Single-cell analysis of long non-coding RNAs in the developing human neocortex

Single cell transcriptomics of lncRNA expression in K562 cell cultures. A Distributions of median lncRNA expression to median mRNA expression ratios (lncRNA:mRNA) in populations, in silico merged single cells, and single cells from K562 cultures. B Proportion of K562 cells that expressed each lncRNA (blue) and mRNA (red), separated by maximum expression in single cells. C Same as in (B) but grouped by maximum expression quantile. D Distributions of non-zero lncRNA (blue) and mRNA (red) expression in 46 single K562 cells. Green squares, housekeeping genes; black triangles, ERCC Spike-In Controls. (PDF 454 kb

Effect of root age on the biomechanics of seminal and nodal roots of barley (<i>Hordeum vulgare L.</i>) in contrasting soil environments

Acknowledgments The James Hutton Institute receives funding from the Scottish Government. The authors would also like to thank Jim McNicol from Biomathematics and Statistics Scotland for his advice on statistical analysis.Peer reviewedPostprin

Normalizing single-cell RNA sequencing data: challenges and opportunities

Single-cell transcriptomics is becoming an important component of the molecular biologist's toolkit. A critical step when analyzing data generated using this technology is normalization. However, normalization is typically performed using methods developed for bulk RNA sequencing or even microarray data, and the suitability of these methods for single-cell transcriptomics has not been assessed. We here discuss commonly used normalization approaches and illustrate how these can produce misleading results. Finally, we present alternative approaches and provide recommendations for single-cell RNA sequencing users

The Spectrum of Angiographic Findings in Transitional Cell Carcinoma of the Kidney

The spectrum of angiographic finding in 20 patients with transitional cell carcinomas of the kidney is described. In 15 of 20 patients (75%), prospective diagnosis of transitional cell carcinomas were made because of a combination of the angiographic findings; tumour vessels, tumour stain, prominent pelviureteric arteries and arterial encasement. In 4 patients with negative angiograms the lesions were relatively small in size and were situated within the renal parenchyma, primarily involving the calyces. The use of pharmacoangiographic agents such as epine-phrine and priscoline improved the angiographic visualization of transitional cell carcinomas of the kidney. For the past several years angiography has had a central role in the evaluation of patients with hematuria and renal masses 1 . 5,6,7,8. Although the use of diagnostic ultrasound and renal puncture have eliminated angiography from the diagnosis of renal cysts, most renal masses which are solid or which have equivocal findings at ultrasound still undergo angiography. At the same time, the decreasing use of retrograde urography has resulted in more frequent angiography in patients with unilateral nonfunctioning kidneys. Transitional cell carcinomas of the renal pelvis are an important cause of both hematuria and non-functioning kidneys. We have therefore reviewed our material to reassess the angiographic abnormalities caused by the transitional cell carcinomas and the overall accuracy of the angiography in the diagnosis of these lesions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73228/1/j.1440-1673.1977.tb03191.x.pd

Effects of root dehydration on biomechanical properties of woody roots of <i>Ulex europaeus</i>

Aims: Effects of root water status on root tensile strength and Young’s modulus were studied in relation to root reinforcement of slopes. Methods: Biomechanical properties of woody roots, Ulex europaeus, were tested during progressive dehydration and after thirty-day moisture equilibration in soil with contrasting water contents. Root diameter, water content and water loss were recorded and root water potential versus water content relation was investigated. Tensile stresses induced by root contraction upon dehydration were measured. Results: Root tensile strength and Young’s modulus increased abruptly when root water content dropped below 0.5 g g −1. The strength increase was due to root radial and axial contraction induced by root water potential drop. Diameter decrease and strength gain were the largest for thin roots because of the relatively larger evaporative surface per volume of thin roots. Largely negative water potentials in dry soil induced root drying, affecting root biomechanical properties. Conclusion: Root water status is a factor that can cause (inappropriately) high strength values and the large variability reported in literature for thin roots. Therefore, all root diameter classes should have consistent moisture for fair comparison. Testing fully hydrated roots should be the routine protocol, given that slope instability occurs after heavy rainfall. </p

The genomic basis of adaptive evolution in threespine sticklebacks

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.National Human Genome Research Institute (U.S.)National Human Genome Research Institute (U.S.) (NHGRI CEGS Grant P50-HG002568

Single-cell analysis tools for drug discovery and development

The genetic, functional or compositional heterogeneity of healthy and diseased tissues presents major challenges in drug discovery and development. Such heterogeneity hinders the design of accurate disease models and can confound the interpretation of biomarker levels and of patient responses to specific therapies. The complex nature of virtually all tissues has motivated the development of tools for single-cell genomic, transcriptomic and multiplex proteomic analyses. Here, we review these tools and assess their advantages and limitations. Emerging applications of single cell analysis tools in drug discovery and development, particularly in the field of oncology, are discussed

Implementation and validation of single-cell genomics experiments in neuroscience

Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors. Here, we present types of orthogonal and functional validation experiment to strengthen preliminary findings obtained using single-cell and single-nucleus transcriptomics as well as the challenges and limitations of these approaches