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  • 99
    Millipore dna probes
    Dna Probes, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 382 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Gen-Probe dna probes
    Dna Probes, supplied by Gen-Probe, used in various techniques. Bioz Stars score: 92/100, based on 229 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Abbott Laboratories pathvysion her 2 dna probe kit
    High EPN3 levels correlate with IBC and independently predict metastasis. a H E staining and EPN3 IHC images of in situ (DCIS) and adjacent infiltrating area (IBC) detected in two different primary human BCs. Images at ×20. Bar, 100 µm. b Summary graph of the differential expression of EPN3 detected by IHC in human BC samples in areas of DCIS vs. adjacent IBC. Data are reported as IHC score in IBC relative to DCIS. N , number of tumor samples. P value, two-sided Wilcoxon signed-rank test. c Cumulative incidence of distant metastasis or loco-regional relapse in BC patients of the IEO consecutive cohort (IEO BC 97-00, N = 2453), stratified by EPN3 protein (top, IHC) or mRNA (bottom, RT-qPCR) levels. HR*, multivariable hazard ratio. Multivariable models were adjusted for tumor grade, tumor size, Ki-67 levels, <t>ERBB2</t> status, ER/PR status, number of positive lymph nodes, and age at surgery, see Supplementary Table 3 . d Forest plot of the multivariable hazard ratios of distant metastasis and 95% Wald confidence intervals (whiskers) in the entire cohort of patients (All) and in the ERBB2-negative (ERBB2-NEG) or lymph node-negative (pN0) subgroups of patients stratified by EPN3 protein (IHC) or mRNA (RT-qPCR) expression levels. The size of the solid squares and diamonds is proportional to the number of distant metastases. The number ( N ) of patients and distant metastases (DM) in each group is indicated. Hazard ratios were estimated with a Cox proportional hazards multivariable model, adjusted for Grade, Ki-67, ERBB2 status, estrogen/progesterone receptor status, tumor size (pT), number of positive lymph nodes (pN), and age at surgery (as appropriate). The number of patients in each subgroup analysis corresponds to those reported in Supplementary Tables 1 and 2 for IHC and RT-qPCR, respectively. P value, Wald test P value. See also Supplementary Tables 1 – 3 14 . Source data are provided as a Source Data file.
    Pathvysion Her 2 Dna Probe Kit, supplied by Abbott Laboratories, used in various techniques. Bioz Stars score: 90/100, based on 581 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pathvysion her 2 dna probe kit/product/Abbott Laboratories
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    Abbott Laboratories pathvysion her2 dna probe kit
    The relationship of subtypes to the <t>DNA</t> ploidy and CIN. The diploid/CIN- status was detected in 72 (64.9%) of the 111 luminal A carcinomas, 39 (41.1%) of the 95 luminal B <t>(HER2-)</t> carcinomas, 8 (11.6%) of the 69 lumminal B (HER2+) carcinomas, 2 (4.9%) of the 41 HER2 carcinomas, and 8 (17.0%) of the 26 basal-like carcinomas. In contrast, the aneuploid/CIN + status was detected in 31 (27.9%) of the 111 luminal A, 47 (49.5%) of the luminal B (HER2-), 56 (81.2%) of the 69 luminal B (HER2+), 37 (90.2%) of the 41 HER2, and 36 (86.6%) of the 47 basal-like subtype tumors. The incidence of diploid/CIN- and aneuploid/CIN+ status was different between the luminal A subtype and luminal B (HER2-), luminal B (HER2+), HER2, and basal-like subtypes (p = 0.0006, p = 5E-13, p = 5E10-12, and p = 8E10-9). In addition, the incidence of diploid/CIN- and aneuploid/CIN+ status was statistically different between the luminal B (HER2-) subtype and luminal B (HER2+), HER2, and basal-like subtypes (p = 0.00002, p = 0.000009, and p = 0.002). Black bar; diploid/CIN- tumors, gray bar; aneuploid/CIN+ tumors, white column; others.
    Pathvysion Her2 Dna Probe Kit, supplied by Abbott Laboratories, used in various techniques. Bioz Stars score: 90/100, based on 591 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Abbott Laboratories dna probes
    Representative examples of conventional cytology and <t>DNA</t> <t>FISH</t> of biliary brushing specimens. ((a) and (b)) Conventional cytology. (a) Reactive changes in the context of PSC with some architectural irregularity, mild variation in nuclear size, and overall intact nuclear to cytoplasmic ratio. (b) Adenocarcinoma in a patient with underlying PSC showing hyperchromatic nuclei, marked variation in nuclear shape and size with nuclear molding, and severely disturbed nuclear to cytoplasmic ratio. In the background, necrotic debris with degenerative cells and granulocytes are observed. ((c) and (d)) Representative examples of FISH signal patterns seen in biliary strictures with probes for CEP7 [aqua], CEP17 [green], 20q [gold], and MYC [red]. (c) A normal cell (2 signals of each probe) and (d) gain of MYC ( > 2 red signals) and gain of CEP7 ( > 2 blue signals).
