Journal: eLife

Article Title: Optogenetics and electron tomography for structure-function analysis of cochlear ribbon synapses

doi: 10.7554/eLife.79494

Figure Lengend Snippet: ( A ) Simplified illustration depicting the components of the external setup installed to control the light stimulation (irradiance and duration), to determine the time point of the freezing onset and command relay (blue, control unit) to the sensors (accelerometer [red, outside, AM], microphone [patterned blue, inside, M], pneumatic pressure sensor, green, inside, PS) to initiate the mechanical sensing process of the HPM100 . ( B ) Fiber – cartridge arrangement in the HPM100 with the fiber at an angle of 60° to the upper half-cylinder: Sample plane: black, fiber: gray, Light rays: red. Mechanical components of HPM100 are not shown. ( C ) Sample loading scheme. ( D ) Re-build chamber replica to enable irradiance calculation externally. ( E ) CCD image of the photodiode in the sample plane. ( F ) The spatial irradiance distribution with a peak irradiance of ~6 mW/mm 2 at 80% intensity of the light-emitting diode (LED) was calculated using a self-written MATLAB routine intensityprofilcalculator.m . Depicted are pixel values in irradiance. The complete workflow for Opto-HPF is presented in .

Article Snippet: Methodology, Resources, Software, Writing – review and editing, programmed the MATLAB GUI, MATLAB interface, installed the sensors to the Opto-HPF.

Techniques: Control

Journal: eLife

Article Title: Optogenetics and electron tomography for structure-function analysis of cochlear ribbon synapses

doi: 10.7554/eLife.79494

Figure Lengend Snippet: ( A ) Pneumatic pressure sensor inside the HPM100. ( B ) Scheme of the localization of the pneumatic pressure sensor below the pneumatic needle valve, which allows LN 2 influx in the chamber for freezing. ( C ) Depicted are the curves from the different sensors aligned by using the MATLAB GUI . The curves of the pressure build-up start and temperature corresponding decline are aligned to the steep drop in the pneumatic pressure curve (green arrowhead, inset). ( D ) The outline of the optical stimulation incorporated with HPF: 100 ms light pulse set to a 390 ms delay from HPM start resulted in a stimulation duration of 48–76 ms before freezing (‘LongStim’) and that set to a 425 ms delay from HPM start in a stimulation of 17–25 ms (‘ShortStim’).

Article Snippet: Methodology, Resources, Software, Writing – review and editing, programmed the MATLAB GUI, MATLAB interface, installed the sensors to the Opto-HPF.

Techniques:

Journal: eLife

Article Title: Optogenetics and electron tomography for structure-function analysis of cochlear ribbon synapses

doi: 10.7554/eLife.79494

Figure Lengend Snippet:

Article Snippet: Methodology, Resources, Software, Writing – review and editing, programmed the MATLAB GUI, MATLAB interface, installed the sensors to the Opto-HPF.

Techniques: Sequencing, Knock-In, Recombinant, Software, Microscopy, Control

Journal: bioRxiv

Article Title: Cold Tolerance is Governed by Diverse Genetic Mechanisms Including Those Regulated by NB-LRR-type Receptor Proteins in Arabidopsis

doi: 10.1101/2022.01.18.476799

Figure Lengend Snippet: Schematic representation of the steps taken in identifying genes involved in cold stress using a high-throughput phenotyping platform. After suspending in low melting agarose (a) , seeds were stratified, and sown (b), and grown in the Arabidopsis growth chambers fitted with digital cameras (c) . Two-dimensional images of the rosette leaves of individual genotypes were captured and analyzed using Matlab GUI software (Method S2) (d) . The digital images were converted to pixel data for conducting easyGWAS to identify putative cold-stress-related genes. The candidate cold-stress-related genes were validated by studying knockout mutants. Homozygous knockout mutants were identified (e) . SALK_104944, knockout T-DNA insertion mutant for AT1G68320 ; HM, homozygous line; HZ, heterozygous line; WT (Col-0 ecotype), wild-type with no insertion. Knockout mutants were phenotyped to determine if any of the 33 putative cold-stress-related genes play a role in cold tolerance (f) .

Article Snippet: Two-dimensional images of the rosette leaves of individual mutants were captured and analyzed by Matlab GUI software (Method S2).

