Journal: Oncogene

Article Title: Hepatitis C virus upregulates B-cell receptor signaling: a novel mechanism for HCV-associated B-cell lymphoproliferative disorders

doi: 10.1038/onc.2015.364

Figure Lengend Snippet: The BCR signaling pathway is the top-ranked network with increasing association with HuR in response to NS3/4A overexpression. ( a ) KEGG pathway analysis revealed that the BCR signaling pathway has the largest number of transcripts with increasing association with HuR in response to NS3/4A overexpression. Red and pink represent upregulated genes; and green, downregulated genes. ( b ) The top-ranked network of genes was centered on the increase in HuR binding to CD79A mRNA, surrounded by other interacting genes whose association with HuR was affected by NS3/4A overexpression.

Article Snippet: Immunoblotting was performed using standard methods with the following antibodies: anti-NS3 (Abcam, ab18664), anti-pBlk (Tyr388, ab151726), anti-actin (ab8226) anti-pCHK2 (Thr68, Cell Signaling Technology, Inc., CST2661), anti-CARD11 (CST4435), anti-Blk (CST3262), anti-BTK (CST8547), anti-pBTK (Tyr223, CST5082), anti-CD79A (CST3351), anti-CD79A (Tyr182, CST5173), anti-CHK2 (Santa Cruz Biotechnology Inc., Dallas, TX, USA; sc-9064) and anti-SYK (sc-1077).

Techniques: Over Expression, Binding Assay

Journal: Oncogene

Article Title: Hepatitis C virus upregulates B-cell receptor signaling: a novel mechanism for HCV-associated B-cell lymphoproliferative disorders

doi: 10.1038/onc.2015.364

Figure Lengend Snippet: Analysis of HuR targets modulated by NS3/4A overexpression. ( a ) The levels of selected HuR target mRNAs in control and SUDHL6-NS3/4A (mass culture) cells were detected by ribonucleoprotein (RNP)-IP with anti-HuR antibody, followed by RT–qPCR analysis. Data show mean and s.d. from at least three separate experiments. * and ** indicate values significantly greater (* P <0.05, and ** P <0.01) in SUDHL6-NS3/4A cells (black column) over control cells (white column). ( b ) Western blot analysis showing protein expression of selected HuR targets in whole cell lysates of vector control (V) and SUDHL6-NS3/4A (NS3/4A) cells. Actin was used as a loading control. ( c ) Telaprevir treatment attenuates the upregulation of CD79A and CD79B protein levels by NS3/4A. SUDHL6 vector control and NS3/4A-overexpressing cells were treated with 10 μ M Telaprevir and its vehicle control (DMSO) for 24 h. Protein level of CD79A, CD79B and NS3 was examined by western blot analysis.

Article Snippet: Immunoblotting was performed using standard methods with the following antibodies: anti-NS3 (Abcam, ab18664), anti-pBlk (Tyr388, ab151726), anti-actin (ab8226) anti-pCHK2 (Thr68, Cell Signaling Technology, Inc., CST2661), anti-CARD11 (CST4435), anti-Blk (CST3262), anti-BTK (CST8547), anti-pBTK (Tyr223, CST5082), anti-CD79A (CST3351), anti-CD79A (Tyr182, CST5173), anti-CHK2 (Santa Cruz Biotechnology Inc., Dallas, TX, USA; sc-9064) and anti-SYK (sc-1077).

Techniques: Over Expression, Quantitative RT-PCR, Western Blot, Expressing, Plasmid Preparation

Journal: Oncogene

Article Title: Hepatitis C virus upregulates B-cell receptor signaling: a novel mechanism for HCV-associated B-cell lymphoproliferative disorders

doi: 10.1038/onc.2015.364

Figure Lengend Snippet: HCV infection upregulates BCR signaling in human primary B cells and Raji cells. ( a ) Western blot analysis showing protein expression of NS3, CARD11, Blk and CD79A in lysates isolated from normal (five discrete patients) and HCV-infected (mix: pooled from eight patients) purified B cells. Actin was used as a loading control. ( b ) Protein expression of NS3, core, CD79A and CD79B in lysates isolated from control and HCV-infected Raji cells was detected by western blot analysis. ( c ) The model depicts a proposed mechanism for HCV-associated B-cell lymphoproliferative disorders. HCV NS3/4A interacts with CHK2 and downregulates CHK2 activity. Subsequently, this repressed CHK2 activity modulates HuR posttranscriptional regulation of a network of target mRNAs associated with B-cell lymphoproliferative disorders, preferentially those involved in the BCR signaling pathway.

Article Snippet: Immunoblotting was performed using standard methods with the following antibodies: anti-NS3 (Abcam, ab18664), anti-pBlk (Tyr388, ab151726), anti-actin (ab8226) anti-pCHK2 (Thr68, Cell Signaling Technology, Inc., CST2661), anti-CARD11 (CST4435), anti-Blk (CST3262), anti-BTK (CST8547), anti-pBTK (Tyr223, CST5082), anti-CD79A (CST3351), anti-CD79A (Tyr182, CST5173), anti-CHK2 (Santa Cruz Biotechnology Inc., Dallas, TX, USA; sc-9064) and anti-SYK (sc-1077).

