Mechanisms of chromosome banding

A series of biochemical investigations were undertaken to determine the mechanism of Q-banding. The results were as follows: 1. In agreement with previous studies, highly AT-rich DNA, such as poly(dA)-poly(dT), markedly enhanced quinacrine fluorescence while GC containing DNA quenched fluorescence. These effects persisted at DNA concentrations comparable to those in the metaphase chromosome. 2. Studies of quinacrine-DNA complexes in regard to the hypochromism of quinacrine, DNA Tm, DNA viscosity, and equilibrium dialysis, indicated the quinacrine was bound by intercalation with relatively little side binding. 3. Single or double stranded nucleotide polymers, in the form of complete or partial helices, were 1000-fold more effective in quenching than solutions of single nucleotides, suggesting that base stacking is required for quenching. 4. Studies of polymers in the A conformation, such as transfer RNA and DNA-RNA hybrids, indicated that marked base tilting does not affect the ability of nucleic acids to cause quenching or enhancement of quinacrine fluorescence. 5. Salts inhibit the binding of quinacrine to DNA. 6. Spermine, polylysine and polyarginine, which bind in the small groove of DNA, inhibited quinacrine binding and quenching, while histones, which probably bind in the large groove, had little effect. This correlated with the observation that removal of histones with acid has no effect on Q-banding. 7. Mouse liver chromatin was separated into five fractions. At concentrations of quinacrine from 2×10^?6 to 2×10^?5 M all fractions inhibited to varying degrees the ability of the chromatin DNA to bind quinacrine and quench quinacrine fluorescence. At saturating levels of quinacrine two fractions, the 400 g pellet (rich in heterochromatin) and a dispersed euchromatin supernatant fraction, showed a decreased number of binding sites for quinacrine. These two fractions were also the richest in non-histone proteins. 8. DNA isolated from the different fractions all showed identical quenching of quinacrine fluorescence. 9. Mouse GC-rich, mid-band, AT-rich, and satellite DNA, isolated by CsCl and Cs₂SO₄-Ag⁺ centrifugation all showed identical quenching of quinacrine fluorescence, indicating that within a given organism, except for very AT or GC-rich satellites, the variation in base composition is not adequate to explain Q-banding. — We interpret these results to indicate that: (a) quinacrine binds to chromatin by intercalation of the three planar rings with the large group at position 9 lying in the small groove of DNA, (b) most pale staining regions are due to a decrease binding of quinacrine, and (c) this inhibition of binding is predominately due to non-histone proteins.     

Mechanisms of chromosome banding

The binding of methylene blue to DNA and chromatin treated in various ways was examined by equilibrium dialysis. The maximum r value (moles of bound dye/mole of nucleotide) was 1.0 for DNA, 0.6 for unfixed chromatin, and 0.83 for chromatin fixed in methanol-acetic acid. When fixed chromatin was treated with saline-citrate at 60° C for 3 hours, as used for G-banding chromosomes, the r value decreased from 0.83 to 0.55. When unfixed chromatin was treated as for R-banding the r values also dropped. Equilibrium dialysis indicated there was no disproportionate increase of dye binding as the concentration of DNA increased. — These results, and others, suggest that some of the Giemsa negative regions of G- and R-banded chromosomes are due to the denaturation of non-histone proteins so that they more effectively cover the DNA and prevent side binding of the thiazin dyes.     

