Journal: Frontiers in Genetics

Article Title: Discovering novel reproductive genes in a non-model fly using de novo GridION transcriptomics

doi: 10.3389/fgene.2022.1003771

Figure Lengend Snippet: De novo transcriptome pipelines for (A) ONT long-read technology, and (B) Illumina short-read technology. mRNA from the accessory glands of Sepsis punctum , was used for cDNA library preparation and RNAseq using ONT long-read and Illumina short-read technologies. ONT transcripts were generated by de novo gene clustering, consensus generation, and gene polishing, whereas for Illumina short-reads were de novo assembled to reconstruct contigs. Preliminary transcriptomes were filtered using common steps (shown in green), using six-frame Open Reading Frame (ORF) searches, ≥ 200 bp length, and dereplication at 100% protein identity, to derive final transcriptomes. Gene expression was quantified using read count as a proxy for ONT and Transcript per Million (TPM) for Illumina.

Article Snippet: Thus far, novel insect reproductive genes and gene products have been primarily discovered using Illumina based RNAseq and microarrays ( ; ; ; ; ), as well as using traditional protein or proteomics analyses ( ; ; ; ; ; ).

Techniques: cDNA Library Assay, Generated, Expressing

Journal: Nature medicine

Article Title: EPIDURAL STIMULATION OF THE CERVICAL SPINAL CORD FOR POST-STROKE UPPER LIMB PARESIS

doi: 10.1038/s41591-022-02202-6

Figure Lengend Snippet: (a) An image of the stimulator (DS8R, left) and 1-to-8 channel multiplexer (D188, right) used to deliver stimulation pulses. (b) An overview of the control scheme used to deliver patterns of stimulation. A PC running a (c) MATLAB based GUI communicated with a microcontroller using a custom (d) communication protocol over a virtual serial port. The microcontroller’s firmware delivered pulse triggers and amplitude control signals to the stimulator as well as an 8 bit parallel channel selection signal to the multiplexer in order to control pulse timing, amplitude, and output channel. Current was delivered from the stimulator through the multiplexer and ultimately to the selected electrode on the implanted spinal array. (c) The GUI interface allowed for configuring all stimulation parameters including active channels, stimulation frequency, pulse train duration (or continuous), pulse train latency, and stimulation amplitude for each active channel. Once configured, stimulation was initiated or terminated via the software interface. The software also allowed for rapid changes in either global stimulation frequency (nudge frequency) or channel amplitude (nudge amplitude). (d) A custom command protocol layer was developed on top of a UART serial interface to enable communication between the GUI and microcontroller. Each packet from the master (PC) to the slave (microcontroller) comprised a 1 byte packet length, 1 byte command, and 0–6 bytes of payload. A payload comprised a 1 byte parameter (to be read or written), a 1 byte channel number (when appropriate), and the value to be written (when ‘write’ command was used). Microcontroller response packets comprised a 1 byte packet length, 1 byte command echo, 0–32 bytes of payload (used to return parameter values during ‘read’ command), and a 1 byte success flag. (e) The microcontroller firmware allowed for pseudo-synchronous stimulation across multiple channels by interleaving pulses on all active channels. A delay of at least 1 ms between each pulse allowed enough time for the multiplexer to fully switch channels. The same pattern of pulses was delivered every period as defined by the stimulation frequency. Each channel could also be configured to deliver a single pulse, a pulse train with finite duration and/or latency, continuous stimulation, or a ‘recruitment curve’ in which the amplitude was gradually increased for successive pulse trains of specified length.

Article Snippet: A PC running a (c) MATLAB based GUI communicated with a microcontroller using a custom (d) communication protocol over a virtual serial port.

Techniques: Selection, Software