Journal: Nature Communications

Article Title: The role of alternative polyadenylation in the antiviral innate immune response

doi: 10.1038/ncomms14605

Figure Lengend Snippet: ( a ) Characteristics of the average tandem 3′ UTR length during the anti-VSV immune response. Human and mouse showed similar patterns. ( b ) The number of poly(A) site-switched genes at consecutive time points in human MDMs upon VSV infection. ( c ) Poly(A) site switching at consecutive time points in human MDMs upon VSV infection. The x axis denotes TSI, and a larger positive value indicates that longer tandem 3′ UTRs were observed at later time points. Genes with significant switching to longer (blue) or shorter (red) tandem 3′ UTRs at later time points (FDR=0.01) are coloured accordingly. The y axis denotes the logarithm of the expression level of genes from later time points relative to earlier samples. ( d ) Venn diagram showing the overlap of DEGs and poly(A) site-switched genes.

Article Snippet: MDMs and mouse peritoneal macrophages were infected with VSV (strain Indiana, ATCC) at 0.5 MOI in serum-free DMEM for 1 h, washed by 1 × PBS, and incubated with fresh complete medium for various periods of time (0, 2, 4, 8, 16 and 24 h).

Techniques: Infection, Expressing

Journal: Nature Communications

Article Title: The role of alternative polyadenylation in the antiviral innate immune response

doi: 10.1038/ncomms14605

Figure Lengend Snippet: ( a ) siRNAs were transfected into A549 cells, and the interference efficiency was determined with qRT-PCR at 48 h. ( b ) We transfected A549 cells with individual siRNAs for 48 h and infected them with VSV-eGFP at an MOI of 1 for 6 h or 12 h. Then, qRT-PCR was performed to detect VSV replication at the mRNA level. Data are mean±s.d. * P <0.05; ** P <0.01. ( c ) FACS analysis of A549 cells transfected with control siRNA (siCon) or the indicated siRNAs and then infected with VSV-eGFP at an MOI of 2 for 6 h. FACS gating strategies from one representative experiment have been provided as . ( d ) A549 cells were transfected with individual siRNAs for 48 h and infected with VSV at an MOI of 1 for 12 h. Then, western blotting was performed to detect VSV replication at the protein level. The uncropped scans of western blots have been provided as . ( e ) Relative mRNA expression of the core 3′ processing factors in VSV-infected MDMs. Data were obtained from two biological duplicates of IVT-SAPAS. The x axis denotes six time points post infection and the y axis denotes relative expression. ( f ) Relative 3′ UTR length of the core 3′ processing genes with switched poly(A) sites during the antiviral immune response. Data were obtained from IVT-SAPAS. The x axis denotes six infection time points and the y axis denotes e UTR/c UTR, which represents the ratio of longer 3′ UTR isoforms to total mRNA isoforms.

Article Snippet: MDMs and mouse peritoneal macrophages were infected with VSV (strain Indiana, ATCC) at 0.5 MOI in serum-free DMEM for 1 h, washed by 1 × PBS, and incubated with fresh complete medium for various periods of time (0, 2, 4, 8, 16 and 24 h).

Techniques: Transfection, Quantitative RT-PCR, Infection, Control, Western Blot, Expressing

Journal:

Article Title: Vesicular Stomatitis Virus Glycoprotein Is a Determinant of Pathogenesis in Swine, a Natural Host

doi: 10.1128/JVI.77.14.8039-8047.2003

Figure Lengend Snippet: (A) Schematic representation of recombinant VSV genomes. The negative-strand recombinant VSIV genomic RNAs indicating the gene order and expressed proteins are shown. VSIV leader (le), trailer (tr) and viral (N, P, M, GI, and L) genes are represented. GNJ refers to the glycoprotein gene from the VSNJV field isolate 95COB (shaded boxes). The lengths of the genomes are shown on the right. (B) Viral proteins incorporated in virus particles. Virions were labeled with [35S]methionine and purified by centrifugation through 10% sucrose, and the virion proteins were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The infecting viruses are indicated above the lanes, and synthesized proteins are indicated on the left for the recombinant VSIV viruses and on the right for 95COB.

Article Snippet: Serial threefold dilutions of antibodies specific for VSIV (ATCC VR-1238AF) or VSNJV (ATCC VR-1239AF) in Dulbecco's modified Eagle medium plus 2% fetal calf serum (DMEM2) were mixed with an equal volume of the same medium containing 200 PFU of the corresponding virus.

Techniques: Recombinant, Virus, Labeling, Purification, Centrifugation, Polyacrylamide Gel Electrophoresis, Synthesized

Journal:

Article Title: Vesicular Stomatitis Virus Glycoprotein Is a Determinant of Pathogenesis in Swine, a Natural Host

doi: 10.1128/JVI.77.14.8039-8047.2003

Figure Lengend Snippet: Neutralization of recombinant and wild-type viruses by antibodies specific for Indiana or New Jersey serotype. Two hundred PFU of virus were incubated for 30 min at 37°C with serial threefold dilutions (starting at 1:40) of antibody prior to inoculation of Vero-76 cells. After 16 to 18 h of incubation at 37°C, individual plaques were counted. Px and Pn represent the numbers of plaques in the presence and absence of antibody, respectively. The percentages of GI (VSIV) and GNJ (VSNJV) in the total G protein present in the different virions, as determined in Fig. ​Fig.1B,1B, are indicated at the bottom.

Article Snippet: Serial threefold dilutions of antibodies specific for VSIV (ATCC VR-1238AF) or VSNJV (ATCC VR-1239AF) in Dulbecco's modified Eagle medium plus 2% fetal calf serum (DMEM2) were mixed with an equal volume of the same medium containing 200 PFU of the corresponding virus.

Techniques: Neutralization, Recombinant, Virus, Incubation