A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Background

Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties by gene expression profile. Lamb et al first proposed the Connectivity Map [Lamb et al (2006), Science 313, 1929–1935] to make successful connections among small molecules, genes, and diseases using genomic signatures.

Results

Here we have built on the principles of the Connectivity Map to present a simpler and more robust method for the construction of reference gene-expression profiles and for the connection scoring scheme, which importantly allows the valuation of statistical significance of all the connections observed. We tested the new method with two randomly generated gene signatures and three experimentally derived gene signatures (for HDAC inhibitors, estrogens, and immunosuppressive drugs, respectively). Our testing with this method indicates that it achieves a higher level of specificity and sensitivity and so advances the original method.

Conclusion

The method presented here not only offers more principled statistical procedures for testing connections, but more importantly it provides effective safeguard against false connections at the same time achieving increased sensitivity. With its robust performance, the method has potential use in the drug development pipeline for the early recognition of pharmacological and toxicological properties in chemicals and new drug candidates, and also more broadly in other 'omics sciences.

Use of breakpoint combination sensitivity testing as a simple and convenient method to evaluate the combined effects of ceftazidime and tobramycin on Pseudomonas aeruginosa and Burkholderia cepacia complex isolates in vitro

An in vitro method of determining the activity of antibiotics in combination which is simple and convenient to perform and which could be used routinely in clinical microbiology laboratories is desirable. We investigated the activity, against Pseudomonas aeruginosa and Burkholderia cepacia complex clinical isolates, of ceftazidime and tobramycin in combination using a broth macrodilution sensitivity method based on breakpoint minimum inhibitory concentrations and compared the results obtained using this method with those obtained using the microtitre checkerboard method. There was good agreement in interpretation of results between the two methods for both P. aeruginosa (90%) and B. cepacia complex isolates (70%) with tobramycin and for P. aeruginosa isolates (70%) with ceftazidime. As the breakpoint combination sensitivity testing method employs only four tubes and does not require initial determination of individual antibiotic minimum inhibitory concentrations, it is simpler and more convenient for determining the activity of antibiotics in combination than the microtitre checkerboard method. The use of this method in routine microbiology laboratories to determine the activity of antibiotic combinations against clinical isolates should optimise treatment of infection by ensuring that appropriate antibiotic combinations are prescribed. (C) 2004 Elsevier B.V. All rights reserved.

Effect of composition, solvent exchange liquid and drying method on the porous structure of phenol-formaldehyde gels

Organic gels have been synthesized by sol–gel polycondensation of phenol (P) and formaldehyde (F) catalyzed by sodium carbonate (C). The effect of synthesis parameters such as phenol/catalyst ratio (P/C), solvent exchange liquid and drying method, on the porous structure of the gels have been investigated. The total and mesopore volumes of the PF gels increased with increasing P/C ratio in the range of P/C B 8, after this both properties started to decrease with P/C ratio for P/C[8 and the gel with P/C = 8 showed the highest total and mesopore volumes of 1.281 and 1.279 cm3 g-1 respectively. The gels prepared by freeze drying possessed significantly higher porosities than the vacuum dried gels. The pore volume and average pore diameter of the freeze dried gels were significantly higher than those of the vacuum dried gels. T-butanol emerged as the preferred solvent for the removal of water from the PF hydrogel prior to drying, as significantly higher pore volumes and specific surface areas were obtained in the corresponding dried gels. The results showed that freeze drying with t-butanol and lower P/C ratios were favourable conditions for the synthesis of highly mesoporous phenol–formaldehyde gels.