    Dna Probes, supplied by Abbott Laboratories, used in various techniques. Bioz Stars score: 93/100, based on 308 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Boehringer Mannheim dna probe
    Transmission of rhGH <t>transgene</t> to rabbits of F1 generation. Presence of transgene was observed in both female and male heterozygote rabbits. A screening of the transgene was performed by polymerase chain reaction (PCR) encompassing 313-bp and 524-bp (not shown) <t>DNA</t> fragments. PCR primers were located upstream and downstream of histidine tag and thrombin recognition site of the gene construct. The red arrows indicate transgene in founder rabbit No. 61 and his F1 male and female offspring of the same size as the input DNA fragment (positive control in line 38). PCR observation was confirmed by sequencing. The black arrow indicates the internal marker of 268 bp. The purple arrow indicates the internal marker of 113 bp (Color figure online)
    Dna Probe, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 92/100, based on 221 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore dna probe
    Transmission of rhGH <t>transgene</t> to rabbits of F1 generation. Presence of transgene was observed in both female and male heterozygote rabbits. A screening of the transgene was performed by polymerase chain reaction (PCR) encompassing 313-bp and 524-bp (not shown) <t>DNA</t> fragments. PCR primers were located upstream and downstream of histidine tag and thrombin recognition site of the gene construct. The red arrows indicate transgene in founder rabbit No. 61 and his F1 male and female offspring of the same size as the input DNA fragment (positive control in line 38). PCR observation was confirmed by sequencing. The black arrow indicates the internal marker of 268 bp. The purple arrow indicates the internal marker of 113 bp (Color figure online)
    Dna Probe, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 244 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher dna probes
    Exclusion of RIG-I from compartments containing plus-strand and minus-strand HCV RNA. A and B) Uninfected and HCV-infected Huh7.5 cells were transfected with constructs encoding for FLAG-tagged RIG-I-K207A 2 days after HCV infection. On day 4 after infection, cells were probed with antibodies directed against the FLAG epitope (grey) and either HCV core or NS5A (green). <t>DNA</t> probes (Affymetrix) targeted to either the positive-strand or the negative-strand of the HCV RNA (red) were then hybridized to the viral RNA. DNA was stained with DAPI (blue) and cells were examined by confocal fluorescence microscopy. Boxed regions in the middle row of both panels outline the area of magnification presented in the bottom rows. Scale bars represent 5 μm.
    Dna Probes, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 2169 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Stratagene dna probes
    Generation of ISP2 and ISP3 double null mutants. A. Schematic representation of the ISP2–ISP3 locus in WT L. major (upper) and the constructs for gene deletion. ORFs are shown as grey arrows and 5′ FR and 3′ FR boxes represent the FR <t>DNA</t> sequences used for gene targeting. The predicted DNA fragment sizes after restriction digest are shown. HYG , hygromycin-resistance gene; BLE , phleomycin-resistance gene. B. Southern blot of the WT L. major (lanes 1, 3 and 5) and Δ isp2/3 (lanes 2, 4 and 6) digested with AgeI or EcoRI/BamHI and probed with <t>radiolabelled</t> 5′ FR, ISP3 ORF and 3′ FR probes. C. Western blot of cell extracts from 0.5 × 10 7 purified metacyclic promastigotes of WT L. major (lane 1), Δ isp2/3 (lane 2) and Δ isp2/3 : ISP2–ISP3 (lane 3) using antibodies against ISP2, HASPB and EF1α.
    Dna Probes, supplied by Stratagene, used in various techniques. Bioz Stars score: 92/100, based on 415 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Boehringer Mannheim dna hybridization probes
    Replicon localization of mob DNAs in cosmids pRmOR69 and pRmOR65. Blots of Eco RI-digested genomic DNAs were hybridized against <t>digoxigenin-labeled</t> cosmid probes. Lanes: M, digoxigenin-labeled molecular weight marker; 1, R. meliloti 2011 (wild-type); 2, A. tumefaciens C58; 3, A. tumefaciens C58(pRme2011a); 4, R. meliloti GR4 (wild type); 5, R. meliloti GRM6 (cured of plasmid pRmeGR4b); 6, R. meliloti GRM10 (cured of plasmid pRmeGR4a); 7, R. meliloti GRM8 (cured of pRmeGR4a and pRmeGR4b); 8, R. meliloti GRT3 (carrying pSym1 deletion); 9, Eco RI-digested cosmid <t>DNA.</t>
