Issues and Prospects of the Library in Japan : From the Answer of the Examination in Asistant Librarian Training

articl

SARTools workflow.

<p>Left part (black): successive steps of the analysis; Right part (blue): SARTools functions associated with each step when running either DESeq2 or edgeR.</p

Example of target file for a KO vs. WT experiment including 3 replicates in each biological condition.

<p>Example of target file for a KO vs. WT experiment including 3 replicates in each biological condition.</p

Several ways to detect an outlier (d3-WT).

<p>(a) Low total number of reads for d3-WT, (b) High proportion of null counts for d3-WT, (c) Most expressed sequence different for d3-WT, (d) Different distribution of counts for d3-WT, (e-f) d3-WT falls far from the other samples on the first component of the PCA and on the dendrogram.</p

Common gene expression profile in response to the mucus layer contact.

<p>Genes showing increased expression in both <i>E. histolytica</i> HM1:IMSS and Rahman during contact with the human colon.</p><p>FC: Fold Change; BF: Bonferroni adjusted p value≤0.05.</p

Schematic of <i>Entamoeba histolytica</i> activities leading to mucus layer depletion and invasion of the human colon.

<p>During its vegetative life style (A), <i>E. histolytica</i> exploits lipids (from lipid-rich food particles, bacteria, and shed epithelial cells) and carbohydrates (undigested glycan-rich food particles provided by the bolus or shed mucus fragment) present in the colonic environment. (B) When dietary polysaccharides are scarce, we hypothesize that <i>E. histolytica</i> turns to host mucus by first deploying a set of polysaccharide hydrolases that depletes the protective oligosaccharide side chains of mucin which can be then targeted by cysteine proteases leading to the depletion of the protective mucus barrier and allowing subsequent invasion of the mucosa. This adaptive foraging could reflect the coevolved functional versatility of <i>E. histolytica</i> glycobiome and the structural diversity of host mucus glycans involved in the interaction.</p

Summary of the microarray data.

<p>The transcriptomic modulations obtained in the 4 comparisons. In total, 614 transcripts with a fold change greater than two were significantly modulated (Bonferroni adjusted p-value<0.05).</p

The <i>E. histolytica</i> HM1: IMSS ubiquitous gene expression profile.

<p>Genes showing increased expression in <i>E. histolytica</i> HM1:IMSS compared to Rahman both in culture and during contact with the human colon.</p><p>FC: Fold Change; BF: Bonferroni adjusted p value≤0.05.</p

Classification of modulated transcripts into functional categories.

<p>Proteins were annotated according to Pathema and NCBI databases web sites.</p

Human colon explants incubated with <i>E. histolytica</i> HM1:IMSS or Rahman trophozoites.

<p>Longitudinal tissue sections of colon explants incubated during 1 or 7<i>E. histolytica</i> HM1:IMSS or Rahman trophozoites. The upper panel (A) corresponds to the alcian blue staining of the mucus in the top followed by staining of the tissue where the epithelial cells and the crypts of Liberkün (counterstain in red with Safranin) are visible. The lower panel (B) corresponds to immunohistochemistry revealing the presence of trophozoites in the top by immunostaining for the Gal/GalNAc lectin and the tissue by counterstaining with Hematoxylin/Eosin (bleu). Note the presence of Rahman trophozoites on top of the mucus layer even after 7 h of incubation and the massive destruction of the mucosa in the presence of HM1:IMSS. Scale bar = 50 µm.</p