BackgroundGene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model.ResultsWe generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models.ConclusionsWe demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0694-1) contains supplementary material, which is available to authorized users.

There are remarkable disparities among patients of different races with prostate cancer; however, the mechanism underlying this difference remains unclear. Here, we present a comprehensive landscape of the transcriptome profiles of 14 primary prostate cancers and their paired normal counterparts from the Chinese population using RNA-seq, revealing tremendous diversity across prostate cancer transcriptomes with respect to gene fusions, long noncoding RNAs (long ncRNA), alternative splicing and somatic mutations. Three of the 14 tumors (21.4%) harbored a TMPRSS2-ERG fusion, and the low prevalence of this fusion in Chinese patients was further confirmed in an additional tumor set (10/54=18.5%). Notably, two novel gene fusions, CTAGE5-KHDRBS3 (20/54=37%) and USP9Y-TTTY15 (19/54=35.2%), occurred frequently in our patient cohort. Further systematic transcriptional profiling identified numerous long ncRNAs that were differentially expressed in the tumors. An analysis of the correlation between expression of long ncRNA and genes suggested that long ncRNAs may have functions beyond transcriptional regulation. This study yielded new insights into the pathogenesis of prostate cancer in the Chinese population.

Black soldier fly (BSF) larvae, Hermetia illucens L., develops on organic wastes, reducing ecological pollution and converting waste biomass into protein and fat rich insect biomass. BSF can replace increasingly expensive protein sources used in poultry, aquaculture and livestock compound diet formulation, such as fish meal and soybean meal, which holds the potential to alleviate future food and feed insecurity. The fate of nutritional spectra in BSF during its life cycle phases is still poorly understood. This study assessed metabolic changes in nutrition composition of BSF from egg to adult. A rapid increase of crude fat content was observed since the development of 4–14 days of larvae with its maximum level reaching 28.4% in dry mass, whereas the crude protein displayed a continuous decreasing trend in the same development phases with minimum level of 38% at larval phase (12 days) and peak level of 46.2% at early pupa stage. A sharp drop in crude fat was noticed from early prepupae to late pupae (24.2%, 8.2% respectively). However crude protein shows its maximum value being 57.6% at postmortem adult stage with 21.6% fat level. In addition, fatty acids, amino acids, minerals and vitamins composition in different development stages of BSF were presented and compared. Findings from this study could provide podium to food and feed industry for framing a strategy for specific molecular nutritional component intake into the diets of humans, aquaculture and animals. It is also indicated that BSF is a possible insect which can be applied to combating the food scarcity of countries where micronutrient deficiency is prevalent. Moreover it contributes to advance exploring for developmental and metabolic biology of this edible insect.

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Metal halide perovskites have aroused tremendous interest in the past several years for their promising applications in display and lighting. However, the development of blue perovskite light‐emitting diodes (PeLEDs) still lags far behind that of their green and red cousins due to the difficulty in obtaining high‐quality blue perovskite emissive layers. In this study, a simple approach is conceived to improve the emission and electrical properties of blue perovskites. By introducing an alkali metal ion to occupy some sites of peripheral suspended organic ligands, the nonradiative recombination is suppressed, and, consequently, blue CsPb(Br/Cl)3 nanocrystals with a high photoluminescence quantum efficiency of 38.4% are obtained. The introduced K+ acts as a new type of metal ligand, which not only suppresses nonradiative pathways but also improves the charge carrier transport of the perovskite nanocrystals. With further engineering of the device structure to balance the charge injection rate, a spectrally stable and efficient blue PeLED with a maximum external quantum efficiency of 1.96% at the emission peak of 477 nm is fabricated.