    Dna Hybridization Probes, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 88/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Abbott Laboratories aneuvysion multicolor dna probe kit
    Replicon localization of mob DNAs in cosmids pRmOR69 and pRmOR65. Blots of Eco RI-digested genomic DNAs were hybridized against <t>digoxigenin-labeled</t> cosmid probes. Lanes: M, digoxigenin-labeled molecular weight marker; 1, R. meliloti 2011 (wild-type); 2, A. tumefaciens C58; 3, A. tumefaciens C58(pRme2011a); 4, R. meliloti GR4 (wild type); 5, R. meliloti GRM6 (cured of plasmid pRmeGR4b); 6, R. meliloti GRM10 (cured of plasmid pRmeGR4a); 7, R. meliloti GRM8 (cured of pRmeGR4a and pRmeGR4b); 8, R. meliloti GRT3 (carrying pSym1 deletion); 9, Eco RI-digested cosmid <t>DNA.</t>
    Aneuvysion Multicolor Dna Probe Kit, supplied by Abbott Laboratories, used in various techniques. Bioz Stars score: 91/100, based on 75 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Boehringer Mannheim digoxigenin labeled dna probes
    RNA Gel Blot Analysis of the Orchid DOH1 Sense and Antisense Transgenic Plants. (A) Expression of DOH1 in orchid 35S :: DOH1se transformants. Total RNA was isolated from mature CLLs from wild-type plants (wt) and the independent 35S :: DOH1se transgenic lines (lines se1, se7, se17, se28, and se33). The gel blot, containing 10 μg of total RNA in each lane, was hybridized with the <t>digoxigenin-labeled</t> full-length DOH1 <t>DNA</t> probe. (B) Expression of the DOH1 sense and antisense genes in 35S :: DOH1as transformants. Total RNA was isolated from 6-week-old VSAMs (length, 1.5 mm) from wild-type plants (wt) and independent 35S :: DOH1as transformants (lines as4, as10, as15, as23, as27, as31, and as38). The gel blot, containing 20 μg of total RNA in each lane, was hybridized with the digoxigenin-labeled full-length DOH1 RNA sense probe (SP) or antisense probe (AP). The rRNAs, stained by methylene blue, indicate the amount of total RNA in each lane.
    Digoxigenin Labeled Dna Probes, supplied by Boehringer Mannheim, used in various techniques. Bioz Stars score: 90/100, based on 126 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Ventana Medical inform her2 dual ish dna probe cocktail assay
    RNA Gel Blot Analysis of the Orchid DOH1 Sense and Antisense Transgenic Plants. (A) Expression of DOH1 in orchid 35S :: DOH1se transformants. Total RNA was isolated from mature CLLs from wild-type plants (wt) and the independent 35S :: DOH1se transgenic lines (lines se1, se7, se17, se28, and se33). The gel blot, containing 10 μg of total RNA in each lane, was hybridized with the <t>digoxigenin-labeled</t> full-length DOH1 <t>DNA</t> probe. (B) Expression of the DOH1 sense and antisense genes in 35S :: DOH1as transformants. Total RNA was isolated from 6-week-old VSAMs (length, 1.5 mm) from wild-type plants (wt) and independent 35S :: DOH1as transformants (lines as4, as10, as15, as23, as27, as31, and as38). The gel blot, containing 20 μg of total RNA in each lane, was hybridized with the digoxigenin-labeled full-length DOH1 RNA sense probe (SP) or antisense probe (AP). The rRNAs, stained by methylene blue, indicate the amount of total RNA in each lane.
    Inform Her2 Dual Ish Dna Probe Cocktail Assay, supplied by Ventana Medical, used in various techniques. Bioz Stars score: 88/100, based on 87 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Hologic Inc b dermatitidis dna probe
    RNA Gel Blot Analysis of the Orchid DOH1 Sense and Antisense Transgenic Plants. (A) Expression of DOH1 in orchid 35S :: DOH1se transformants. Total RNA was isolated from mature CLLs from wild-type plants (wt) and the independent 35S :: DOH1se transgenic lines (lines se1, se7, se17, se28, and se33). The gel blot, containing 10 μg of total RNA in each lane, was hybridized with the <t>digoxigenin-labeled</t> full-length DOH1 <t>DNA</t> probe. (B) Expression of the DOH1 sense and antisense genes in 35S :: DOH1as transformants. Total RNA was isolated from 6-week-old VSAMs (length, 1.5 mm) from wild-type plants (wt) and independent 35S :: DOH1as transformants (lines as4, as10, as15, as23, as27, as31, and as38). The gel blot, containing 20 μg of total RNA in each lane, was hybridized with the digoxigenin-labeled full-length DOH1 RNA sense probe (SP) or antisense probe (AP). The rRNAs, stained by methylene blue, indicate the amount of total RNA in each lane.
    B Dermatitidis Dna Probe, supplied by Hologic Inc, used in various techniques. Bioz Stars score: 92/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Abbott Laboratories vysis pathvysion her2 dna probe kit
