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Biology subjects

Yu, A. D.

Publications and source records attributed to Yu, A. D..

2 recordsLinked to original sources

FlyBox: A Flexible Open-Source Behavior Monitoring System

Over the past two decades, the vast majority of circadian behavior in Drosophila has been recorded in Drosophila Activity Monitor (DAM) boards. Though simple and robust, locomotor behavior recording via DAM boards can be prohibitively expensive, especially when taking incubator costs into consideration. Furthermore, their simplicity limits their experimental options and resolution. Here, we present the FlyBox: a simple, open-source benchtop locomotor activity recording system. FlyBox was designed to monitor activity in animals loaded into a standard laboratory multi-well plate. It features light-tight construction and multiple programmable LEDs for simulating day/night cycles and optogenetic manipulation. In total, a single FlyBox costs approximately $750 to build and around two days of labor. In addition, we also present the FlyBoxScanner software to simplify activity monitoring while maintaining compatibility with DAM analysis software. FlyBox is an attractive and affordable package for behavior monitoring that also offers considerable room for customization. Materials and instructions for the FlyBox are available at https://github.com/Rosbash-Lab-FlyBox/FlyBox, and FlyBoxScanner is available at https://github.com/jose-elias-alvarez/flybox-scanner.

neuroscience↗

BuTT-Seq: a new method for facile profiling of transcription

A wide range of sequencing methods have been developed to assess nascent RNA transcription and resolve the single-nucleotide position of RNA polymerase genome-wide. These techniques are often burdened with high input material requirements and lengthy protocols. We leveraged the template-switching properties of thermostable group II intron reverse transcriptase (TGIRT) and developed BuTT-Seq (BUlk analysis of nascent Transcript Termini sequencing), which can produce libraries from purified nascent RNA in 6 hours and from as few as 10,000 cells - an improvement of at least 25-fold over existing techniques. BuTT-Seq shows that inhibition of the superelongation complex (SEC) causes promoter-proximal pausing to move upstream in a fashion correlated with subnucleosomal fragments. To address transcriptional regulation in a tissue, BuTT-Seq was used to measure the circadian regulation of transcription from fly heads. All the results indicate that BuTT-Seq is a simple and powerful technique to analyze transcription at a high level of resolution.

molecular biology↗