Neighborhood functions and hill-climbing strategies dedicated to the generalized ungapped local multiple alignment

Ungapped Local Multiple Alignment is a widely used procedure in bioinformatics. It roughly consists of locating in a given set of nucleotide (DNA) or amino acid (proteins) sequences, a number of non-overlapping fixed-size factors (also called occurrences), that are likely to have evolved from a common ancestor. In addition to the widely known statistical approaches, we define the problem from a pure combinatorial optimization point of view, by defining specific neighborhood functions and a hill-climbing strategy for each of four particular instances of this problem: (1) one occurrence per sequence, (2) at most one occurrence per sequence, (3) at least one occurrence per sequence, and (4) any number of occurrences per sequence. The method is implemented in a tool called Nomad (Neighborhood Optimization for Multiple Alignment Discovery) and a web interface is available at www.expasy.org/tools/nomad.html.     

An International Laboratory Comparison Study of Volumetric and Gravimetric Hydrogen Adsorption Measurements

In order to determine a material's hydrogen storage potential, capacity measurements must be robust, reproducible, and accurate. Commonly, research reports focus on the gravimetric capacity, and often times the volumetric capacity is not reported. Determining volumetric capacities is not as straight-forward, especially for amorphous materials. This is the first study to compare measurement reproducibility across laboratories for excess and total volumetric hydrogen sorption capacities based on the packing volume. The use of consistent measurement protocols, common analysis, and figure of merits for reporting data in this study, enable the comparison of the results for two different materials. Importantly, the results show good agreement for excess gravimetric capacities amongst the laboratories. Irreproducibility for excess and total volumetric capacities is attributed to real differences in the measured packing volume of the material.     

Aggregation-Enhanced Photoluminescence and Photoacoustics of Atomically Precise Gold Nanoclusters in Lipid Nanodiscs (NANO2)

The authors designed a structurally stable nano-in-nano (NANO²) system highly capable of bioimaging via an aggregation-enhanced NIR excited emission and photoacoustic response achieved based on atomically precise gold nanoclusters protected by linear thiolated ligands [Au₂₅(SC_nH_2n+1)₁₈, n  = 4–16] encapsulated in discoidal phospholipid bicelles through a one-pot synthesis. The detailed morphological characterization of NANO² is conducted using cryogenic transmission electron microscopy, small/wide angle X-ray scattering with the support of molecular dynamics simulations, providing information on the location of Au nanoclusters in NANO². The photoluminescence observed for NANO² is 20–60 times more intense than that of the free Au nanoclusters, with both excitation and emission wavelengths in the near-infrared range, and the photoacoustic signal is more than tripled. The authors attribute this newly discovered aggregation-enhanced photoluminescence and photoacoustic signals to the restriction of intramolecular motion of the clusters’ ligands. With the advantages of biocompatibility and high cellular uptake, NANO² is potentially applicable for both in vitro and in vivo imaging, as the authors demonstrate with NIR excited emission from in vitro A549 human lung and the KB human cervical cancer cells.     

Controlling the shape of the molecular weight distribution for tailored tensile and rheological properties in thermoplastics and thermoplastic elastomers

Thermoplastics and thermoplastic elastomers compose roughly 80 percent of all polymeric materials manufactured today and play an important role in numerous sectors of modern society. While the effects of molecular weight and dispersity (Ð) on the tensile and rheological properties of these materials are well-known, only recent studies have evidenced the profound influence of the shape of the molecular weight distribution (MWD) on polymer properties. This development is largely due to the emergence of new synthetic strategies to control higher moments of the MWD. In this Perspective, we describe recent advancements by our group in understanding the effect of MWD shape on the mechanical and rheological properties of thermoplastics and thermoplastic elastomers. We highlight means to exploit MWD shape for improved processability and performance and discuss future directions in this field.     

Catalytic properties of transition metal salts immobilized on nanoporous silica polyamine composites II: hydrogenation

The transition metal compounds Pd(OAc)₂, RhCl₃·4H₂O and RuCl₃ · nH₂O were adsorbed onto the nanoporous silica polyamine composite (SPC) particles (150–250 µm), WP‐1 [poly(ethyleneimine) on amorphous silica], BP‐1 [poly(allylamine) on amorphous silica], WP‐2 (WP‐1 modified with chloroacetic acid) and BP‐2 (BP‐1 modified with chloroacetic acid). Inductively coupled plasma‐atomic emission spectrometry analysis of the dried samples after digestion indicated metal loadings of 0.4–1.2 mmol g^?1 except for RhCl₃·4H₂O on BP‐2 which showed a metal loading of only 0.1 mmol g^?1. The metal loaded composites were then screened as hydrogenation catalysts for the reduction of 1‐octene, 1‐decene, 1‐hexene and 1, 3‐cyclohexadiene at a hydrogen pressure of 5 atm in the temperature range of 50–90 °C. All 12 combinations of SPC and transition metal compound proved active for the reduction of the terminal olefins, but isomerization to internal alkenes was competitive in all cases. Under these conditions, selective hydrogenation of 1,3‐cyclohexadiene to cyclohexene was observed with some of the catalysts. Turnover frequencies were estimated for the hydrogenation reactions based on the metal loading and were in some cases comparable to more conventional heterogeneous hydrogenation catalysts. Examination of the catalysts before and after reaction with X‐ray photoelectron spectroscopy and transmission electron microscopy revealed that, in the cases of Pd(OAc)₂ on WP‐2, BP‐1 and BP‐2, conversion of the surface‐ligand bound metal ions to metal nano‐particles occurs. This was not the case for Pd(OAc)₂ on WP‐1 or for RuCl₃ · nH₂O and RhCl₃· 4H₂O on all four composites. The overall results are discussed in terms of differences in metal ion coordination modes for the composite transition‐metal combinations. Suggested ligand interactions are supported by solid state CPMAS ¹³C NMR analyses and by analogy with previous structural investigations of metal binding modes on these composite materials. Copyright © 2011 John Wiley & Sons, Ltd.     

TDPAC studies of the iron–molybdenum cofactor in nitrogenase

The uptake and the processing of molybdenum in nitrogen fixing bacteria was studied applying the TDPAC-technique with radioactive ⁹⁹Mo. The observation of the nuclear quadrupole frequencies allowed a ‘finger-printing’ of the characteristic binding states in three bacteria species. The measurements have been carried out with intact cells and with the isolated proteins. In one bacterium a molybdenum storage protein was identified. This revised version was published online in August 2006 with corrections to the Cover Date.     

Attrition-enhanced total resolution leads to homochiral families of amino acid derivatives

The total resolution of five structurally similar racemizable amino acid derivatives, three of which have racemic crystal structures, was performed simultaneously. By enantioselective incorporation in an amino acid derivative that forms a conglomerate the other four were deracemized on attrition-induced grinding. The outcome of the resolution was random (R) or (S), but all compounds had the same absolute configuration and high enantiomeric purities.