Impact of variance components on reliability of absolute quantification using digital PCR

Background

Digital polymerase chain reaction (dPCR) is an increasingly popular technology for detecting and quantifying target nucleic acids. Its advertised strength is high precision absolute quantification without needing reference curves. The standard data analytic approach follows a seemingly straightforward theoretical framework but ignores sources of variation in the data generating process. These stem from both technical and biological factors, where we distinguish features that are 1) hard-wired in the equipment, 2) user-dependent and 3) provided by manufacturers but may be adapted by the user. The impact of the corresponding variance components on the accuracy and precision of target concentration estimators presented in the literature is studied through simulation.

Results

We reveal how system-specific technical factors influence accuracy as well as precision of concentration estimates. We find that a well-chosen sample dilution level and modifiable settings such as the fluorescence cut-off for target copy detection have a substantial impact on reliability and can be adapted to the sample analysed in ways that matter. User-dependent technical variation, including pipette inaccuracy and specific sources of sample heterogeneity, leads to a steep increase in uncertainty of estimated concentrations. Users can discover this through replicate experiments and derived variance estimation. Finally, the detection performance can be improved by optimizing the fluorescence intensity cut point as suboptimal thresholds reduce the accuracy of concentration estimates considerably.

Conclusions

Like any other technology, dPCR is subject to variation induced by natural perturbations, systematic settings as well as user-dependent protocols. Corresponding uncertainty may be controlled with an adapted experimental design. Our findings point to modifiable key sources of uncertainty that form an important starting point for the development of guidelines on dPCR design and data analysis with correct precision bounds. Besides clever choices of sample dilution levels, experiment-specific tuning of machine settings can greatly improve results. Well-chosen data-driven fluorescence intensity thresholds in particular result in major improvements in target presence detection. We call on manufacturers to provide sufficiently detailed output data that allows users to maximize the potential of the method in their setting and obtain high precision and accuracy for their experiments.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-283) contains supplementary material, which is available to authorized users.     

Electric Field and Mobility Dependent First‐Order Recombination Losses in Organic Solar Cells

The origin of photocurrent losses in the power‐generating regime of organic solar cells (OSCs) remains a controversial topic, although recent literature suggests that the competition between bimolecular recombination and charge extraction determines the bias dependence of the photocurrent. Here the steady‐state recombination dynamics is studied in bulk‐heterojunction OSCs with different hole mobilities from short‐circuit to maximum power point. It is shown that in this regime, in contrast to previous transient extracted charge and absorption spectroscopy studies, first‐order recombination outweighs bimolecular recombination of photogenerated charge carriers. This study demonstrates that the first‐order losses increase with decreasing slower carrier mobility, and attributes them to either mobilization of charges trapped at the donor:acceptor interface through the Poole–Frenkel effect, and/or recombination of photogenerated and injected charges. The dependence of both first‐order and higher‐order losses on the slower carrier mobility explains why the field dependence of OSC efficiencies has historically been attributed to charge‐extraction losses.     

3, 3′-diindolylmethane Enhances the Effectiveness of Herceptin against HER-2/Neu-Expressing Breast Cancer Cells

Herceptin failure is a major clinical problem in breast cancer. A subset of breast cancer patients with high HER-2/neu levels eventually experience metastatic disease progression when treated with Herceptin as a single agent. Mechanistic details of development of this aggressive disease are not clear. Therefore, there is a dire need to better understand the mechanisms by which drug resistance develops and to design new combined treatments that benefit patients with aggressive breast cancer and have minimal toxicity. We hypothesized that 3, 3′-diindolylmethane (DIM), a non-toxic agent can be combined with Herceptin to treat breast cancers with high levels of HER-2/neu. Here, we evaluated the effects of Herceptin alone and in combination with DIM on cell viability, apoptosis and clonogenic assays in SKBR3 (HER-2/neu-expressing) and MDA-MB-468 (HER-2/neu negative) breast cancer cells. We found that DIM could enhance the effectiveness of Herceptin by significantly reducing cell viability, which was associated with apoptosis-induction and significant inhibition of colony formation, compared with single agent treatment. These results were consistent with the down-regulation of Akt and NF-kB p65. Mechanistic investigations revealed a significant upregulation of miR-200 and reduction of FoxM1 expression in DIM and Herceptin-treated breast cancer cells. We, therefore, transfected cells with pre-miR-200 or silenced FoxM1 in these cells for understanding the molecular mechanism involved. These results provide experimental evidence, for the first time, that DIM plus Herceptin therapy could be translated to the clinic as a therapeutic modality to improve treatment outcome of patients with breast cancer, particularly for the patients whose tumors express high levels of HER-2/neu.     