    RNA Gel Blot Analysis of the Orchid DOH1 Sense and Antisense Transgenic Plants. (A) Expression of DOH1 in orchid 35S :: DOH1se transformants. Total RNA was isolated from mature CLLs from wild-type plants (wt) and the independent 35S :: DOH1se transgenic lines (lines se1, se7, se17, se28, and se33). The gel blot, containing 10 μg of total RNA in each lane, was hybridized with the <t>digoxigenin-labeled</t> full-length DOH1 <t>DNA</t> probe. (B) Expression of the DOH1 sense and antisense genes in 35S :: DOH1as transformants. Total RNA was isolated from 6-week-old VSAMs (length, 1.5 mm) from wild-type plants (wt) and independent 35S :: DOH1as transformants (lines as4, as10, as15, as23, as27, as31, and as38). The gel blot, containing 20 μg of total RNA in each lane, was hybridized with the digoxigenin-labeled full-length DOH1 RNA sense probe (SP) or antisense probe (AP). The rRNAs, stained by methylene blue, indicate the amount of total RNA in each lane.
    Vysis Pathvysion Her2 Dna Probe Kit, supplied by Abbott Laboratories, used in various techniques. Bioz Stars score: 85/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Hologic Inc dna probes
    RNA Gel Blot Analysis of the Orchid DOH1 Sense and Antisense Transgenic Plants. (A) Expression of DOH1 in orchid 35S :: DOH1se transformants. Total RNA was isolated from mature CLLs from wild-type plants (wt) and the independent 35S :: DOH1se transgenic lines (lines se1, se7, se17, se28, and se33). The gel blot, containing 10 μg of total RNA in each lane, was hybridized with the <t>digoxigenin-labeled</t> full-length DOH1 <t>DNA</t> probe. (B) Expression of the DOH1 sense and antisense genes in 35S :: DOH1as transformants. Total RNA was isolated from 6-week-old VSAMs (length, 1.5 mm) from wild-type plants (wt) and independent 35S :: DOH1as transformants (lines as4, as10, as15, as23, as27, as31, and as38). The gel blot, containing 20 μg of total RNA in each lane, was hybridized with the digoxigenin-labeled full-length DOH1 RNA sense probe (SP) or antisense probe (AP). The rRNAs, stained by methylene blue, indicate the amount of total RNA in each lane.
    Dna Probes, supplied by Hologic Inc, used in various techniques. Bioz Stars score: 90/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher strip ez dna probe synthesis kit
    Calcineurin enhances AP-1 binding to the endogenous cytoglobin promoter. A–C , utilizing EMSA, AP-1 was demonstrated to bind to the endogenous <t>Cygb</t> promoter. The binding affinity of AP-1 to <t>DNA</t> was enhanced in the presence of CnA* and in response
    Strip Ez Dna Probe Synthesis Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    High EPN3 levels correlate with IBC and independently predict metastasis. a H E staining and EPN3 IHC images of in situ (DCIS) and adjacent infiltrating area (IBC) detected in two different primary human BCs. Images at ×20. Bar, 100 µm. b Summary graph of the differential expression of EPN3 detected by IHC in human BC samples in areas of DCIS vs. adjacent IBC. Data are reported as IHC score in IBC relative to DCIS. N , number of tumor samples. P value, two-sided Wilcoxon signed-rank test. c Cumulative incidence of distant metastasis or loco-regional relapse in BC patients of the IEO consecutive cohort (IEO BC 97-00, N = 2453), stratified by EPN3 protein (top, IHC) or mRNA (bottom, RT-qPCR) levels. HR*, multivariable hazard ratio. Multivariable models were adjusted for tumor grade, tumor size, Ki-67 levels, ERBB2 status, ER/PR status, number of positive lymph nodes, and age at surgery, see Supplementary Table 3 . d Forest plot of the multivariable hazard ratios of distant metastasis and 95% Wald confidence intervals (whiskers) in the entire cohort of patients (All) and in the ERBB2-negative (ERBB2-NEG) or lymph node-negative (pN0) subgroups of patients stratified by EPN3 protein (IHC) or mRNA (RT-qPCR) expression levels. The size of the solid squares and diamonds is proportional to the number of distant metastases. The number ( N ) of patients and distant metastases (DM) in each group is indicated. Hazard ratios were estimated with a Cox proportional hazards multivariable model, adjusted for Grade, Ki-67, ERBB2 status, estrogen/progesterone receptor status, tumor size (pT), number of positive lymph nodes (pN), and age at surgery (as appropriate). The number of patients in each subgroup analysis corresponds to those reported in Supplementary Tables 1 and 2 for IHC and RT-qPCR, respectively. P value, Wald test P value. See also Supplementary Tables 1 – 3 14 . Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: A self-sustaining endocytic-based loop promotes breast cancer plasticity leading to aggressiveness and pro-metastatic behavior

