Multiplexed microsphere diagnostic tools in gene expression applications: factors and futures

Microarrays have received significant attention in recent years as scientists have firstly identified factors that can produce reduced confidence in gene expression data obtained on these platforms, and secondly sought to establish laboratory practices and a set of standards by which data are reported with integrity. Microsphere-based assays represent a new generation of diagnostics in this field capable of providing substantial quantitative and qualitative information from gene expression profiling. However, for gene expression profiling, this type of platform is still in the demonstration phase, with issues arising from comparative studies in the literature not yet identified. It is desirable to identify potential parameters that are established as important in controlling the information derived from microsphere-based hybridizations to quantify gene expression. As these evolve, a standard set of parameters will be established that are required to be provided when data are submitted for publication. Here we initiate this process by identifying a number of parameters we have found to be important in microsphere-based assays designed for the quantification of low abundant genes which are variable between studies.     

Carbohydrate liquid crystals: synthesis and characterisation of the methyl-6-O-(n-acyl)-α-D-glucopyranosides

Seven members of the methyl-6-O-(n-acyl)-α-d-glucopyranosides have been synthesised and their transitional properties determined. The undecanoyl and octadecanoyl members do not exhibit liquid crystallinity while the members having chain lengths between dodecanoyl and hexadecanoyl exhibit a monotropic smectic A phase. Variable temperature infrared spectroscopy reveals that the hydrogen bonding within the system shows a marked change at the melting point but apparently no change at the smectic A-isotropic transition. This observation is interpreted in terms of Goodby's model for the smectic A phase in which the carbohydrate moieties are located at the centre of the smectic bilayer and assuming that hydrogen bonded aggregates persist into the isotropic phase. Within this framework, the unusually low values of the entropy change associated with the smectic A-isotropic transition may also be accounted for.     

Validation of alternative methods for the analysis of drinking water and their application to Escherichia coli

In Europe, the Drinking Water Directive of the European Commission indicates which methods (most of which are CEN/ISO-standardized methods) should be used for the analysis of microbiological parameters (European Commission, Environment, Council Directive 98/83/EC of 3 November 1998). According to the Directive, alternative methods “may be used, providing it can be demonstrated that the results obtained are at least as reliable as those produced by the methods specified.” The prerequisite for the routine use of any alternative method is to provide evidence that this method performs equivalently to the corresponding reference method. In this respect, the ISO 16140 standard (ISO, ISO 16140. Microbiology of Food and Animal Feeding Stuffs—Protocol for the Validation of Alternative Methods, 2003) represents a key issue in generating such a procedure based on an interlaboratory study. A new statistical tool, called the accuracy profile, has been developed to better interpret the data. The study presented here is based upon the enumeration of Escherichia coli bacteria in water. The reference method may require up to 72 h to provide a confirmed result. The aim of this publication is to present data for an alternative method by which results can be obtained in 18 h (Colilert-18/Quanti-Tray) based upon defined substrate technology (DST). The accuracy profile is a statistical and graphical decision-making tool and consists of simultaneously combining, in a single graphic, β expectation tolerance intervals (β-ETIs) and acceptability limits (λ). The study presents the validation criteria calculated at the three levels of contamination used in the trial for a β equal to 80% and a λ equal to ±0.3 and combines the accuracy profiles of Escherichia coli for a λ of ±0.3 log₁₀ unit/100 ml, a λ of ±0.4 log₁₀ unit/100 ml, and a β of 80% or 90%. Several interesting conclusions can be drawn from these data. The accuracy profile method has been applied to the validation of the Colilert-18/Quanti-Tray method against reference method ISO 9308-1 (ISO, ISO 9308-1. Water Quality—Detection and Enumeration of Escherichia coli and Coliform Bacteria. Part 1. Membrane Filtration Method, 2000), using a β of 80% and a λ of 0.4; the alternative method can be validated between 1.00 and 2.05 log₁₀ units/100 ml, equivalent to 10 to 112 CFU/100 ml.     

Relationships of risk factors for pre-eclampsia with patterns of occurrence of isolated gestational proteinuria during normal term pregnancy

Background

Isolated gestational proteinuria may be part of the pre-eclampsia disease spectrum. Confirmation of its association with established pre-eclampsia risk factors and higher blood pressure in uncomplicated pregnancies would support this concept.

Methods

Data from 11,651 women from the Avon Longitudinal Study of Parents and Children who had a term live birth but did not have pre-existing hypertension or diabetes or develop gestational diabetes or preeclampsia were used. Proteinuria was assessed repeatedly (median 12 measurements per woman) by dipstick and latent class analysis was used to identify subgroups of the population with different patterns of proteinuria in pregnancy.

Results

Higher maternal pre-pregnancy body mass index (BMI), younger age, nulliparity and twin pregnancy were independently associated with increased odds of any proteinuria in pregnancy. Women who experienced proteinuria showed five patterns: proteinuria in early pregnancy only (≤20 weeks gestation), and onset at 21–28 weeks, 29–32 weeks, 33–36 weeks and ≥37 weeks gestation. There were higher odds of proteinuria onset after 33 weeks in obese women and after 37 weeks in nulliparous women compared with normal weight and multiparous women respectively. Smoking in pregnancy was weakly negatively associated with odds of proteinuria onset after 37 weeks. Twin pregnancies had higher odds of proteinuria onset from 29 weeks. In women with proteinuria onset after 33 weeks blood pressure was higher in early pregnancy and at the end of pregnancy.

Conclusions

Established pre-eclampsia risk factors were related to proteinuria occurrence in late gestation in healthy term pregnancies, supporting the hypothesis that isolated gestational proteinuria may represent an early manifestation of pre-eclampsia.     

Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012

This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation.     

Inhibition of MT1-MMP activity using functional antibody fragments selected against its hemopexin domain

The membrane associated MMP, MT1-MMP, is a critical pericellular protease involved in tumour cell invasion and angiogenesis and is highly up-regulated in numerous human cancers. It therefore represents an exciting new therapeutic cancer-specific target. We have generated recombinant human scFv antibodies against the non-catalytic, hemopexin domain of MT1-MMP that modulate its interactions with collagen. One of these is an effective inhibitor of the invasive capacity of cancer cells and of angiogenesis in model systems. This demonstrates that targeting sites outside the catalytic domain presents a potential novel approach to proteinase inhibition that could have applications in cancer therapeutics.