Techniques: Infection, Western Blot, Expressing, Isolation, Purification, Activity Assay

Journal: Fems Microbiology Letters

Article Title: Evidence for recombination between a sialidase ( nanH ) of Actinomyces naeslundii and Actinomyces oris , previously named ‘ Actinomyces naeslundii genospecies 1 and 2’

doi: 10.1111/j.1574-6968.2008.01336.x

Figure Lengend Snippet: Neighbour-joining tree showing relationships between type and reference strains of Actinomyces naeslundii, Actinomyces oris, Actinomyces johnsonii and Actinomyces viscosus and oral and clinical isolates determined by partial nanH gene sequence analysis. Actinomyces naeslundii strains 25, 51 and CCUG 34725 and A. oris strains 60 and 61 (each shown with the nanH sequence accession number) did not cluster with the majority of strains of the same species and were identified as strains with significant evidence of interspecies recombination. Scale bar=0.01 substitutions per site.

Article Snippet: The strains included in this study were 30 A. naeslundii (CCUG 33521, CCUG 33522, CCUG 33519, CCUG 33523, ATCC 12104, CCUG 34725, CCUG 35334 and CCUG 37599 and 22 human clinical and oral isolates); 71 A. oris (P2G, P5K, P6K, P7K, P8K, P9K, Pn4D, Pn5D, CCUG 33915, CCUG 33919, CCUG 33920, CCUG 33914, CCUG 34285, CCUG 34286 and ATCC 27044 and 56 human clinical and oral isolates); two A. johnsonii (CCUG 33932 and CCUG 34287) isolates and one A. viscosus (NCTC 10951).

Techniques: Sequencing

Journal: Fems Microbiology Letters

Article Title: Evidence for recombination between a sialidase ( nanH ) of Actinomyces naeslundii and Actinomyces oris , previously named ‘ Actinomyces naeslundii genospecies 1 and 2’

doi: 10.1111/j.1574-6968.2008.01336.x

Figure Lengend Snippet: Genetic variation of partial nanH sequences of type and reference strains and clinical isolates of Actinomyces oris and Actinomyces naeslundii

Article Snippet: The strains included in this study were 30 A. naeslundii (CCUG 33521, CCUG 33522, CCUG 33519, CCUG 33523, ATCC 12104, CCUG 34725, CCUG 35334 and CCUG 37599 and 22 human clinical and oral isolates); 71 A. oris (P2G, P5K, P6K, P7K, P8K, P9K, Pn4D, Pn5D, CCUG 33915, CCUG 33919, CCUG 33920, CCUG 33914, CCUG 34285, CCUG 34286 and ATCC 27044 and 56 human clinical and oral isolates); two A. johnsonii (CCUG 33932 and CCUG 34287) isolates and one A. viscosus (NCTC 10951).

Techniques:

Journal: Fems Microbiology Letters

Article Title: Evidence for recombination between a sialidase ( nanH ) of Actinomyces naeslundii and Actinomyces oris , previously named ‘ Actinomyces naeslundii genospecies 1 and 2’

doi: 10.1111/j.1574-6968.2008.01336.x

Figure Lengend Snippet: Recombination events found in nanH of Actinomyces oris strains 60 (EU805671) and 61 (EU805672) and Actinomyces naeslundii strains 51 (EU805620), 25 (EU805612) and CUG 34725 (EU805609). Solid line indicates portion of sequence derived from nanH of A. naeslundii and broken line indicates portion of sequence derived from nanH of A. oris . Insertion in strain 25 between 365 and 1038, in strain 51 between 629 and 1038, in strain 60 between 1 and 477, in strain 61 between 432 and 1038 and between 1 and 655 in CUG 34725. Breakpoints determined using RDP suite of programs with significant evidence ( P <0.001) for recombination obtained with ≥5 recombination tests in all cases.

Article Snippet: The strains included in this study were 30 A. naeslundii (CCUG 33521, CCUG 33522, CCUG 33519, CCUG 33523, ATCC 12104, CCUG 34725, CCUG 35334 and CCUG 37599 and 22 human clinical and oral isolates); 71 A. oris (P2G, P5K, P6K, P7K, P8K, P9K, Pn4D, Pn5D, CCUG 33915, CCUG 33919, CCUG 33920, CCUG 33914, CCUG 34285, CCUG 34286 and ATCC 27044 and 56 human clinical and oral isolates); two A. johnsonii (CCUG 33932 and CCUG 34287) isolates and one A. viscosus (NCTC 10951).

Techniques: Sequencing, Derivative Assay

Journal: Fems Microbiology Letters

Article Title: Evidence for recombination between a sialidase ( nanH ) of Actinomyces naeslundii and Actinomyces oris , previously named ‘ Actinomyces naeslundii genospecies 1 and 2’

doi: 10.1111/j.1574-6968.2008.01336.x

Figure Lengend Snippet: Reverse transcriptase (RT)-PCR assays showing expression of nanH and the housekeeping gene atpA in the type strains of Actinomyces oris (CCUG 34288; EU805602), and Actinomyces johnsonii (CCUG 34287; EU805600), Actinomyces naeslundii (CCUG 2238; EU805601) and Actinomyces viscosus (NCTC 10951; EU805603). Negative controls, omitting the RT in the reaction mix, yielded no amplicons from any strain.

Article Snippet: The strains included in this study were 30 A. naeslundii (CCUG 33521, CCUG 33522, CCUG 33519, CCUG 33523, ATCC 12104, CCUG 34725, CCUG 35334 and CCUG 37599 and 22 human clinical and oral isolates); 71 A. oris (P2G, P5K, P6K, P7K, P8K, P9K, Pn4D, Pn5D, CCUG 33915, CCUG 33919, CCUG 33920, CCUG 33914, CCUG 34285, CCUG 34286 and ATCC 27044 and 56 human clinical and oral isolates); two A. johnsonii (CCUG 33932 and CCUG 34287) isolates and one A. viscosus (NCTC 10951).

Techniques: Reverse Transcription, Reverse Transcription Polymerase Chain Reaction, Expressing