    doi: 10.1038/s41467-020-16836-y

    Figure Lengend Snippet: High EPN3 levels correlate with IBC and independently predict metastasis. a H E staining and EPN3 IHC images of in situ (DCIS) and adjacent infiltrating area (IBC) detected in two different primary human BCs. Images at ×20. Bar, 100 µm. b Summary graph of the differential expression of EPN3 detected by IHC in human BC samples in areas of DCIS vs. adjacent IBC. Data are reported as IHC score in IBC relative to DCIS. N , number of tumor samples. P value, two-sided Wilcoxon signed-rank test. c Cumulative incidence of distant metastasis or loco-regional relapse in BC patients of the IEO consecutive cohort (IEO BC 97-00, N = 2453), stratified by EPN3 protein (top, IHC) or mRNA (bottom, RT-qPCR) levels. HR*, multivariable hazard ratio. Multivariable models were adjusted for tumor grade, tumor size, Ki-67 levels, ERBB2 status, ER/PR status, number of positive lymph nodes, and age at surgery, see Supplementary Table 3 . d Forest plot of the multivariable hazard ratios of distant metastasis and 95% Wald confidence intervals (whiskers) in the entire cohort of patients (All) and in the ERBB2-negative (ERBB2-NEG) or lymph node-negative (pN0) subgroups of patients stratified by EPN3 protein (IHC) or mRNA (RT-qPCR) expression levels. The size of the solid squares and diamonds is proportional to the number of distant metastases. The number ( N ) of patients and distant metastases (DM) in each group is indicated. Hazard ratios were estimated with a Cox proportional hazards multivariable model, adjusted for Grade, Ki-67, ERBB2 status, estrogen/progesterone receptor status, tumor size (pT), number of positive lymph nodes (pN), and age at surgery (as appropriate). The number of patients in each subgroup analysis corresponds to those reported in Supplementary Tables 1 and 2 for IHC and RT-qPCR, respectively. P value, Wald test P value. See also Supplementary Tables 1 – 3 14 . Source data are provided as a Source Data file.

