaM infection brought about a significant increase of syncytium formation under conditions in which the fusion protein was proteolytically cleaved and activated by trypsin-like protease. This shows that SeV/DeltaM spreads markedly to neighboring cells in a cell-to-cell manner, because both hemagglutinin-neuraminidase and active fusion proteins are present at very high levels on the surface of cells infected with SeV/DeltaM. Thus, SeV/DeltaM is a novel type of vector with the characteristic features of loss of virus particle formation and gain of cell-to-cell spreading via a mechanism dependent on the activation of the fusion protein.     

A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates

Background  

Studies of differential expression that use Affymetrix GeneChip arrays are often carried out with a limited number of replicates. Reasons for this include financial considerations and limits on the available amount of RNA for sample preparation. In addition, failed hybridizations are not uncommon leading to a further reduction in the number of replicates available for analysis. Most existing methods for studying differential expression rely on the availability of replicates and the demand for alternative methods that require few or no replicates is high.     

Evidence that gingko biloba extract does not inhibit MAO A and B in living human brain

Extracts of Ginkgo biloba have been reported to reversibly inhibit both monoamine oxidase (MAO) A and B in rat brain in vitro leading to speculation that MAO inhibition may contribute to some of its central nervous system effects. Here we have used positron emission tomography (PET) to measure the effects of Ginkgo biloba on human brain MAO A and B in 10 subjects treated for 1 month with 120 mg/day of the Ginkgo biloba extract EGb 761, using [11C]clorgyline and [11C]L-deprenyl-D2 to measure MAO A and B respectively. A three-compartment model was used to calculate the plasma to brain transfer constant K1 which is related to blood flow, and lambdak3, a model term which is a function of the concentration of catalytically active MAO molecules. Ginkgo biloba administration did not produce significant changes in brain MAO A or MAO B suggesting that mechanisms other than MAO inhibition need to be considered as mediating some of its CNS effects.