Techniques: High Throughput Screening Assay, Software, Knock-Out, Mutagenesis

Journal: Cell reports

Article Title: D1 and D2 neurons in the nucleus accumbens enable positive and negative control over sugar intake in mice

doi: 10.1016/j.celrep.2023.112190

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit-anti-mCherry Abcam RRID: AB_2571870 TRITC-conjugated affinipure Goat anti-Rabbit IgG (H + L) Jackson ImmunoResearch Labs RRID: AB_2337932 Goat Anti-GFP antibody (FITC) Abcam RRID: AB_305635 Anti-c-Fos Rabbit polyclonal to c-Fos Abcam RRID: AB_2231989 Biotinylated Goat Anti-Rabbit IgG antibody Vector Laboratories RRID: AB_2313606 Chemicals, peptides, and recombinant proteins Sucralose Sigma PubChem Substance ID: 329769983 Rebaudioside A Sigma PubChem Substance ID: 329747271 Glucose Sigma PubChem Substance ID: 24895335 Methyl α-D-glucopyranoside Sigma PubChem Substance ID: 24897328 Denatonium Benzoate Sigma PubChem Substance ID: 57654112 Lithium chloride Sigma PubChem Substance ID: 24896459 Victoza (liraglutide) injection Novo Nordisk N/A DiI lipophiliccarbocyanine dye Sigma PubChem Substance ID: 57650110 PubChem Substance ID: Invitrogen Cat #D1817 Dextran, Tetramethylrhodamine, 10,000 MW, Lysine Fixable (Fluoro-Ruby) Critical commercial assays VECTASTAIN Elite ABC HRP Kit (Peroxidase, Standard) Vector Laboratories Cat# PK-6100 C&B Metabond Parkell SKU: S380 Experimental models: Organisms/strains Mouse: B6.FVB(Cg)-Tg(Drd1-cre)EY262Gsat/Mmucd University of California, Davis MMRRC RRID:MMRRC_030989-UCD Mouse: B6.FVB(Cg)-Tg(Drd2-cre)ER44Gsat/Mmucd University of California, Davis MMRRC RRID:MMRRC_032108-UCD Mouse: B6(Cg)-Tg(Phox2b-cre)3Jke/J The Jackson Laboratory RRID:IMSR_JAX:016223 Mouse: B6; 129S6-Gt(ROSA)26Sortm9 (CAG-tdTomato)Hze/J The Jackson Laboratory RRID:IMSR_JAX:007905 Recombinant DNA and virus strains H129 CAG-LSL-TK-tdTomato NIH Center for Neuroanatomy with Neurotropic Virus ΔTK-TT PRV CMV-EGFP NIH Center for Neuroanatomy with Neurotropic Virus Ba-152 PRV CAG-DIO-TK-GFP NIH Center for Neuroanatomy with Neurotropic Virus Ba-2017 AAV-flex-taCasp3-TEVp Addgene Cat # 45580-AAV5; RRID:Addgene_45580 AAV-EF1a-DIO-hChR2(H134R)-EYFP Addgene Cat # 20298-AAV5; RRID:Addgene_20298 Software and algorithms MATLAB R2017b MathWorks https://www.mathworks.com/products/matlab/ GraphPad Prism 8 GraphPad https://www.graphpad.com/scientific-software/prism/ Adobe Illustrator CC 2017 Adobe https://shop.adobe.com/ Open Ephys GUI Open Ephys https://open-ephys.org/software Neuroscope, NDManager and Klusters Lynn Hazan & Michaël Zugaro http://neurosuite.sourceforge.net/ KlustaKwik Ken Harris http://klustakwik.sourceforge.net/ BukaLab Asapti Labs https://asapti.com/ BioRender BioRender https://biorender.com Other Implantable Optical Fibers Doric Lenses, Canada MFC_200/240–0.22_6mm_ZF1.25(G)_FLT 32 CH Microelectrode (Electrophysiological recordings) NeuroNexus A2x16–10mm-50–500-177-A32 Micro-Renathane (tubing) Braintree SKU: MRE033 Open in a separate window KEY RESOURCES TABLE.

Techniques: Plasmid Preparation, Recombinant, Injection, Software