Rchimerism: An R Package for Automated Chimerism Data Analysis.

A quantitative chimerism test monitors engraftment of donor hematopoietic stem cells or relapse of leukemias or lymphomas in hematopoietic stem cell transplantation patients. The most common method used for chimerism testing is PCR amplification of short tandem repeat loci, followed by capillary gel electrophoresis. Manual data analysis is tedious and time consuming, as it involves the selection of informative loci and the repetition of quantifying chimerism percentage for multiple loci from multiple cell types. It is also susceptible to human errors. Currently, there is no free software to fully automate chimerism data analysis. Rchimerism, an R shiny package, was developed to automatically pick informative loci, calculate chimerism percentage, and display the results through a user-friendly interface. The accuracy of the program was compared with manual calculation on 60 patient samples with 100% concordance. Compared with manual calculation, Rchimerism drastically reduces analysis time from 20 to 40 minutes for single donor transplantation samples and from 40 to 80 minutes for double donor transplantation samples to >1 minute. Rchimerism can be downloaded and used freely by noncommercial laboratories.

Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana.

BACKGROUND: Riboswitches are mRNA elements that change conformation when bound to small molecules. They are known to be key regulators of biosynthetic pathways in both prokaryotes and eukaryotes. PRESENTATION OF THE HYPOTHESIS: The hypothesis presented here is that riboswitches function as receptors in hormone perception. We propose that riboswitches initiate or integrate signaling cascades upon binding to classic signaling molecules. The molecular interactions for ligand binding and gene expression control would be the same as for biosynthetic pathways, but the context and the cadre of ligands to consider is dramatically different. The hypothesis arose from the observation that a compound used to identify adenine binding RNA sequences is chemically similar to the classic plant hormone, or growth regulator, cytokinin. A general tenet of the hypothesis is that riboswitch-binding metabolites can be used to make predictions about chemically related signaling molecules. In fact, all cell permeable signaling compounds can be considered as potential riboswitch ligands. The hypothesis is plausible, as demonstrated by a cursory review of the transcriptome and genome of the model plant Arabidopsis thaliana for transcripts that i) contain an adenine aptamer motif, and ii) are also predicted to be cytokinin-regulated. Here, one gene, CRK10 (for Cysteine-rich Receptor-like Kinase 10, At4g23180), contains an adenine aptamer-related sequence and is down-regulated by cytokinin approximately three-fold in public gene expression data. To illustrate the hypothesis, implications of cytokinin-binding to the CRK10 mRNA are discussed. TESTING THE HYPOTHESIS: At the broadest level, screening various cell permeable signaling molecules against random RNA libraries and comparing hits to sequence and gene expression data bases could determine how broadly the hypothesis applies. Specific cases, such as CRK10 presented here, will require experimental validation of direct ligand binding, altered RNA conformation, and effect on gene expression. Each case will be different depending on the signaling pathway and the physiology involved. IMPLICATIONS OF THE HYPOTHESIS: This would be a very direct signal perception mechanism for regulating gene expression; rivaling animal steroid hormone receptors, which are frequently ligand dependent transcription initiation factors. Riboswitch-regulated responses could occur by modulating target RNA stability, translatability, and alternative splicing - all known expression platforms used in riboswitches. The specific illustration presented, CRK10, implies a new mechanism for the perception of cytokinin, a classic plant hormone. Experimental support for the hypothesis would add breadth to the growing list of important functions attributed to riboswitches. REVIEWERS: This article was reviewed by Anthony Poole, Rob Knight, Mikhail Gelfand.

Rho-kinase-mediated Ca2+-independent contraction in rat embryo fibroblasts.

Thus far, determining the relative contribution of Ca2+/calmodulin-dependent myosin light chain kinase (MLCK) and Ca2+-independent Rho-kinase pathways to myosin II activation and contraction has been difficult. In this study, we characterize the role of Rho-kinase in a rat embryo fibroblast cell line (REF-52), which contains no detectable MLCK. No endogenous MLCK could be detected in REF-52 cells by either Western or Northern blot analysis. In the presence or absence of Ca2+, thrombin or lysophosphatidic acid (LPA) increased RhoA activity and Rhokinase activity, correlating with isometric tension development and myosin II regulatory light chain (RLC) phosphorylation. Resting tension is associated with a basal phosphorylation of 0.31 +/- 0.02 mol PO4/mol RLC, whereas upon LPA or thrombin treatment myosin II RLC phosphorylation increases to 1.08 +/- 0.05 and 0.82 +/- 0.05 mol PO4/mol RLC, respectively, within 2.5 min. Ca2+ chelation has minimal effect on the kinetics and magnitude of isometric tension development and RLC phosphorylation. Treatment of REF-52 cells with the Rho-kinase-specific inhibitor Y-27632 abolished thrombin- and LPA-stimulated contraction and RLC phosphorylation. These results suggest that Rho-kinase is sufficient to activate myosin II motor activity and contraction in REF-52 cells.