    Article Snippet: Once labeled, the DNA probe was hybridized on dried slides of the BC TMAs, following the protocol of the PathVysion HER-2 DNA Probe Kit (Abbott Molecular Inc.).

    Techniques: Staining, Immunohistochemistry, In Situ, Expressing, Quantitative RT-PCR

    Amplification/overexpression of EPN3 in human BCs. a Schematic representation of human chromosome 17. b Venn diagram of EPN3 and ERBB2 amplification in different BC cohorts: BC METABRIC cohort ( N = 2137, available at http://www.cbioportal.org ) 71 , 72 , TCGA invasive BC cohort ( N = 1080, TCGA Research Network: http://cancergenome.nih.gov/ ), and the IEO cohort ( N = 219). Percentage (%) of amplification is shown in parentheses. In the IEO cohort, EPN3 and ERBB2 were considered amplified when the EPN3/CEP17 ratio was > 2.5, and the ERBB2/CEP17 ratio was ≥2.0 60 , respectively. P, P value of the association between the indicated variables by two-sided Fisher’s exact test. c Representative images of EPN3 IHC (quantification scores are indicated). Top, images at 20× (bar, 200 μm); bottom, magnification of the boxed insets (bar, 200 μm). d Venn diagram representation of EPN3 amplification (FISH) and overexpression (IHC; score > 1.0) in the IEO cohort ( N = 212). P, P value of the association between the indicated variables by two-sided Fisher’s exact test. Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: A self-sustaining endocytic-based loop promotes breast cancer plasticity leading to aggressiveness and pro-metastatic behavior

    doi: 10.1038/s41467-020-16836-y

    Figure Lengend Snippet: Amplification/overexpression of EPN3 in human BCs. a Schematic representation of human chromosome 17. b Venn diagram of EPN3 and ERBB2 amplification in different BC cohorts: BC METABRIC cohort ( N = 2137, available at http://www.cbioportal.org ) 71 , 72 , TCGA invasive BC cohort ( N = 1080, TCGA Research Network: http://cancergenome.nih.gov/ ), and the IEO cohort ( N = 219). Percentage (%) of amplification is shown in parentheses. In the IEO cohort, EPN3 and ERBB2 were considered amplified when the EPN3/CEP17 ratio was > 2.5, and the ERBB2/CEP17 ratio was ≥2.0 60 , respectively. P, P value of the association between the indicated variables by two-sided Fisher’s exact test. c Representative images of EPN3 IHC (quantification scores are indicated). Top, images at 20× (bar, 200 μm); bottom, magnification of the boxed insets (bar, 200 μm). d Venn diagram representation of EPN3 amplification (FISH) and overexpression (IHC; score > 1.0) in the IEO cohort ( N = 212). P, P value of the association between the indicated variables by two-sided Fisher’s exact test. Source data are provided as a Source Data file.

    Article Snippet: Once labeled, the DNA probe was hybridized on dried slides of the BC TMAs, following the protocol of the PathVysion HER-2 DNA Probe Kit (Abbott Molecular Inc.).

    Techniques: Amplification, Over Expression, Immunohistochemistry, Fluorescence In Situ Hybridization

    The relationship of subtypes to the DNA ploidy and CIN. The diploid/CIN- status was detected in 72 (64.9%) of the 111 luminal A carcinomas, 39 (41.1%) of the 95 luminal B (HER2-) carcinomas, 8 (11.6%) of the 69 lumminal B (HER2+) carcinomas, 2 (4.9%) of the 41 HER2 carcinomas, and 8 (17.0%) of the 26 basal-like carcinomas. In contrast, the aneuploid/CIN + status was detected in 31 (27.9%) of the 111 luminal A, 47 (49.5%) of the luminal B (HER2-), 56 (81.2%) of the 69 luminal B (HER2+), 37 (90.2%) of the 41 HER2, and 36 (86.6%) of the 47 basal-like subtype tumors. The incidence of diploid/CIN- and aneuploid/CIN+ status was different between the luminal A subtype and luminal B (HER2-), luminal B (HER2+), HER2, and basal-like subtypes (p = 0.0006, p = 5E-13, p = 5E10-12, and p = 8E10-9). In addition, the incidence of diploid/CIN- and aneuploid/CIN+ status was statistically different between the luminal B (HER2-) subtype and luminal B (HER2+), HER2, and basal-like subtypes (p = 0.00002, p = 0.000009, and p = 0.002). Black bar; diploid/CIN- tumors, gray bar; aneuploid/CIN+ tumors, white column; others.