Novel Mutations and Deletions of the KIT (Steel Factor Receptor) Gene in Human Piebaldism

Piebaldism is an autosomal dominant genetic disorder of pigmentation characterized by white patches of skin and hair. Melanocytes are lacking in these hypopigmented regions, the result of mutations of the KIT gene, which encodes the cell surface receptor for steel factor (SLF). We describe the analysis of 26 unrelated patients with piebaldism-like hypopigmentation—17 typical patients, 5 with atypical clinical features or family histories, and 4 with other disorders that involve white spotting. We identified novel pathologic mutations or deletions of the KIT gene in 10 (59%) of the typical patients, and in 2 (40%) of the atypical patients. Overall, we have identified pathologic KIT gene mutations in 21 (75%) of 28 unrelated patients with typical piebaldism we have studied. Of the patients without apparent KIT mutations, none have apparent abnormalities of the gene encoding SLF itself (MGF), and genetic linkage analyses in two of these families are suggestive of linkage of the piebald phenotype to KIT. Thus, most patients with typical piebaldism appear to have abnormalities of the KIT gene.     

Adjustment of juvenile tuatara to a cooler,southern climate: operative temperatures,emergence behaviour and growth rate

Translocations for conservation often involve species limited to relict distributions. However, uncertainty can exist regarding the ability of source individuals to acclimatise following a shift to a distant location. We investigated the ability of captive-reared juvenile tuatara (Sphenodon punctatus) of Cook Strait stock (41°S) to adjust to outdoor, predator-protected pens within Orokonui Ecosanctuary (45 °S). We examined potential basking and within burrow temperatures, the influence of temperature on emergence, and growth rates in comparison with other locations. Tuatara at Orokonui reached their preferred temperature when basking over summer, and burrows provided protection from freezing over winter. Emergence was temperature-dependent and essentially ceased during winter. Growth rates of Orokonui-held juveniles were within the range for four other captive-rearing facilities and faster than for wild juveniles from a Cook Strait population. As all Orokonui-held juveniles have survived and grown we conclude that the climate at this southern location is suitable to consider a free-release.     

Aspects of inorganic nitrogen assimilation in yeasts

Cultures of Candida utilis utilise glutamate in preference to ammonia and ammonia in preference to nitrate. The nitrate reductase of this organism is induced by nitrate and repressed in cultures grown on glutamate or ammonia. Nitrate-grown cultures of C. utilis, irrespective of the medium nitrate concentration, behave as though nitrogen-limited. In contrast to C. utilis, Saccharomyces cerevisiae utilises ammonia in preference to glutamate. In eight yeasts studied the highest cellular contents of biosynthetic NADP-linked glutamate dehydrogenase were found in batch cultures containing low concentrations of ammonia or in nitrogen-limited chemostat cultures. NAD-linked glutamate dehydrogenase activity was detected in extracts of cells grown in the presence of glutamate but not in those grown in the presence of ammonia.     

A Small Molecule Non‐fullerene Electron Acceptor for Organic Solar Cells

Organic bulk heterojunction photovoltaic devices predominantly use the fullerene derivatives [C60]PCBM and [C70]PCBM as the electron accepting component. This report presents a new organic electron accepting small molecule 2‐[{7‐(9,9‐di‐n‐propyl‐9H‐fluoren‐2‐yl)benzo[c][1,2,5]thiadiazol‐4‐yl}methylene]malononitrile (K12) for organic solar cell applications. It can be processed by evaporation under vacuum or by solution processing to give amorphous thin films and can be annealed at a modest temperature to give films with much greater order and enhanced charge transport properties. The molecule can efficiently quench the photoluminescence of the donor polymer poly(3‐n‐hexylthiophene‐2,5‐diyl) (P3HT) and time resolved microwave conductivity measurements show that mobile charges are generated indicating that a truly charge separated state is formed. The power conversion efficiencies of the photovoltaic devices are found to depend strongly on the acceptor packing. Optimized K12:P3HT bulk heterojunction devices have efficiencies of 0.73±0.01% under AM1.5G simulated sunlight. The efficiencies of the devices are limited by the level of crystallinity and nanoscale morphology that was achievable in the blend with P3HT.