Biomedical subjects

Chris Chambers

Publications and source records attributed to Chris Chambers.

4 recordsLinked to original sources

PubMed2006

A novel method for analyzing [Ca2+] flux kinetics in high-throughput screening.

Driven by multiparameter fluorescence readouts and the analysis of kinetic responses from biological assay systems, the amount and complexity of high-throughput screening data are constantly increasing. As a consequence, the reduction of data to a simple number, reflecting a percentage activity/inhibition, is no longer an adequate approach because valuable additional information, for example, about compound-or process-induced artifacts, is lost. Time series data such as the transient calcium flux observed after activation of Gq-coupled G protein-coupled receptors (GPCRs), are especially challenging with respect to quantity of data; typically, responses are followed for several minutes. Based on measurements taken on the fluorometric imaging plate reader, the authors have introduced a mathematical model to describe the time traces of cellular calcium fluxes mediated by the activation of GPCRs. The model describes the time series using 13 parameters, reducing the amount of data by 90% while guiding the detection of compound-induced artifacts as well as the selection of compounds for further characterization.

Animals↗

PubMed2005

Evaluating real-life high-throughput screening data.

High-throughput screening (HTS) is the result of a concerted effort of chemistry, biology, information technology, and engineering. Many factors beyond the biology of the assay influence the quality and outcome of the screening process, yet data analysis and quality control are often focused on the analysis of a limited set of control wells and the calculated values derived from these wells. Taking into account the large number of variables and the amount of data generated, multiple views of the screening data are necessary to guarantee quality and validity of HTS results. This article does not aim to give an exhaustive outlook on HTS data analysis but tries to illustrate the shortfalls of a reductionist approach focused on control wells and give examples for further analysis.

Biological Assay↗

PubMed2004

Nitrogen uptake and turnover in riparian woody vegetation.

The nutrient balance of streams and adjacent riparian ecosystems may be modified by the elimination of anadromous fish runs and perhaps by forest fertilization. To better understand nitrogen (N) dynamics within stream and riparian ecosystems we fertilized two streams and their adjacent riparian corridors in central Idaho. On each stream two nitrogen doses were applied to a swathe approximately 35 m wide centered on the stream. The fertilizer N was enriched in 15N to 18 per thousand. This enrichment is light relative to many previous labeling studies, yet sufficient to yield a traceable signal in riparian and stream biota. This paper reports pre-treatment differences in delta15N and the first-year N response to fertilizer within the riparian woody plant community. Future papers will describe the transfer of allochthonous litter N to the stream and its subsequent processing by stream biota. Pre-treatment delta15N differed between the two creeks (P=0.0002), possibly due to residual salmon nitrogen in one of the creeks. Pre-treatment delta15N of current-year needles was enriched compared to leaf litter, which was in turn enriched compared to needles aged 4 years and older. We conclude that fractionation due to retranslocation occurs in at least two phases. The first phase, which optimizes allocation of N in younger needle age classes, is distinctly different from the second, which conserves N prior to abscission. The delta15N difference between creeks was eliminated by the fertilization (P=0.42). In the two dominant conifer species, Abies lasiocarpa and Picea engelmannii, most fertilizer N was found in the current-year foliage; little was found in older needles and none was detected in litter (P=0.53). The only N-fixing shrub species, Alnus incana, took up only a small amount of fertilizer N [mean percent N derived from fertilizer (%Ndff) 5.0+/-1.6% (SE)]. Far more fertilizer N was taken up by other deciduous shrubs (mean %Ndff=33.9+/-4.5%). Fertilizer N made up 25% (+/-4.2%) of the N in deciduous shrub litter. These results demonstrate the feasibility of light labeling with 15N and the potential influence of riparian plant species composition on stream nutrient dynamics via allochthonous leaf litter inputs.

Animals↗

PubMed2003

Measuring intracellular calcium fluxes in high throughput mode.

The measurement of intracellular calcium fluxes in real time is widely applied within the pharmaceutical industry to measure the activation of G-protein coupled receptors (GPCRhyp;s), either for pharmacological characterisation or to screen for new surrogate ligands. Initially restricted to G(q) coupled GPCRs, the introduction of promiscuous and chimeric G-proteins has further widened the application of these assays. The development of new calcium sensitive dyes and assays has provided sensitive, homogeneous assays which can be readily applied to high throughput screening (HTS). In this paper we describe the full automation of this assay type using a fluorometric imaging plate reader (FLIPR ) integrated into a Beckman/Sagian system to establish a simple robotic system that is well suited for the current medium throughput screening in this area of lead discovery. Using a recently completed HTS we discuss important determinants for FLIPR based screening, highlight some limitations of the current approach, and look at the requirements for future automated systems capable of keeping up with expanding compound files.

Automation↗