Genome Trees from Conservation Profiles

The concept of the genome tree depends on the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. In this respect, genome trees have often been identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping global trends for the phylogenetic signals that mutually link the various genomes. We therefore derive here the methodological concept of genome trees based on protein conservation profiles in multiple species. The basic idea in this derivation is that the multi-component “presence-absence” protein conservation profiles permit tracking of common evolutionary histories of genes across multiple genomes. We show that a significant reduction in informational redundancy is achieved by considering only the subset of distinct conservation profiles. Beyond these basic ideas, we point out various pitfalls and limitations associated with the data handling, paving the way for further improvements. As an illustration for the methods, we analyze a genome tree based on the above principles, along with a series of other trees derived from the same data and based on pair-wise comparisons (ancestral duplication-conservation and shared orthologs). In all trees we observe a sharp discrimination between the three primary domains of life: Bacteria, Archaea, and Eukarya. The new genome tree, based on conservation profiles, displays a significant correspondence with classically recognized taxonomical groupings, along with a series of departures from such conventional clusterings

Amino-Modified Polymer Immobilized Ionic Liquid Stabilized Ruthenium Nanoparticles: Efficient and Selective Catalysts for the Partial and Complete Reduction of Quinolines

RuNPs stabilised by amino-decorated imidazolium-based polymer immobilized ionic liquids catalyse the dimethylamine borane mediated reduction of quinolines to 1,2-dihydroquinoline (DHQ) and 1,2,3,4-tetrahydroquinoline (THQ). Partial reduction of 3-substituted quinolines to the corresponding 1,2-dihydroquinoline was achieved with 100 % selectivity in toluene under mild conditions. This is the first report of the selective partial reduction of 3-substituted quinolines to the corresponding 1,2-dihydroquinolines with a heterogeneous nanoparticle-based catalyst. A wide range of substituted quinolines have also been reduced to the corresponding 1,2,3,4-tetrahydroquinoline with high selectivity and good yields by adjusting the reaction time. The 1,2-dihydroquinolines readily release dihydrogen in toluene at 60 °C in the absence of catalyst with no evidence for disproportionation and as such are potential organo-hydride reagents. The initial TOF of 610 mol quinoline converted mol Ru−1 h−1 for the reduction of quinoline is among the highest to be reported for a metal nanoparticle-based catalyst and the conversion of 96 % obtained after 4 h at 65 °C is significantly higher than its platinum nanoparticle counterpart PtNP@NH2-PEGPIILS as well as 5 wt/% Ru/C, which only reached 9 % and 11 % conversion, respectively, at the same time. Hot filtration experiments showed that the active species was heterogeneous

No improvement in long-term wear and revision rates with the second-generation Biomet cup (RingLoc) in young patients: 141 hips followed for median 12 years

Optimising joint reconstruction management in arthritis and bone tumour patient

Highly efficient and selective partial reduction of nitroarenes to N-arylhydroxylamines catalysed by phosphine oxide-decorated polymer immobilized ionic liquid stabilized ruthenium nanoparticles

RuNPs stabilised by a polymer immobilised ionic liquid derived from co-polymerisation of a PEG-substituted imidazolium-based styrene monomer and diphenyl(4-vinylphenyl)phosphine oxide, RuNP@O = PPh2-PEGPIILS, (2) is a remarkably efficient and selective catalyst for the hydrazine hydrate-mediated partial reduction of nitroarenes to the corresponding N-arylhydoxylamine. Near quantitative conversion to N-phenylhydroxylamine with > 99 % selectivity was obtained after only 2 h when the reaction was conducted at 25 °C in ethanol under an inert atmosphere using 0.1 mol% catalyst. Under these conditions, the composition-time profile showed that the reduction occurred via the direct pathway whereas reactions in air gave a mixture of azoxy-based products due to competing condensation resulting from reversible formation of N-phenylhydroxylamine. The initial TOF of 6,100 h−1 obtained after 10 min at 40 °C with 0.1 mol% 2 is among the highest to be reported for the metal nanoparticle catalysed reduction of nitrobenzene to N-phenylhydroxylamine and a significant improvement on 5 wt% Ru/C which gave a modest conversion of 21 % (initial TOF = 240 h−1) to a mixture of N-phenylhydroxylamine and aniline. A broad range of substituted N-aryl and N-heteroaryl nitroarenes were reduced to the corresponding N-arylhydroxylamine in high yield and with excellent selectivity by adjusting the reaction times. However, reduction of electron rich amino-substituted nitroarenes was extremely slow and resulted in reduction to the aniline with no evidence for the corresponding hydroxylamine. Complete reduction of amino substituted nitroarene is proposed to be facilitated by amine-assisted elimination of hydroxide from the hydroxylamine to afford a readily reducible quinondiimine-derived iminium intermediate that reacts with a surface hydride to liberate the amine. Under optimum conditions the catalyst could be reused five times for the reduction of nitrobenzene to N-phenylhydroxylamine with no detectable change in activity and only slight decrease in selectivity

Raman study of the anharmonicity in YBa2_2Cu3_3Ox_x

A systematic Raman study in the visible carried out on the YBa2Cu316,18Ox (x=6-7) compounds, with isotopic substitution of 18O for 16O, has detected a doping dependent deviation from harmonic behavior for the frequency shift of the in-phase mode, a smaller amount of anharmonicity for the apex mode, and almost no effect for the out-of-phase B1g-symmetry phonon. It appears that the amount of anharmonicity depends strongly on the oxygen concentration; it diminishes close to the tetragonal to orthorhombic structural phase transition and close to optimal doping, while it reaches its maximum value for the ortho-II and a tetragonal phase. The almost zero anharmonicity at optimal doping persists even at 77K. The data in the overdoped oxygen concentration, where a softening of the in-phase phonon frequency occurs, indicate that the anharmonicity is not enhanced by the sudden increase in the CuO2 buckling. The results fully agree with recent studies of the ortho-II phase but they do not comply with a static double-well potential of the apical oxygen atom at optimal doping.Comment: Dedicated to Prof. K. A. M\"uller on the Occasion of his 90th Birthda

Occurrence and Treatment of Bone Atrophic Non-Unions Investigated by an Integrative Approach

Recently developed atrophic non-union models are a good representation of the clinical situation in which many nonunions develop. Based on previous experimental studies with these atrophic non-union models, it was hypothesized that in order to obtain successful fracture healing, blood vessels, growth factors, and (proliferative) precursor cells all need to be present in the callus at the same time. This study uses a combined in vivo-in silico approach to investigate these different aspects (vasculature, growth factors, cell proliferation). The mathematical model, initially developed for the study of normal fracture healing, is able to capture essential aspects of the in vivo atrophic non-union model despite a number of deviations that are mainly due to simplifications in the in silico model. The mathematical model is subsequently used to test possible treatment strategies for atrophic non-unions (i.e. cell transplant at post-osteotomy, week 3). Preliminary in vivo experiments corroborate the numerical predictions. Finally, the mathematical model is applied to explain experimental observations and identify potentially crucial steps in the treatments and can thereby be used to optimize experimental and clinical studies in this area. This study demonstrates the potential of the combined in silico-in vivo approach and its clinical implications for the early treatment of patients with problematic fractures

Gated Diffusion-controlled Reactions

The binding and active sites of proteins are often dynamically occluded by motion of the nearby polypeptide. A variety of theoretical and computational methods have been developed to predict rates of ligand binding and reactivity in such cases. Two general approaches exist, "protein centric" approaches that explicitly treat only the protein target, and more detailed dynamical simulation approaches in which target and ligand are both treated explicitly. This mini-review describes recent work in this area and some of the biological implications