Hybridization Chain Reaction Fluorescence In Situ Hybridization (HCR-FISH) in Ambystoma mexicanum Tissue.

In situ hybridization is a standard procedure for visualizing mRNA transcripts in tissues. The recent adoption of fluorescent probes and new signal amplification methods have facilitated multiplexed RNA imaging in tissue sections and whole tissues. Here we present protocols for multiplexed hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) staining, imaging, cell segmentation, and mRNA quantification in regenerating axolotl tissue sections. We also present a protocol for whole-mount staining and imaging of developing axolotl limbs.

singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality.

Single-cell assays have transformed our ability to model heterogeneity within cell populations. As these assays have advanced in their ability to measure various aspects of molecular processes in cells, computational methods to analyze and meaningfully visualize such data have required matched innovation. Independently, Virtual Reality (VR) has recently emerged as a powerful technology to dynamically explore complex data and shows promise for adaptation to challenges in single-cell data visualization. However, adopting VR for single-cell data visualization has thus far been hindered by expensive prerequisite hardware or advanced data preprocessing skills. To address current shortcomings, we present singlecellVR, a user-friendly web application for visualizing single-cell data, designed for cheap and easily available virtual reality hardware (e.g., Google Cardboard, ∼$8). singlecellVR can visualize data from a variety of sequencing-based technologies including transcriptomic, epigenomic, and proteomic data as well as combinations thereof. Analysis modalities supported include approaches to clustering as well as trajectory inference and visualization of dynamical changes discovered through modelling RNA velocity. We provide a companion software package, scvr to streamline data conversion from the most widely-adopted single-cell analysis tools as well as a growing database of pre-analyzed datasets to which users can contribute.

Normalization of markedly elevated alpha-fetoprotein in a virologic nonresponder with HCV-related cirrhosis.

Measurement of serum AFP can be useful in the diagnosis of hepatocellular carcinoma (HCC). AFP is a fetal protein that is not normally present in the serum of adults but is elevated in most patients with HCC. The diagnosis of HCC is generally made in patients with a mass lesion in a cirrhotic liver if the AFP is over 400 ng/ml. Unfortunately, AFP is elevated in other conditions such as nonseminomatous germ cell tumor, chronic hepatitis, cirrhosis, pregnancy, and hepatic metastasis. A high AFP cutoff value for HCC would increase the specificity of the test, but would decrease the sensitivity considerably. We report the case of a patient with HCV and cirrhosis with a markedly elevated AFP of 1257 ng/ml in whom no evidence of HCC could be found after a thorough radiologic and histologic evaluation. Despite a virologic nonresponse to IFN-alpha2b and ribavirin therapy, there was a complete normalization of AFP.