Chloride, sodium, potassium and faecal bacteria levels in surface runoff and subsurface percolates from grassland plots amended with cattle slurry

This study investigated the effectiveness of vegetated buffer strips for removing contaminants in runoff from grassed plots (slope 15%) after application of cattle slurry. Plots (8 x 8 m2 or 8 x 3 m2) received slurry or inorganic fertilizer, and then simulated rainfall (1, 7 and 21 days after slurry/fertilizer application); after each event, runoff and percolates were sampled at various distances downslope (2, 4, 6, and 8 m), and analysed for Cl-, Na+, K+ and faecal bacteria contents. Contaminant concentrations were markedly higher in runoff from the slurry-amended plots than in runoff from the fertiliser-amended plots. After the first rainfall event, some contaminant concentrations in runoff from the slurry-amended plots declined with distance downslope (i.e. with buffer strip width), supporting the relative efficacy of the strip for retaining pollutants. After the second and third rainfall events, by contrast, our results suggest remobilisation of contaminants retained during the first event. Faecal bacteria levels (especially streptococcus levels) remained high throughout the study, even in percolates and runoff collected 8 m downslope after the third rainfall event, and indeed even downslope of the adjacent fertilizer-amended plots (indicating lateral movement): this suggests that bacterial contamination may be the most significant risk arising from slurry application.     

Influence of force fields on the selective diffusion of para-xylene over ortho-xylene in 10-ring zeolites

A molecular dynamics study of diffusion of p-xylene and o-xylene has been performed over three different pure silica 10-ring zeolites, MFI, SFG and TUN. The shape selective properties of the frameworks of these three materials have been tested using four different types of force fields commonly used based on united atom, rigid-ion and core-shell approximations. The performance of each force field is analysed in order to find which force fields can give sufficiently accurate estimations that allow to select appropriate zeolites for selective separation of para/ortho xylene. This performance was found to depend on the quality of the structural properties of the zeolite, in particular the size and shape of the 10 rings which act as bottlenecks for the diffusion. The computational results allow us to define some optimum characteristics for the selective diffusion of p-xylene.     

Functional homology among human and fission yeast Cdc14 phosphatases

Budding and fission yeast Cdc14 homologues, a conserved family of serine-threonine phosphatases, play a role in the inactivation of mitotic cyclin-dependent kinases (CDKs) by molecularly distinct mechanisms. Saccharomyces cerevisiae Cdc14 protein phosphatase inactivates CDKs by promoting mitotic cyclin degradation and the accumulation of a CDK inhibitor to allow budding yeast cells to exit from mitosis. Schizosaccharomyces pombe Flp1 phosphatase down-regulates CDK/cyclin activity, controlling the degradation of the Cdc25 tyrosine phosphatase for fission yeast cells to undergo cytokinesis. In the present work, we show that human Cdc14 homologues (hCdc14A and hCdc14B) rescued flp1-deficient fission yeast strains, indicating functional homology. We also show that hCdc14A and B interacted in vivo with S. pombe Cdc25 and that hCdc14A dephosphorylated this mitotic inducer both in vitro and in vivo. Our results support a Cdc14 conserved inhibitory mechanism acting on S. pombe Cdc25 protein and suggest that human cells may regulate Cdc25 in a similar manner to inactivate Cdk1-mitotic cyclin complexes.     

Heterogenised Rh(I), Ir(I) metal complexes with chiral triaza donor ligands: a cooperative effect between support and complex

Rhodium and iridium complexes of the chiral triaza ligands, {N,N^′-bis{[(2S)-(1-benzylpyrrolidinyl)]methyl}amine (2), N,N^′-bis{[(2S)-(1-benzylpyrrolidinyl)]methyl}-N-propylamine (3), N,N^′-bis{[(2S)-(1-benzylpyrrolidinyl)]methyl}-N-[3-(triethoxysilyl)propyl]amine (4)}, are described. All ligands form one to one [ML] species with the above metal ions. The structures of these complexes were elucidated by analytical and spectroscopic data (elemental analysis, mass spectroscopy, IR, ¹H and ¹³C NMR). The fixation of the preformed triethoxysilyl-rhodium and iridium complexes, on mesoporous solids (MCM-41, SBA-15), and their use, under heterogeneous conditions, for the hydrogenation reactions are reported. The catalytic activity and selectivity of heterogenised complexes are higher to that observed under homogeneous conditions, as a consequence of the complex- and/or reagents-to-support interaction. The stable covalent bond between support and complex allows the recovery and recycling of the heterogenised catalysts for a number of cycles, moreover atomic absorption analysis of the reaction solutions shows that there is not any metal leaching into the solutions.     

