Quantitative and Systematical Designing Fluorophores Enables Ultrasensitive Distinguishing Carbonyls

Although the sophisticated fluorescent probes can improve detection sensitivity, either the lack of quantitative design for fluorophores or the deficiency of selectivity towards individual species makes it extremely difficult to...

Queryfuse is a sensitive algorithm for detection of gene-specific fusions

ABSTRACTRecurrent chromosomal translocations, known as fusions, play important roles in carcinogenesis. They can serve as valuable diagnostic and therapeutic targets. RNA-seq is an ideal platform for detecting transcribed fusions, and computational methods have been developed to identify fusion transcripts from RNA-seq data. However, some transciptome realignment procedures for these methods are unnecessary, making this task computationally expensive and time consuming. Therefore, we have developed QueryFuse, a novel hypothesis-based algorithm that identifies gene-specific fusion from pre-aligned RNA-seq data. It is designed to help biologists quickly find and/or computationally validate fusions of interest, together with visualization and detailed properties of supporting reads. By aligning reads to Query genes at the pre-processing step with a more sensitive, memory intensive local aligner, QueryFuse can reduce alignment time and improve detection sensitivity.QueryFuse performed better or at comparable levels with two popular tools (deFuse and TopHatFusion) on both simulated and well-annotated cell-line datasets. Finally, using QueryFuse, we identified a novel fusion event with a potential therapeutic implication in clinical samples. Taken together, our results showed that QueryFuse is efficient and reliable for detecting gene-specific fusion events.

Trapping Brown Marmorated Stink Bugs: “The Nazgȗl” Lure and Kill Nets

Improvements to current brown marmorated stink bug (BMSB), Halyomorpha halys, surveillance and killing systems are needed to improve detection sensitivity and to reduce pesticide use. Detection of BMSB in New Zealand with traps is reliant on sticky panels with aggregation pheromone, which are low cost but inefficient compared with beating foliage. Trapping for BMSB adults and nymphs was conducted daily with lethal traps consisting of an aggregation pheromone-baited-coat hanger covered with dark-colored long-lasting insecticide-treated mesh, we termed “The Nazgȗl”, based on its sinister appearance. A deep tray lined with white plastic was attached centrally at the base for collecting the dead BMSB. The lethal traps killed and caught up to 3.5-fold more nymphs and adult BMSB than identically-baited sticky panels in the 3 weeks of deployment, and provided a snapshot of phenology by instar. We expect that lure-and-kill stations could contribute to the suppression of a delimited population and could be included as part of a semiochemical-based eradication program. Attracting and killing females and nymphs, thus removing future offspring, could contribute to population suppression during an eradication.

Applying DNA rolling circle amplification in fluorescence imaging of cell surface glycans labeled by a metabolic method

We report herein imaging cell surface glycosylation by using click chemistry and DNA rolling circle amplification (RCA) to improve detection sensitivity..

Quantitative analysis with a two-detector measuring system in in-air PIXE-design to improve detection sensitivity at low energies

In this paper, a two-detector measuring system in in-air PIXE system composed of two Si(Li) detectors has been developed for simultaneous measurement of low- and high-Z elements. In order to improve detection sensitivity of the detector for low energy region, a new device which is attached at the tip of the detector has been designed. It is made of acryl and has a thin end on which a 1.5 μm-thick Mylar film is stuck. As a result, it exhibited a miraculous effect in improving detection sensitivity at low energies and it became possible to detect K X-rays of aluminium. In order to perform quantitative analysis in in-air system, we have measured detection efficiencies for the two Si(Li) detectors including the effect of X-ray absorption in air on the basis of the method that we developed. Concerning the beam energy at the target and corresponding X-ray production cross-sections, the same values as were reported in the previous paper were applicable since conditions of irradiating system were unchanged. It was confirmed that the new method allows us to quantitatively analyze all the elements heavier than aluminum and to obtain mostly the same results as those by in-vacuum PIXE for various kinds of samples. Accuracy of analysis was also confirmed by using a standard material.