Journal: Cell

Article Title: Discovery of natural-product-derived sequanamycins as potent oral anti-tuberculosis agents

doi: 10.1016/j.cell.2023.01.043

Figure Lengend Snippet:

Article Snippet: Final Fourier Shell Correlation plots for the density maps were generated using MATLAB R2021a.

Techniques: Mutagenesis, Recombinant, Cell Culture, Methylation, Amplification, Software, Microscopy, RNA Extraction, Real-time Polymerase Chain Reaction

Journal: Scientific Reports

Article Title: Temporal ablation of the ciliary protein IFT88 alters normal brainwave patterns

doi: 10.1038/s41598-024-83432-1

Figure Lengend Snippet: Inducible IFT88 KO mice have reduced EEG power over a broad spectrum. ( a. ) Power spectrum density plots (PSDs) of EEG waveform power broken down by frequency ranges reveals a shift in brainwave activity. Delta = 1 – 4 Hz, Theta = 4 – 8 Hz, Alpha = 8 – 13 Hz, Beta = 13 – 30 Hz, Gamma = 30 – 50 Hz. ( b. ) Cumulative distribution plots of the above PSDs show a shift in EEG waveform to a lower power. Overall EEG waveform activity was reduced in inducible IFT88 KOs in both the wake (p = 0.017) and non-REM (p = 0.034) states (Kolmogorov–Smirnov test).

Article Snippet: To characterize if IFT88 KO mice share this pathology the 24-h EEG/EMG recordings were filtered to remove the DC offset as well as line current and then further processed in MATLAB to generate power spectrum density plots (PSDs; Fig. ).

Techniques: Activity Assay

Journal: Scientific Reports

Article Title: Temporal ablation of the ciliary protein IFT88 alters normal brainwave patterns

doi: 10.1038/s41598-024-83432-1

Figure Lengend Snippet: Ciliary ablation shifts EEG activity in a frequency dependent manner. ( a. ) Decomposition of PSDs reveals that during the awake state, low-frequency delta wave activity was reduced by 75.1% (p = 0.0059) and theta wave power was attenuated by 52.8% in inducible IFT88 KOs (p = 0.0013). This response was sleep-state dependent as slow-wave power was not attenuated in Non-REM and REM sleep. During sleep states only power of high frequency waveforms was impacted. During non-REM sleep alpha and beta wave power was reduced by 44.2% (p = 0.0167) and 45.9% (p = 0.0265). This remained consistent in REM sleep where alpha wave power was attenuated 43.9% (p = 0.0179) and beta wave power by 40.65% (p = 0.0492) (Tukey’s HSD test). ( b. ) Density distribution plots of this data further illustrate how IFT88 ablation shifts peak brain power in these frequencies (Kolmogorov–Smirnov test).

Article Snippet: To characterize if IFT88 KO mice share this pathology the 24-h EEG/EMG recordings were filtered to remove the DC offset as well as line current and then further processed in MATLAB to generate power spectrum density plots (PSDs; Fig. ).

Techniques: Activity Assay

Journal: Nature Communications

Article Title: Identification of a neural crest stem cell niche by Spatial Genomic Analysis

doi: 10.1038/s41467-017-01561-w

Figure Lengend Snippet: Reproducibility of subclusters between different embryos. a Violin plots show modality and gene expression levels for the 35 genes used in the study. Plots are based on Gaussian kernel density estimation and MatLab (R2015a v8.0) default settings for ksdensity command. b The five clusters (see heat map in Fig. with pooled data from five samples) form reproducible spatial patterns in the dorsal neural tube. Spatial mapping of the pooled clusters into two additional embryo sections reproduce the pattern seen in Fig. . c The early migratory neural crest population (shown in green in Fig. ) consists of three separate subpopulations (NC mig 1–3) with spatially distinct locations. All populations express the epidermal marker Krt19 , whereas the cells that emigrated first and have thus migrated the furthest express pluripotency markers and high levels of the neuroectodermal gene Pax6 . The following populations (NC mig 2–3) have high Msx2 expression. For the subcluster reproducibility analysis, five samples from three different embryos were compared and three representatives were chosen for the images ( n = 5). Scale bar, 10 μm

Article Snippet: Plots are based on Gaussian kernel density estimation and MatLab (R2015a v8.0) default settings for ksdensity command. b The five clusters (see heat map in Fig. with pooled data from five samples) form reproducible spatial patterns in the dorsal neural tube.

Techniques: Gene Expression, Marker, Expressing