The semantic smart laboratory: a system for supporting the chemical eScientist

One goal of eScience is to enable the end-to-end publication of experiments and results. In the Combechem project we have developed an innovative human-centred system which captures the process of a chemistry experiment from plan to execution. The system comprises an electronic lab book replacement, which has been successfully trialled in a synthetic organic chemistry laboratory, and a flexible back-end storage system. Working closely with the users, we found that a light touch and a high degree of flexibility was required in the user interface. In this paper, we concentrate on the representation and storage of human-scale experiment metadata, introducing an ontology to describe the record of an experiment, and a storage system for the data from our lab book software. Just as the interfaces need to be flexible to cope with whatever a chemist wishes to record, so the back end solutions need to be similarly flexible to store any metadata that may be created. The storage system is based on Semantic Web technologies, such as RDF, and Web Services. It gives a much higher degree of flexibility to the type of metadata it can store, compared to the use of rigid relational databases.     

Inequalities for the h-Vectors and Flag h-Vectors of Geometric Lattices

We prove that the order complex of a geometric lattice has a convex ear decomposition. As a consequence, if (L) is the order complex of a rank (r + 1) geometric lattice L, then for all i r/2 the h-vector of (L) satisfies h_i-1 h_i and h_i h_r-i. We also obtain several inequalities for the flag h-vector of (L) by analyzing the weak Bruhat order of the symmetric group. As an application, we obtain a zonotopal cd-analogue of the Dowling–Wilson characterization of geometric lattices which minimize Whitney numbers of the second kind. In addition, we are able to give a combinatorial flag h-vector proof of h_i-1 h_i when i (2/7)(r + (5/2)).     

Single nucleotide polymorphism analysis in the human phosphatase PTPrj gene using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

Data derived from analysis of single nucleotide polymorphisms (SNPs) are being applied in many diverse fields, from medical studies of disease mechanisms and individual drug response, to population genetics for tracking migration and mixing of ancestral groups and also in forensic science for the identification of human remains and identification of individuals from bodily samples. All these applications have in common the need to generate data for multiple loci from large numbers of samples. Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) is a promising platform for the generation of such data and we present a simple, flexible and robust technique for SNP determination. We demonstrate these features by typing two SNPs (Q276P and R326Q) in the human phosphatase gene PTPrj, which has been implicated in the aetiology of colon, lung, breast and thyroid cancers. A nucleotide depletion primer extension assay using no commercial kits or dideoxyNTPs was used to genotype a panel of DNAs derived from thyroid cancer patients and normal volunteers. The results obtained were in perfect agreement with those generated via restriction fragment length polymorphism analysis. No significant association was noted between possession of either allelic variant and a disease state, but the technique was validated as simple, flexible and appropriate for application in this context. Furthermore, it was highly cost-effective and required minimal optimisation, rendering it ideal for this type of pilot study.     

Triple-quantum dynamics in multiple-spin systems undergoing magic-angle spinning: application to 13C homonuclear correlation spectroscopy

We analyze the multiple-quantum dynamics governed by a new homonuclear recoupling strategy effecting an average dipolar Hamiltonian comprising three-spin triple-quantum operators (e.g., S(p)+S(q)+S(r)+) under magic-angle spinning conditions. Analytical expressions are presented for polarization transfer processes in systems of three and four coupled spins-1/2 subject to triple-quantum filtration (3QF), and high-order multiple-quantum excitation is investigated numerically in moderately large clusters, comprising up to seven spins. This recoupling approach gives highly efficient excitation of triple-quantum coherences: ideally, up to 67% of the initial polarization may be recovered by 3QF in three-spin systems in polycrystalline powders. Two homonuclear 2D correlation strategies are demonstrated experimentally on powders of uniformly 13C-labeled alanine and tyrosine: the first correlates the single-quantum spectrum in the first dimension with the corresponding 3QF spectrum along the other. The second protocol correlates triple-quantum coherences with their corresponding single-quantum coherences within triplets of coupled spins.     

1,3-dialkylimidazolium-based room-temperature ionic liquids as background electrolyte and coating material in aqueous capillary electrophoresis

The 1-ethyl-3-methylimidazolium (EMIM) cation was found to have constant mobility of 4.5 x 10(-4) cm2 V(-1) s(-1) over the pH range of 3 to 11. The electroosmotic flow of bare silica capillary was reversed by the covalently bonded room-temperature ionic liquid (RTIL) coating. With run buffer of 5 mM EMIM (pH 8.5), NH4+ in human urine was separated from the K+ matrix and was detected to be 0.37 +/- 0.012%. K+, Na+, Li+, Ca2+, Mg2+ and Ba2+ were baseline separated in RTIL-coated capillary with run buffer of 10 mM EMIMOH-acetic acid at pH 5, and the concentration of the above ions in a red wine were detected to be 907, 27.9, 0, 71.0, 83.4 and 31.1 microg/ml, respectively. The RTIL-coated capillary showed stable electroosmotic flow for at least 80 h in the run buffer.     

Electrophoresis of DNA in ionic liquid coated capillary

An ionic liquid (IL) coated capillary was prepared and investigated for DNA separation. The electroosmotic flow of the capillary was reversed between pH 4.5 and 9. Below 900 base pairs the larger DNA fragment suffered more retardation in the IL coated capillary due to the increasing charge density of the fragment with size. In the presence of 4% hydroxyethylcellulose, the phiX174 DNA-Hae III digest fragments were baseline separated in both IL- and polyacrylamide-coated capillary except for the fragments of 271 and 281 base pairs; while the analysis time was shorter in the IL-coated capillary. Our experiments indicated that the IL-coated capillary could work stably in the run buffer for at least 96 h with no notable deterioration in performance.     

Synthesis of (-)-gloeosporone, a fungal autoinhibitor of spore germination using a pi-allyltricarbonyliron lactone complex as a templating architecture for 1,7-diol construction

The synthesis of the germination self-inhibitor (-)-Gloeosporone is reported. The embedded 1,7-diol motif in the product is constructed by an ironcarbonyl tether controlled Mukaiyama aldol reaction. The key step in the synthesis is the reductive removal of the ligating iron species by treatment of an acetoxycomplex 6 with lithium naphthalenide.     

Pyrrolidine-5,5-trans-lactams. 5. Pharmacokinetic optimization of inhibitors of hepatitis C virus NS3/4A protease

[reaction: see text] In this, the second of two Letters, the optimization of the pyrrolidine-5,5-trans-lactam template (exemplified by 1a) as a mechanism-based inhibitor of hepatitis C NS3/4A protease is described. "Right Box" analysis of cassette dosing screening pharmacokinetic data was used to rapidly categorize the compounds. GW0014 (compound 4d) emerged as the compound displaying an optimal balance of biochemical and replicon potency, along with low i.v. clearance in the dog.