Journal: Biophysical Journal

Article Title: Modeling the Dynamics of Cdc42 Oscillation in Fission Yeast

doi: 10.1016/j.bpj.2017.12.007

Figure Lengend Snippet: Numerical solutions for ODE Model 2 ((11a), (11b)). Note that time is plotted in dimensional units (minutes) here. (a and d) Plots of c1,2, g1,2 given by (11a), (11b) with Ctot = 1.58 (above the limit point of asymmetric branch) as a function of time with koff = 1. (b and e) Plots of c1,2, g1,2 as a function of time with koff = 0.9, respectively. The period of the oscillation is ∼2 min. (c and f) Plots of c1,2 and cytosolic concentrations Ctot – c1– c2 (Gtot – g1– g2) for koff = 0.791 and Ctot = 1.5. The solution has a larger period (∼10 min) compared to solution plotted in figures (b and d). (g–i) Change of transition time from asymmetric state to symmetric oscillation as the strength of negative feedback κ changes. (h) Solutions of c1,2 with κ near the saddle-node point κ = 8.39. For κ = 8.4, the numerical solution undergoes a transition from an asymmetric state to converges to a periodic solution. The transition time is sensitive to the parameter κ. As κ increases from 8.4 to 8.41, the transition time decreases by half (from 80 to 40 min). Initial condition: c1 = 1.3, c2 = 0.01, g1 = 0.23, g2 = 0.64. ODEs ((11a), (11b)) are solved by the software MATLAB’s stiff solver ode15s (MathWorks, Natick, MA). Initial conditions for (e–g): c1 = 0.7181, c2 = 0.1842, g1 = 0.1853, and g2 = 0.585. To see this figure in color, go online.

Article Snippet: ODEs ( (11a) , (11b) ) are solved by the software MATLAB’s stiff solver ode15s (MathWorks, Natick, MA).

Techniques: Software

Journal: Cell reports

Article Title: Unexpected Rule-Changes in a Working Memory Task Shape the Firing of Histologically Identified Delay-Tuned Neurons in the Prefrontal Cortex.

doi: 10.1016/j.celrep.2019.12.102

Figure Lengend Snippet: Figure 4. Identified Layer III Neuron Exhibiting Elevated Spiking Activity during the Delay Period of the Working Memory Task and Its Distinct Rate Adaptation during Cognitive Flexibility (A) Reconstruction of the identified delay-elevated pyramidal neuron, TO34, located in layer III of the prelimbic cortex (section thickness: 50 mm, 5 sections) (blue, basal dendrites; red, apical dendrite; and green, main axon). Red dot indicates the position of the cell body (D, dorsal; M, medial; and L, lateral). (B) Position of the labeled cell body (shown with a red dot) in the tissue section (D, dorsal; L, lateral; M, medial). (C) Left: raster plot of the delay-elevated cell, TO34, across all trials during working memory and cognitive flexibility. Right: trial identifier as in Figure 3D. (D) Identified cell, TO34, showed ramping neuronal activity during the delay period of the working memory task (rule 1). Horizontal bars with asterisks indicate significance in firing rate change (*adjusted alpha = 0.0096, significance thresholds were calculated using a shuffling procedure on all correct trials; FDR for multiple comparison; see STAR Methods for details). Bottom: firing activity during delay is stimulus specific (chocolate versus cherry trials) during the working memory paradigm (rule 1) (Nchocolate = 9, Ncherry = 14 trials; *adjusted alpha = 0.0093, permutation test on all correct trials with two conditions; FDR correction; see STAR Methods for details). Dark lines, mean firing rate; shading, mean ± SEM. (E) Delay-elevated cell, TO34, exhibited significant decrease in firing rate upon rule change (Nrule 1 = 24, Nnaive = 23, and Nlearned = 10 trials; p = 0.0126, Kruskal- Wallis test, post hoc Dunn’s multiple comparisons test). Error bars denote ± SEM. **p < 0.01. (F) Delay firing activity of cell TO34 during rule 2 across correct non-conflicting trials, and correct or incorrect conflicting trials (Nnon-conf. correct = 15, Nconf. error = 11, and Nconf. correct = 6 trials; p = 0.0337, Kruskal-Wallis test, n.s. in post hoc Dunn’s multiple comparisons test). Error bars denote ± SEM. (G) Neurobiotin-labeled delay-elevated cell, TO34 (green, soma), was BRN1+ (arrowhead, nucleus; cyan), SATB2+ (arrowhead, nucleus; magenta), and CTIP2+

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Coup-TFI interacting protein 2 (CTIP2) [host Rb; Dil 1:1000] Abcam Cat# ab28448; RRID: AB_1140055 Wolfram syndrome-1 (WFS1) [host rb; Dil 1:1500] Proteintech Cat# 11558-1; RRID: AB_2216046 BRN1 [host gt; Dil 1:500] Santa Cruz Cat# sc6028, gift from Tibor Harkany, used in Keays et al. (2007) SATB2 [host m; Dil 1:100] Abcam Cat# ab51502; RRID: AB_882455 Chemicals, Peptides, and Recombinant Proteins Neurobiotin Tracer Vector Laboratories Cat# SP-1120; RRID: AB_2313575 Critical Commercial Assays Vectastain ABC kit Vector Laboratories Cat# PK6100; RRID: AB_2336819 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000; RRID: AB_2336789 Experimental Models: Organisms/Strains Long-Evans rats Charles River Laboratories https://www.criver.com/ Software and Algorithms MATLAB R2012b Mathworks https://www.mathworks.com/products/ matlab.html Prism 7 GraphPad https://www.graphpad.com/ Spike2 7.11 Cambridge Electronic Design Limited (CED) http://ced.co.uk/ Klustakwik Harris et al., 2000 http://klustakwik.sourceforge.net/ klusta and KlustaViewA Rossant et al., 2016 https://klusta.readthedocs.io/en/latest/ Zen Zeiss https://www.zeiss.co.uk/corporate/home.html Imaris 9.2 BitPlane, Oxford Instruments https://imaris.oxinst.com/ ImageJ 1.47v ImageJ https://imagej.nih.gov/ij/ Other Silicon Probe; Buzsaki64-H64_30mm NeuroNexus https://neuronexus.com/

Techniques: Activity Assay, Labeling, Comparison, Chocolate