Comparative transcriptomic analysis of rectal tissue from beef steers revealed reduced host immunity in Escherichia coli 0157:H7 super-shedders

Sherpa Romeo green journal. Open access, distributed under the terms of the Creative Commons Attribution LicenseSuper-shedder cattle are a major disseminator of E . coli O157:H7 into the environment, and the terminal rectum has been proposed as the primary E . coli O157:H7 colonization site. This study aimed to identify host factors that are associated with the super-shedding pro- cess by comparing transcriptomic profiles in rectal tissue collected from 5 super-shedder cattle and 4 non-shedder cattle using RNA-Seq. In total, 17,859 ± 354 genes and 399 ± 16 miRNAs were detected, and 11,773 genes were expressed in all animals. Fifty-eight differ- entially expressed (DE) genes (false discovery rate < 0.05) including 11 up-regulated and 47 down-regulated (log 2 (fold change) ranged from -5.5 to 4.2), and 2 up-regulated DE miRNAs (log 2 (fold change) = 2.1 and 2.5, respectively) were identified in super-shedders compared to non-shedders. Functional analysis of DE genes revealed that 31 down-regu- lated genes were potentially associated with reduced innate and adaptive immune functions in super-shedders, including 13 lymphocytes membrane receptors, 3 transcription factors and 5 cytokines, suggesting the decreased key host immune functions in the rectal tissue of super-shedders, including decreased quantity and migration of immune cells such as lym- phocytes, neutrophils and dendritic cells. The up-regulation of bta-miR-29d-3p and the down regulation of its predicted target gene, regulator of G-protein signaling 13 , suggested a potential regulatory role of this miRNA in decreased migration of lymphocytes in super- shedders. Based on these findings, the rectal tissue of super-shedders may inherently exhibit less effective innate and adaptive immune protection. Further study is required to confirm if such effect on host immunity is due to the nature of the host itself or due to actions mediated by E . coli O157:H7.Ye

Viral communities of the human gut: metagenomic analysis of composition and dynamics

Abstract Background The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut. Main body Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained. We then review studies characterizing the virome of the healthy human gut, which reveal that most of the viruses detected are typically uncharacterized phage - the viral dark matter - and that viruses that infect human cells are encountered only rarely. We then review movement of phage between bacterial cells during antibiotic treatment. Here a radical proposal for extensive movement of antibiotic genes on phage has been challenged by a careful reanalysis of the metagenomic annotation methods used. We then review two recent studies of movement of whole phage communities between human individuals during fecal microbial transplantation, which emphasize the possible role of lysogeny in dispersal. Short conclusion Methods for studying the human gut virome are improving, yielding interesting data on movement of phage genes between cells and mammalian host organisms. However, viral populations are vast, and studies of their composition and function are just beginning

Additional file 4: Table S4. of Comparative miRNAome analysis revealed different miRNA expression profiles in bovine sera and exosomes

Pearson correlation of the detected miRNAs among individuals in exosomes. (DOCX 38 kb

Additional file 1: Table S1. of Comparative miRNAome analysis revealed different miRNA expression profiles in bovine sera and exosomes

Compilation of evaluated reads data in the process of generating miRNAs. (DOCX 70 kb

Rhododendron weyrichii Maxim.

原著和名: オンツツジ科名: ツツジ科 = Ericaceae採集地: 高知県 高知市 一宮 (土佐 高知市 一宮)採集日: 1982/4/17採集者: 萩庭丈壽整理番号: JH015511国立科学博物館整理番号: TNS-VS-96551

The MOV10 RNA helicase is a dosage-dependent host restriction factor for LINE1 retrotransposition in mice.