    Journal: BMC Research Notes

    Article Title: Luminal A and luminal B (HER2 negative) subtypes of breast cancer consist of a mixture of tumors with different genotype

    doi: 10.1186/1756-0500-5-376

    Figure Lengend Snippet: The relationship of subtypes to the DNA ploidy and CIN. The diploid/CIN- status was detected in 72 (64.9%) of the 111 luminal A carcinomas, 39 (41.1%) of the 95 luminal B (HER2-) carcinomas, 8 (11.6%) of the 69 lumminal B (HER2+) carcinomas, 2 (4.9%) of the 41 HER2 carcinomas, and 8 (17.0%) of the 26 basal-like carcinomas. In contrast, the aneuploid/CIN + status was detected in 31 (27.9%) of the 111 luminal A, 47 (49.5%) of the luminal B (HER2-), 56 (81.2%) of the 69 luminal B (HER2+), 37 (90.2%) of the 41 HER2, and 36 (86.6%) of the 47 basal-like subtype tumors. The incidence of diploid/CIN- and aneuploid/CIN+ status was different between the luminal A subtype and luminal B (HER2-), luminal B (HER2+), HER2, and basal-like subtypes (p = 0.0006, p = 5E-13, p = 5E10-12, and p = 8E10-9). In addition, the incidence of diploid/CIN- and aneuploid/CIN+ status was statistically different between the luminal B (HER2-) subtype and luminal B (HER2+), HER2, and basal-like subtypes (p = 0.00002, p = 0.000009, and p = 0.002). Black bar; diploid/CIN- tumors, gray bar; aneuploid/CIN+ tumors, white column; others.

    Article Snippet: HER2 amplification was tested on the smear preparations for IHC equivocal cases using a PathVysion HER2 DNA Probe Kit (Abbott Laboratories) according to the manufacturer’s instructions as described previously.

    Techniques:

    Representative examples of conventional cytology and DNA FISH of biliary brushing specimens. ((a) and (b)) Conventional cytology. (a) Reactive changes in the context of PSC with some architectural irregularity, mild variation in nuclear size, and overall intact nuclear to cytoplasmic ratio. (b) Adenocarcinoma in a patient with underlying PSC showing hyperchromatic nuclei, marked variation in nuclear shape and size with nuclear molding, and severely disturbed nuclear to cytoplasmic ratio. In the background, necrotic debris with degenerative cells and granulocytes are observed. ((c) and (d)) Representative examples of FISH signal patterns seen in biliary strictures with probes for CEP7 [aqua], CEP17 [green], 20q [gold], and MYC [red]. (c) A normal cell (2 signals of each probe) and (d) gain of MYC ( > 2 red signals) and gain of CEP7 ( > 2 blue signals).

    Journal: Gastroenterology Research and Practice

    Article Title: Genetic Abnormalities in Biliary Brush Samples for Distinguishing Cholangiocarcinoma from Benign Strictures in Primary Sclerosing Cholangitis

    doi: 10.1155/2016/4381513

    Figure Lengend Snippet: Representative examples of conventional cytology and DNA FISH of biliary brushing specimens. ((a) and (b)) Conventional cytology. (a) Reactive changes in the context of PSC with some architectural irregularity, mild variation in nuclear size, and overall intact nuclear to cytoplasmic ratio. (b) Adenocarcinoma in a patient with underlying PSC showing hyperchromatic nuclei, marked variation in nuclear shape and size with nuclear molding, and severely disturbed nuclear to cytoplasmic ratio. In the background, necrotic debris with degenerative cells and granulocytes are observed. ((c) and (d)) Representative examples of FISH signal patterns seen in biliary strictures with probes for CEP7 [aqua], CEP17 [green], 20q [gold], and MYC [red]. (c) A normal cell (2 signals of each probe) and (d) gain of MYC ( > 2 red signals) and gain of CEP7 ( > 2 blue signals).