Preparation of substituted anilines from nitro compounds by using supported gold catalysts

A protocol for the chemoselective hydrogenation of nitro compounds to the corresponding anilines by means of supported gold catalysts is described. Nitro groups on different compounds--containing double bonds, carbonyl, nitrile or amide groups--have been successfully hydrogenated on supported gold nanoparticles (Au/TiO2 and Au/Fe2O3), using a batch reactor under H2 pressure. Unlike other noble metals, gold shows high chemoselectivity towards reduction of the nitro group, at near-complete conversion of the substrate. The total time to carry out this protocol strongly depends on the reaction step, which is a function of the activity of the catalyst and the nature of the substrate.     

Polymorphisms in rpoS and stress tolerance heterogeneity in natural isolates of Cronobacter sakazakii

Significant phenotypic diversity was observed when we examined the abilities of a number of Cronobacter sakazakii natural isolates to cope with various sublethal stress conditions (acid, alkaline, osmotic, oxidative, or heat stress). Levels of catalase activity and use of acetate as a carbon source, phenotypes commonly used as indirect assays to predict RpoS function, revealed a high correlation between predicted RpoS activity and tolerance to acid, alkaline, osmotic, and oxidative treatments. The rpoS genes were sequenced and analyzed for polymorphisms. Loss-of-function mutations were found in two strains; C. sakazakii DPC 6523 and the genome-sequenced strain C. sakazakii ATCC BAA-894. The complementation of these strains with a functional rpoS gene resulted in an increase in bacterial tolerance to acid, osmotic, and oxidative stresses. The pigmentation status of strains was also assessed, and a high variability in carotenoid content was observed, with a functional rpoS gene being essential for the production of the characteristic yellow pigment. In conclusion, the evidence presented in this study demonstrates that rpoS is a highly polymorphic gene in C. sakazakii, and it supports the importance of RpoS for the tolerance under stress conditions that C. sakazakii may encounter in the food chain and in the host during infection.     

Antibody Protection Reveals Extended Epitopes on the Human TSH Receptor

Stimulating, and some blocking, antibodies to the TSH receptor (TSHR) have conformation-dependent epitopes reported to involve primarily the leucine rich repeat region of the ectodomain (LRD). However, successful crystallization of TSHR residues 22-260 has omitted important extracellular non-LRD residues including the hinge region which connects the TSHR ectodomain to the transmembrane domain and which is involved in ligand induced signal transduction. The aim of the present study, therefore, was to determine if TSHR antibodies (TSHR-Abs) have non-LRD binding sites outside the LRD. To obtain this information we employed the method of epitope protection in which we first protected TSHR residues 1-412 with intact TSHR antibodies and then enzymatically digested the unprotected residues. Those peptides remaining were subsequently delineated by mass spectrometry. Fourteen out of 23 of the reported stimulating monoclonal TSHR-Ab crystal contact residues were protected by this technique which may reflect the higher binding energies of certain residues detected in this approach. Comparing the protected epitopes of two stimulating TSHR-Abs we found both similarities and differences but both antibodies also contacted the hinge region and the amino terminus of the TSHR following the signal peptide and encompassing cysteine box 1 which has previously been shown to be important for TSH binding and activation. A monoclonal blocking TSHR antibody revealed a similar pattern of binding regions but the residues that it contacted on the LRD were again distinct. These data demonstrated that conformationally dependent TSHR-Abs had epitopes not confined to the LRDs but also incorporated epitopes not revealed in the available crystal structure. Furthermore, the data also indicated that in addition to overlapping contact regions within the LRD, there are unique epitope patterns for each of the antibodies which may contribute to their functional heterogeneity.