Changes in the bacterial community in the fermentation process of <i>kôso</i>, a Japanese sugar-vegetable fermented beverage

<p><i>Kôso</i> is a Japanese fermented beverage made with over 20 kinds of vegetables, mushrooms, and sugars. The changes in the bacterial population of <i>kôso</i> during fermentation at 25 °C over a period of 10 days were studied using 454 pyrosequencing of the 16S rRNA gene. The analysis detected 224 operational taxonomic units (OTUs) clustered from 8 DNA samples collected on days 0, 3, 7, and 10 from two fermentation batches. Proteobacteria were the dominant phylum in the starting community, but were replaced by Firmicutes within three days. Seventy-eight genera were identified from the 224 OTUs, in which <i>Bifidobacterium</i>, <i>Leuconostoc</i>, <i>Lactococcus</i>, and <i>Lactobacillus</i> dominated, accounting for over 96% of the total bacterial population after three days’ fermentation. UniFrac–Principal Coordinate Analysis of longitudinal fermented samples revealed dramatic changes in the bacterial community in <i>kôso</i>, resulting in significantly low diversity at the end of fermentation as compared with the complex starting community.</p> <p>Changes in the relative abundance of the 50 species in <i>kôso</i> communities during 10-day fermentation.</p

Additional file 2: of Proteome analysis of shell matrix proteins in the brachiopod Laqueus rubellus

The depth of the isotigs of shell matrix proteins in this study. (TIFF 597 kb

Additional file 1: of Proteome analysis of shell matrix proteins in the brachiopod Laqueus rubellus

RT-PCR analysis of ICP-1 and EF-1ι. M: mantle; L: lophophore. (TIFF 897 kb

A Th2-type humoral response is induced by targeting MGL2⁺ dDCs <i>in vivo</i>.

<p>(A) One day after the injection of biotinylated anti-MGL2 mAbs or rat IgG2a (isotype control) into <i>Mgl2</i>^+/+ or <i>Mgl2</i>^–/– mice, cells from draining LNs were subjected to flow cytometry analysis for biotin residues internalized into CD11c⁺ DCs using PE-SAv. (B) Flow cytometry analysis of surface MGL2 on the cells, gated for the levels of PE-SAv binding and CD11c circled in the panel A. (C) Antibodies specific for rat IgG2a in sera were detected 1 week after the injection of rat anti-MGL2 mAbs or rat IgG2a (isotype control) into <i>Mgl2</i>^+/+ mice or <i>Mgl2</i>^–/– mice. (D) Sera obtained 1 week after the injection of anti-MGL2 mAbs into <i>Mgl2</i>^+/+ mice were assessed for antibody isotypes that were specific for rat IgG2a. (A–D) The experiments were independently performed three times.</p

A Unique Dermal Dendritic Cell Subset That Skews the Immune Response toward Th2

<div><p>Dendritic cell (DC) subsets in the skin and draining lymph nodes (LNs) are likely to elicit distinct immune response types. In skin and skin-draining LNs, a dermal DC subset expressing macrophage galactose-type C-type lectin 2 (MGL2/CD301b) was found distinct from migratory Langerhans cells (LCs) or CD103⁺ dermal DCs (dDCs). Lower expression levels of Th1-promoting and/or cross-presentation-related molecules were suggested by the transcriptome analysis and verified by the quantitative real-time PCR analysis in MGL2⁺ dDCs than in CD103⁺ dDCs. Transfer of MGL2⁺ dDCs but not CD103⁺ dDCs from FITC-sensitized mice induced a Th2-type immune response <i>in vivo</i> in a model of contact hypersensitivity. Targeting MGL2⁺ dDCs with a rat monoclonal antibody against MGL2 efficiently induced a humoral immune response with Th2-type properties, as determined by the antibody subclass. We propose that the properties of MGL2⁺ dDCs, are complementary to those of CD103⁺ dDCs and skew the immune response toward a Th2-type response.</p></div

Characterization of MGL2⁺ dDCs in skin.

<p>Flow cytometry analysis of skin cell suspensions for DC markers. MHCII⁺ cells were analyzed for the expression of MGL2, EpCAM, CD103, and Langerin. The experiments were independently performed three times.</p

Expression of <i>HmVALT</i> and <i>HmPALT</i>1 and accumulation of their gene products in hydrangea.

<p>(<b>A</b>) The amount of <i>HmVALT</i> and <i>HmPALT1</i> mRNA was determined by quantitative RT-PCR. mRNAs were prepared from sepal at each stage and other tissues. The data are relative to the expression of 18S ribosomal RNA and were further normalized to the level of sepal at stage 1 mRNA, which was expressed as 1.0. The error bars represent SD (n = 3). (<b>B</b>) Immunoblot analyses of HmVALT and HmPALT1 in the sepals. Hydrophobic protein fractions were extracted from sepal tissues at each stage and subjected to SDS–PAGE (20 µg of protein).</p

Determination of amino acids responsible for Al transport activity of HmVALT1 or HmPALT1.

<p>(<b>A</b>) Al tolerance assay of amino acid replaced HmVALT transformant. <i>Δhsp150</i> yeast cells that harbored HmVALT-L162T and −G196A were spotted onto LPP medium (pH 3.5) with or without 2 mM Al₂(SO₄)₃, and the plates were incubated at 30°C for 4 d.HmVALT-L162T transformant grew less indicating to become more Al-sensitive but that of HmVALT-G196A grew at similar level. (<b>B</b>) Al tolerance assay of amino acid replaced HmPALT transformant. Wild type yeast cells that harbored HmPALT1-T114G, −E181Δ and −H188P were spotted onto LPP medium (pH 3.5) with or without 1 mM Al₂(SO₄)₃, and the plates were incubated at 30°C for 4 d. HmPALT1-E181Δ transformant was less sensitive to Al, but others showed to be more sensitive.</p

Comparison of HmPALT1 and the NIP proteins.

<p>(<b>A</b>) Phylogenetic tree was generated from a ClustalW alignment of selected NIP and HmPALT1 amino acid sequences using TreeView 1.6.6. (<b>B</b>) Alignment of HmPALT1 and similar amino acid sequences in Figure5A. Black and gray boxes indicate identical and similar amino acids, respectively. The red bars above the alignment denote the positions of the NPA motif. The aligned ar/R selectivity filter residues are highlighted in vertical blue boxes. The positions that are indicated by black arrows were mutated in the analysis of the yeast Al-sensitivity test (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043189#pone-0043189-g008" target="_blank">Figure 8</a>). Sequences acquired from accessions: PtNIP [XP_002297797], RcNIP1;1 [XP_002527308], MtNIP [AAS48063], AtNIP5;1 [NP_192776], HvLsi6 [BAH84977], HvLsi1 [BAH24163].</p

The organic components of <i>H. macrophylla</i> sepals responsible for the blue color development.

<p>All of the colored sepals contained the same anthocyanin component (delphinidin 3-glucoside, <b>1</b>) and co-pigments (chlorogenic acid, <b>2</b>; neochlorogenic acid, <b>3</b>; 5-<i>O-p</i>-coumaroylquinic acid, <b>4</b>). The sepal color is affected by the ratio of co-pigmnets, amount of Al³⁺ and vacuolar pH.</p