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Each analysis included 12 paired expression measurements, one from blood and one from a given brain region, from each animal.
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But the first study to use functional magnetic resonance imaging (fMRI) to examine brain activity in people who've taken psilocybin finds that the drug reduces neural firing in key communication hubs, essentially disconnecting some brain regions from each other.
Twenty-one different brain regions from each individual were isolated and gene expression was performed.
The summary of clinical information and the availability of the brain regions from each case are shown in Tables 1 and 2. Bisulfite sequence analysis was performed for all available brain regions and the % methylation was plotted against various clinical parameters (Figures S1, S2, S3).
Our operationally-matched assessment of DA tissue content and TH measures from all four brain regions from each test subject is a novel state-of-the-art approach to equate the DA tissue content resulting from a respective TH protein and TH phosphorylation profile and to determine their contributions to locomotor activity.
Brain regions from each control and PD patient analyzed included cortex, cerebellum and caudate.
Tissue was obtained from multiple brain regions from each patient: striatum, cerebellum, mid-brain, superior frontal gyrus (SFG) and superior temporal gyrus (STG).
Paraffin-embedded tissue blocks from 12 brain regions from each case were sent to the TBI Brain Bank at BUSM for uniform processing, staining and immunohistochemistry (IHC) (Table 1); 2 of the selected cases were missing the superior temporal block.
We next individually analyzed the raw expression levels of 12 genes showing significant alterations (downregulated: MET, PCSK1, RGS4, HS3ST2, NPTX2, NEUROD6, RAB27B, HCN1, HOMER1; upregulated: GJA1, AEBP1, GALNTL2) in 3 brain regions from each subject (see Supplementary Fig. 1, left panels), confirming that AD hippocampi exhibited the most significant alterations of gene expression (Fig. 2 A).
For technical validation of differentially expressed genes, we performed semi-quantitative RT-PCR using RNA extracted from additional samples that were collected in each brain region from tissue adjacent to that used in the microarray expression study.
Genes identified as differentially expressed between the FSL and FRL rats in each brain region from both animal cohorts were assessed for significant enrichment of particular biological processes using the terms of the fifth level of Gene Ontology (GO) (Supplementary Table S4).
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