Neuroanatomical correlates of interval perception in the amygdala.

<p>The peak voxel is located in the left amygdala. The scatter plot shows distributions of scores on interval perception vs. mean GMV of all the voxels in the cluster after controlling for sex and total GMV. Each dot represents one participant.</p

Clusters of voxels correlated with interval perception.

<p><i>Note</i>: MNI  =  Montreal Neurological Institute.</p

Exemplar stimuli in the interval test.

<p>Note that the second melody was nearly identical to the first melody, except that the second note of the second melody (see arrow pointing downwards) violated the pitch interval structure as indicated by the first melody.</p

Neuroanatomical correlates of interval perception in the temporal cortex.

<p><i>A.</i> The peak voxel in the right temporal cortex is located in the superior temporal gyrus. The scatter plot shows distributions of scores on interval perception vs. mean GMV of all the voxels in the cluster after controlling for sex and total GMV. Each dot represents one participant. <i>B</i>. The peak voxel in the left temporal cortex is located in the planum polare. The scatter plot shows distributions of scores on interval perception vs. mean of GMV of all the voxels in the cluster.</p

Additional file 2 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Additional file 2: TableS6. The metabolites identified in positive ion mode

Additional file 3 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Additional file 3: Table S7. The metabolites identified in negative ionmode

Additional file 4 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Additional file 4: Table S8. The differential expressed genes identified inwillow barks

Additional file 1 of Different color regulation mechanism in willow barks determined using integrated metabolomics and transcriptomics analyses

Additional file 1: TableS1. Information on all metabolites. Table S2. Up- and downregulatedmetabolites. Table S3. RNA-sequencing profiles. Table S4. Number of up- anddownregulated differentially expressed genes. Table S5. The primers designedfor RT-qPCR

Resolving Chromosome-Centric Human Proteome with Translating mRNA Analysis: A Strategic Demonstration

Chromosome-centric human proteome project (C-HPP) aims at differentiating chromosome-based and tissue-specific protein compositions in terms of protein expression, quantification, and modification. We previously found that the analysis of translating mRNA (mRNA attached to ribosome-nascent chain complex, RNC-mRNA) can explain over 94% of mRNA-protein abundance. Therefore, we propose here to use full-length RNC-mRNA information to illustrate protein expression both qualitatively and quantitatively. We performed RNA-seq on RNC-mRNA (RNC-seq) and detected 12 758 and 14 113 translating genes in human normal bronchial epithelial (HBE) cells and human colorectal adenocarcinoma Caco-2 cells, respectively. We found that most of these genes were mapped with >80% of coding sequence coverage. In Caco-2 cells, we provided translating evidence on 4180 significant single-nucleotide variations. While using RNC-mRNA data as a standard for proteomic data integration, both translating and protein evidence of 7876 genes can be acquired from four interlaboratory data sets with different MS platforms. In addition, we detected 1397 noncoding mRNAs that were attached to ribosomes, suggesting a potential source of new protein explorations. By comparing the two cell lines, a total of 677 differentially translated genes were found to be nonevenly distributed across chromosomes. In addition, 2105 genes in Caco-2 and 750 genes in HBE cells are expressed in a cell-specific manner. These genes are significantly and specifically clustered on multiple chromosomes, such as chromosome 19. We conclude that HPP/C-HPP investigations can be considerably improved by integrating RNC-mRNA analysis with MS, bioinformatics, and antibody-based verifications

Genome-Wide and Experimental Resolution of Relative Translation Elongation Speed at Individual Gene Level in Human Cells

<div><p>In the process of translation, ribosomes first assemble on mRNAs (translation initiation) and then translate along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. By integrating three types of RNA-seq methods, we experimentally and computationally resolved elongation speed, with our proposed elongation velocity index (EVI), a relative measure at individual gene level and under physiological condition in human cells. We successfully distinguished slow-translating genes from the background translatome. We demonstrated that low-EVI genes encoded more stable proteins. We further identified cell-specific slow-translating codons, which might serve as a causal factor of elongation deceleration. As an example for the biological relevance, we showed that the relatively slow-translating genes tended to be associated with the maintenance of malignant phenotypes per pathway analyses. In conclusion, EVI opens a new view to understand why human cells tend to avoid simultaneously speeding up translation initiation and decelerating elongation, and the possible cancer relevance of translating low-EVI genes to gain better protein quality.</p></div