Additional file 1 of Positive associations between different circulating trans fatty acids (TFAs) and urinary albumin excretion among adults in the U.S.: a population-based study

Supplementary Material

Additional file 4 of Positive associations between different circulating trans fatty acids (TFAs) and urinary albumin excretion among adults in the U.S.: a population-based study

Supplementary Material

Data from the 24 PCMV clinical isolates and prototype Sichuan strain (GenBank accession no. JN701021.1).

<p>Strains are designated according to accession number and strain name.</p

Scatter plot of the high-throughput sequencing data.

<p>The high-throughput sequencing data (differentially expressed miRNAs) are graphed on the scatter plot to visualize variations in miRNA expression between TGEV infected and control groups. The values on the X axes and Y axes of the scatter plot are the normalized values for the TGEV infected and control groups (log2 scaled). The green lines are fold-change lines (default fold-change value: 1.5).</p

Phylogenetic analysis of <i>Herpesviridae</i> viruses.

<p>Glycoprotein B nucleotide sequences of the alphaherpesviruses, betaherpesviruses, and gammaherpesviruses were obtained from GenBank: PCMV SC strain (accession no. JN701021.1); RhCMV (Rhesus cytomegalovirus; accession no. U76749.1); CyCMV (Cynomolgus macaque cytomegalovirus; accession no. HQ198248.1); MaCMV (Mycobacteriophage Barnyard; accession no. AY129339); PTCMV (Pan troglodytes cytomegalovirus; accession no. FJ538485); HCMV (Human cytomegalovirus; accession no. M6092.1); GgCMV (Gorilla cytomegalovirus; accession no. FJ538490); MuHV-2 (Murine herpesvirus type 2; accession no. AF232689.2); MCMV (Murine cytomegalovirus; M86302.1); HHV-6 (Human herpesvirus; accession no. M97927.1); PRV (Pseudorabies virus; accession no. AF257079.1; HHV-7 (Human herpesvirus; accession no. AF007830.1); AlHV-1 (Alcelaphine herpesvirus 1; accession no. AF005370); BoHV-1 (Bovine herpesvirus type 1; accession no. Z78205); BoHV-2 (Bovine herpesvirus type 2; accession no. Z78205); BoHV-4 (Bovine herpesvirus type 4; accession no. Z15044.1); EBV (Epstein-Barr virus; accession no. V01555.2); EHV-1 (Equine herpesvirus 1 strain Ab4; accession no. AY665713.1); EHV-4 (Equine herpesvirus 4 strain NS80567; accession no. AF030027.1); HHV-8 (Human herpesvirus 8 type M; accession no. U75698.1); VZV (Varicella-Zoster virus; accession no. X04370); PLHV-2 (porcine lymphotropic herpesvirus 2; accession no. AF191043); PLHV-1 (lymphotropic herpesvirus 1; accession no. AF478169.1); MuHV-2 (Murine herpesvirus 2; accession no. GU018179.1); HSV-2 (Herpes simplex virus 2; accession no. Z86099); AHV (Ateles herpesvirus; accession no. AF083424); ILTV (Laryngotracheitis Virus; accession no. X56093.1).Bootstrap values of <b>></b>65% from 1000 pseudo-replicates are indicated at the branch nodes.</p

Index of amino acid substitution propensity.

<p>(A) Analysis of 34 PCMV strains from China. (B) Analysis of global PCMV strains.</p

Stem-loop RT-qPCR confirmation for miRNAs.

<p>Four differentially expressed miRNAs and four novel miRNAs were selected from the high-throughput sequencing datasets and confirmed by stem-loop RT-qPCR. The results showed a general consistency between the stem-loop RT-qPCR and the high-throughput sequencing. The fold changes (miRNA copy numbers of TGEV-infected ST cell sample <i>vs</i>. miRNA copy numbers of normal ST cell sample) are shown in the diagram. The fold change cutoffs of the upregulated miRNAs and the downregulated miRNAs were 1.5 and 0.67, respectively. “+” and “–” indicate upregulated and downregulated miRNAs, respectively. qRT-PCR Ct threshold: 0.015.</p><p>Stem-loop RT-qPCR confirmation for miRNAs.</p

Plots of transition (s) and transversion (v) frequencies against the K80 distance.

<p><i>S</i> denotes transition and <i>V</i> denotes transversion. (A) Analysis of 34 PCMV strains from China. (B) Analysis of global PCMV strains.</p

Phylogenetic analysis of 42 global strains of PCMV based on the 2580 bp <i>gB</i> complete nucleotide sequence and the deduced amino acid sequence.

<p>(A) Phylogenetic tree constructed from nucleotide sequences. (B) Phylogenetic tree constructed from amino acid sequences. The reference PCMV <i>gB</i> nucleotide sequences were obtained from GenBank: SC strain (accession no. JN701021.1); ZZ strain (accession no. FJ870562.1); NB strain (accession no. FJ844360.1, FJ870561.1); FJ strain (accession no. FJ870564.1); JH strain (accession no. FJ870563.1); HN isolate (accession no.HQ686081.1, HQ686080.1, FJ595497.1, EF460488.1); Spanish 55b isolate (accession no. AF268040.2); B6 strain (accession no. AF268039.2); Japanese OF-1 strain (accession no. AF268041.2); Japanese Yamaguchi strain (accession no. AB771707.1, AB771708.1, AB771706.1); Swedish isolate P1 (accession no. AF394057.1); Swedish isolate 1469 (accession no. AF394056).Multiple alignment was performed in the Clustal W program, and MEGA 5.0 software was used to construct the neighbor-joining (NJ) and maximum likelihood (ML) trees. Bootstrap values >65% from 1000 pseudo-replicates are indicated at the branch nodes. Numbers in parentheses are the maximum likelihood. Strains are designated by accession number, country/district, and strain name. The 24 strains analyzed in this study are indicated by (♦). The two major groups were identified as A and B.</p

Length distribution of total sRNAs in TGEV-infected ST cells and normal ST cells.

<p>(A) Bar chart showing the total read counts against the read lengths for the complete adapter-trimmed read set in TGEV-infected ST cells. (B) Bar chart shows the total read counts against the read lengths for the complete adapter-trimmed read set in normal ST cells. The results indicate a successful enrichment of mature miRNAs in the TGEV-infected ST cells and normal ST cell libraries.</p