Benzimidazole carbamate residues in milk: Detection by Surface Plasmon Resonance-biosensor, using a modified QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) method for extraction

A surface plasmon resonance (SPR) biosensor screening assay was developed and validated to detect 11 benzimidazole carbamate (BZT) veterinary drug residues in milk. The polyclonal antibody used was raised in sheep against a methyl 5(6)-[(carboxypentyl)-thio]-2-benzimidazole carbamate protein conjugate. A sample preparation procedure was developed using a modified QuEChERS method. BZT residues were extracted from milk using liquid extraction/partition with a dispersive solid phase extraction clean-up step. The assay was validated in accordance with the performance criteria described in 2002/657/EC. The limit of detection of the assay was calculated from the analysis of 20 known negative milk samples to be 2.7 mu g kg(-1). The detection capability (CC beta) of the assay was determined to be 5 mu g kg(-1) for 11 benzimidazole residues and the mean recovery of analytes was in the range 81-116%. A comparison was made between the SPR-biosensor and UPLC-MS/MS analyses of milk samples (n = 26) taken from cows treated different benzimidazole products, demonstrating the SPR-biosensor assay to be fit for purpose. (C) 2009 Elsevier B.V. All rights reserved.

GELIFICATION - A SIMPLE AND EFFICIENT METHOD FOR ON-CHIP STORAGE OF REAGENTS: TOWARDS LAB-ON-A-CHIP SYSTEMS FOR POINT-OF-CARE DIAGNOSTICS

In this study, we describe a simple and efficient method for on-chip storage of reagents for point-of-care (POC) diagnostics. The method is based on gelification of all reagents required for on-chip PCR-based diagnostics as a ready-to-use product. The result reported here is a key step towards the development of a ready and easy to use fully integrated Lab-on-a-chip (LOC) system for fast, cost-effective and efficient POC diagnostics analysis.

Pepsin in bronchoalveolar lavage fluid:a specific and sensitive method of diagnosing gastro-oesophageal reflux-related pulmonary aspiration

Gastro-oesophageal reflux (GOR)-related aspiration is associated with respiratory disease, but the current "gold standard" investigation, the lipid-laden macrophage index (LLMI), is flawed. A specific marker of GOR-related aspiration should originate in the stomach, but not the lung. An assay to detect gastric pepsin in the bronchoalveolar lavage (BAL) of children was developed and validated.

A proposed model membrane and test method for microneedle insertion studies

A commercial polymeric film (Parafilm M (R), a blend of a hydrocarbon wax and a polyolefin) was evaluated as a model membrane for microneedle (MN) insertion studies. Polymeric MN arrays were inserted into Parafilm M (R) (PF) and also into excised neonatal porcine skin. Parafilm M (R) was folded before the insertions to closely approximate thickness of the excised skin. Insertion depths were evaluated using optical coherence tomography (OCT) using either a force applied by a Texture Analyser or by a group of human volunteers. The obtained insertion depths were, in general, slightly lower, especially for higher forces, for PF than for skin. However, this difference was not a large, being less than the 10% of the needle length. Therefore, all these data indicate that this model membrane could be a good alternative to biological tissue for MN insertion studies. As an alternative method to OCT, light microscopy was used to evaluate the insertion depths of MN in the model membrane. This provided a rapid, simple method to compare different MN formulations. The use of Parafilm M (R), in conjunction with a standardised force/time profile applied by a Texture Analyser, could provide the basis for a rapid MN quality control test suitable for in-process use. It could also be used as a comparative test of insertion efficiency between candidate MN formulations. 

Ionic liquids containing secondary hydroxyl-groups and a method for their preparation.

The invention provides ionic liqs., [R'1CH(OH)CH2]NR'nX (X = anion, R' = alkyl, alkenyl, alkynyl, cycloalkyl, alkylcarbonylalkyl, alkoxy, haloalkyl, haloalkoxy, alkenyloxy, alkynyloxy, cycloalkyloxy, aryl), having a secondary hydroxyl group, and an atom-efficient method for the prepn. of these ionic liqs., by epoxidn. of a protonated nitrogen- contg. org. base (which can optionally be prepd. in situ) in the presence of an anion suitable for supporting ionic liq. formation. Thus, reaction of 1-methylimidazole with HCl in EtOH ∼ 25° followed by treatment with propylene oxide gave 1-(2-hydroxypropyl)-3-methylimidazolium chloride. [on SciFinder(R)]