Unique reporter-based sensor platforms to monitor signalling in cells.

INTRODUCTION: In recent years much progress has been made in the development of tools for systems biology to study the levels of mRNA and protein, and their interactions within cells. However, few multiplexed methodologies are available to study cell signalling directly at the transcription factor level. METHODS: Here we describe a sensitive, plasmid-based RNA reporter methodology to study transcription factor activation in mammalian cells, and apply this technology to profiling 60 transcription factors in parallel. The methodology uses two robust and easily accessible detection platforms; quantitative real-time PCR for quantitative analysis and DNA microarrays for parallel, higher throughput analysis. FINDINGS: We test the specificity of the detection platforms with ten inducers and independently validate the transcription factor activation. CONCLUSIONS: We report a methodology for the multiplexed study of transcription factor activation in mammalian cells that is direct and not theoretically limited by the number of available reporters.

The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cells.

BACKGROUND: The importance of appropriate normalization controls in quantitative real-time polymerase chain reaction (qPCR) experiments has become more apparent as the number of biological studies using this methodology has increased. In developing a system to study gene expression from transiently transfected plasmids, it became clear that normalization using chromosomally encoded genes is not ideal, at it does not take into account the transfection efficiency and the significantly lower expression levels of the plasmids. We have developed and validated a normalization method for qPCR using a co-transfected plasmid. RESULTS: The best chromosomal gene for normalization in the presence of the transcriptional activators used in this study, cadmium, dexamethasone, forskolin and phorbol-12-myristate 13-acetate was first identified. qPCR data was analyzed using geNorm, Normfinder and BestKeeper. Each software application was found to rank the normalization controls differently with no clear correlation. Including a co-transfected plasmid encoding the Renilla luciferase gene (Rluc) in this analysis showed that its calculated stability was not as good as the optimised chromosomal genes, most likely as a result of the lower expression levels and transfection variability. Finally, we validated these analyses by testing two chromosomal genes (B2M and ActB) and a co-transfected gene (Rluc) under biological conditions. When analyzing co-transfected plasmids, Rluc normalization gave the smallest errors compared to the chromosomal reference genes. CONCLUSIONS: Our data demonstrates that transfected Rluc is the most appropriate normalization reference gene for transient transfection qPCR analysis; it significantly reduces the standard deviation within biological experiments as it takes into account the transfection efficiencies and has easily controllable expression levels. This improves reproducibility, data validity and most importantly, enables accurate interpretation of qPCR data.

Medical training and the hospital at night: an oxymoron?

CONTEXT: Attempts to reduce doctors' working hours and streamline postgraduate medical training may mean junior doctors' out-of-hours experience is reduced. It is also proposed that, in the UK, compulsory clinical (Foundation Programme) competencies are to be accomplished in 1 year rather than 2 years as they are at present. This observational study was performed to examine the scope of opportunity available to junior doctors to achieve such competencies while working on a 'Hospital at Night' (H@N) team. METHODS: A database of electronic requests made to the H@N team was used to tabulate the number and type of tasks requested and to define differences between specialties, using local hospital admissions rates to contextualise the data. These requests were then compared with a list of compulsory clinical competencies to assess the scope of opportunity available to trainees to achieve these competencies when working on the H@N team. RESULTS: A total of 8268 referrals were made to our H@N team between 1 October 2007 and 31 January 2008 using the electronic Hospital Information System (HIS). The predefined, online HIS request list included eight of the 20 tasks that represent compulsory competencies and showed that on average there were 247 opportunities per week of night shifts to perform them. Medical wards generated more requests than surgical wards (4767 versus 3170) and afforded greater opportunity to attain compulsory competencies (139 opportunities/week versus 96 opportunities/week; extra requests could not be attributed to either medical or surgical wards as original request did not include ward number). CONCLUSIONS: The H@N initiative provides adequate opportunities for junior doctors to attain important clinical (Foundation) competencies. There appears to be sufficient opportunity to achieve these competencies within 1 year rather than the 2 years currently allowed in the UK Foundation Programme.

Structure-function dissection of D6, an atypical scavenger receptor.

Chemokines direct leukocyte migration by activating intracellular signalling pathways through G-protein coupled chemokine receptors. However, they also bind to other surface proteins, including a group of molecules which we refer to as 'atypical' chemokine receptors. One such molecule is D6. D6 is structurally-related to other chemokine receptors, and binds specific pro-inflammatory chemokines with high affinity, but surprisingly, when expressed in heterologous cell lines, it is unable to transduce signals after chemokine engagement. Instead, by using the approaches outlined in this chapter, evidence has emerged that D6 acts as a chemokine scavenger which uses unique intracellular trafficking properties to continuously sequester extracellular chemokines into cells. It is envisaged that this suppresses inflammation in vivo by limiting pro-inflammatory chemokine bioavailability, and indeed, D6 deficient mice show exaggerated inflammatory responses to a variety of challenges. In addition to the in vitro functional studies, we also describe the methods we have used to express, purify and analyse large quantities of D6 protein. The unusually high stability of D6 and its broad subcellular distribution enables D6 to be expressed to very high levels in transfected cells, making it possible, at least in principal, to produce enough D6 to allow for purification of quantities suitable for crystallisation. This is a key step on the path towards generating a three-dimensional structure of the molecule. Thus, the protocols we outline have helped establish chemokine scavenging as a novel paradigm in chemokine biology, and may also ultimately provide unprecedented insight into the structure of D6 and other chemokine receptors.

The chemokine receptor D6 limits the inflammatory response in vivo.

How the inflammatory response is initiated has been well defined but relatively little is known about how such responses are resolved. Here we show that the D6 chemokine receptor is involved in the post-inflammatory clearance of beta-chemokines from cutaneous sites. After induction of inflammation by phorbol esters, wild-type mice showed a transient inflammatory response. However, in D6-deficient mice, an excess concentration of residual chemokines caused a notable inflammatory pathology with similarities to human psoriasis. These results suggest that D6 is involved in the resolution of the cutaneous inflammatory response.

The chemokine ESkine/CCL27 displays novel modes of intracrine and paracrine function.

We have previously shown that the beta-chemokine ESkine/CCL27 is differentially spliced to produce two alternative forms. One is a secreted chemokine (ESkine), whereas the other (PESKY) lacks a signal peptide and is translocated to the nucleus. The role of this nuclear-targeted chemokine has not so far been defined, and it was the purpose of this study to examine this chemokine variant in more depth. To identify the region of PESKY involved in the nuclear translocation we tagged fragments with enhanced green fluorescent protein and expressed them in Chinese hamster ovary cells. We show PESKY nuclear translocation to be dependent on C-terminal residues that are shared with the signal peptide-bearing variant ESkine. Indeed we further demonstrate that ESkine can also use these C-terminal residues to enter the nucleus of cells following receptor (CCR10)-mediated internalization. To examine biological roles for PESKY we have overexpressed it in 3T3 cells. Such overexpression results in marked cytoskeletal rearrangements that are coincident with a radical reorganization of the cellular actin cytoskeleton. Microarray analyses and Ab neutralization studies indicate that these changes are mediated in part by insulin-like growth factor-1. Furthermore, monolayer wounding assays indicate that PESKY expression correlates with markedly increased migratory capacity. Thus, it is our contention that nuclear PESKY and ESkine both enter the nucleus by either intracrine or paracrine mechanisms and may facilitate cellular migration by inducing actin cytoskeletal relaxation. Therefore, nuclear ESkine/PESKY represents a novel paradigm for chemokine function.