Transposable elements constitute nearly half of the mammalian genome and play important roles in genome evolution. While a multitude of both transcriptional and post-transcriptional mechanisms exist to silence transposable elements, control of transposition in vivo remains poorly understood. MOV10, an RNA helicase, is an inhibitor of mobilization of retrotransposons and retroviruses in cell culture assays. Here we report that MOV10 restricts LINE1 retrotransposition in mice. Although MOV10 is broadly expressed, its loss causes only incomplete penetrance of embryonic lethality, and the surviving MOV10-deficient mice are healthy and fertile. Biochemically, MOV10 forms a complex with UPF1, a key component of the nonsense-mediated mRNA decay pathway, and primarily binds to the 3' UTR of somatically expressed transcripts in testis. Consequently, loss of MOV10 results in an altered transcriptome in testis. Analyses using a LINE1 reporter transgene reveal that loss of MOV10 leads to increased LINE1 retrotransposition in somatic and reproductive tissues from both embryos and adult mice. Moreover, the degree of LINE1 retrotransposition inhibition is dependent on the Mov10 gene dosage. Furthermore, MOV10 deficiency reduces reproductive fitness over successive generations. Our findings demonstrate that MOV10 attenuates LINE1 retrotransposition in a dosage-dependent manner in mice

Potential Regulatory Role of MicroRNAs in the Development of Bovine Gastrointestinal Tract during Early Life

<div><p>This study aimed to investigate the potential regulatory role of miRNAs in the development of gastrointestinal tract (GIT) during the early life of dairy calves. Rumen and small intestinal (mid-jejunum and ileum) tissue samples were collected from newborn (30 min after birth; n = 3), 7-day-old (n = 6), 21-day-old (n = 6), and 42-day-old (n = 6) dairy calves. The miRNA profiling was performed using Illumina RNA-sequencing and the temporal and regional differentially expressed miRNAs were further validated using qRT-PCR. Analysis of 16S rRNA gene copy numbers was used to quantify total bacteria, <i>Bifidobacterium</i> and <i>Lactobacillus</i> species. The expression of miR-143 was abundant in all three gut regions, at all time points and it targets genes involved primarily in the proliferation of connective tissue cells and muscle cells, suggesting a role in regulating rapid tissue development during the early life of calves. The expression of miR-146, miR-191, miR-33, miR-7, miR-99/100, miR-486, miR-145, miR-196 and miR-211 displayed significant temporal differences (FDR <0.05), while miR-192/215, miR-194, miR-196, miR-205 and miR-31 revealed significant regional differences (FDR <0.05). The expression levels of miR-15/16, miR-29 and miR-196 were positively correlated with the copy numbers of 16S rRNA gene of <i>Bifidobacterium</i> or <i>Lactobacillus</i> species or both (<i>P</i><0.05). Functional analysis using Ingenuity Pathway Analysis identified the above mentioned differentially expressed miRNAs as potential regulators of gut tissue cell proliferation and differentiation. The bacterial density-associated miRNAs were identified as modulators of the development of lymphoid tissues (miR-196), maturation of dendritic cells (miR-29) and development of immune cells (miR-15/16). The present study revealed temporal and regional changes in miRNA expression and a correlation between miRNA expression and microbial population in the GIT during the early life, which provides further evidence for another mechanism by which host-microbial interactions play a role in regulating gut development.</p></div

Functions of 31 down-regulated DE genes in super-shedders that are associated with immune functions predicted by IPA.

<p>Functions of 31 down-regulated DE genes in super-shedders that are associated with immune functions predicted by IPA.</p

Expression of selected differentially expressed (DE) genes as detected by qRT-PCR and RNA-Sequencing.

<p>Differentially expressed genes as measured by qPCR are shown by lines on the top and values are indicated by the right Y-axis as relative expression level (ΔCq). Lower ΔCt values represent higher gene expression levels and <i>vice versa</i>. Gene expression as measured by RNA-Seq are shown by bar graphs on the bottom and values are indicated by the left Y-axis as log2 (FPKM). A, B indicate a significant difference in the relative expression detected by qPCR (P-value < 0.05); a, b indicate a significant difference in expression of genes detected by RNA-Seq (FDR < 0.05). Data are presented as mean ± standard deviation. NS and SS represent non-shedders and super-shedders, respectively.</p

Differentially expressed miRNAs in recto-anal junction.

<p>The heatmap was created using pheatmap function in R package. Blue colors represent lower expression, and red color represent higher expression. Scaled reads per million (RPM) values were indicated by the color bar. NS, non-shedders; SS, super-shedders.</p