    Article Snippet: FISH was performed as previously described using seven different DNA probes including the centromeric probes CEP7 and CEP17 and the locus-specific probes to CDKN2A , TP53 , ERBB2 , 20q , and MYC (Abbott Molecular, Abbott Park, Illinois) [ ].

    Techniques: Fluorescence In Situ Hybridization

    Transmission of rhGH transgene to rabbits of F1 generation. Presence of transgene was observed in both female and male heterozygote rabbits. A screening of the transgene was performed by polymerase chain reaction (PCR) encompassing 313-bp and 524-bp (not shown) DNA fragments. PCR primers were located upstream and downstream of histidine tag and thrombin recognition site of the gene construct. The red arrows indicate transgene in founder rabbit No. 61 and his F1 male and female offspring of the same size as the input DNA fragment (positive control in line 38). PCR observation was confirmed by sequencing. The black arrow indicates the internal marker of 268 bp. The purple arrow indicates the internal marker of 113 bp (Color figure online)

    Journal: Journal of Applied Genetics

    Article Title: Expression of human growth hormone in the milk of transgenic rabbits with transgene mapped to the telomere region of chromosome 7q

    doi: 10.1007/s13353-012-0110-4

    Figure Lengend Snippet: Transmission of rhGH transgene to rabbits of F1 generation. Presence of transgene was observed in both female and male heterozygote rabbits. A screening of the transgene was performed by polymerase chain reaction (PCR) encompassing 313-bp and 524-bp (not shown) DNA fragments. PCR primers were located upstream and downstream of histidine tag and thrombin recognition site of the gene construct. The red arrows indicate transgene in founder rabbit No. 61 and his F1 male and female offspring of the same size as the input DNA fragment (positive control in line 38). PCR observation was confirmed by sequencing. The black arrow indicates the internal marker of 268 bp. The purple arrow indicates the internal marker of 113 bp (Color figure online)

    Article Snippet: The DNA probe specific for the transgene was labeled with biotin-dUTP by the Nick Translation Kit (Boehringer Mannheim) and purified on a Sephadex G-50 column.

    Techniques: Transmission Assay, Polymerase Chain Reaction, Construct, Positive Control, Sequencing, Marker

    Southern blot analysis of selected wzx mutants. Chromosomal DNA from representative A L (S2 and X10) and A + (S7 and X24) wzx mutants from the wzx s and wzx x series and a representative A − (X14) wzx x mutant was digested with Hin dIII and separated on a 0.8% agarose gel, transferred to a nylon membrane, and probed with a dUTP-digoxigenin-labelled Bam HI- Bgl II fragment corresponding to the insert of pFV162-26. All mutants show an increase in the size of the Hin dIII fragment of approximately 0.9 kb, corresponding to the size of the Gm r cassette. No gross rearrangements that could be responsible for the varied A-band LPS phenotypes of these mutants were found in this region.

    Journal: Journal of Bacteriology

    Article Title: Effect of wzx (rfbX) Mutations on A-Band and B-Band Lipopolysaccharide Biosynthesis in Pseudomonas aeruginosa O5

    doi:

    Figure Lengend Snippet: Southern blot analysis of selected wzx mutants. Chromosomal DNA from representative A L (S2 and X10) and A + (S7 and X24) wzx mutants from the wzx s and wzx x series and a representative A − (X14) wzx x mutant was digested with Hin dIII and separated on a 0.8% agarose gel, transferred to a nylon membrane, and probed with a dUTP-digoxigenin-labelled Bam HI- Bgl II fragment corresponding to the insert of pFV162-26. All mutants show an increase in the size of the Hin dIII fragment of approximately 0.9 kb, corresponding to the size of the Gm r cassette. No gross rearrangements that could be responsible for the varied A-band LPS phenotypes of these mutants were found in this region.

    Article Snippet: For detection of specific fragments, probe DNA was labelled with digoxigenin-dUTP (Boehringer Mannheim, Laval, Quebec, Canada), and hybridization and detection were performed according to the manufacturer’s directions.

    Techniques: Southern Blot, Mutagenesis, Agarose Gel Electrophoresis

    Exclusion of RIG-I from compartments containing plus-strand and minus-strand HCV RNA. A and B) Uninfected and HCV-infected Huh7.5 cells were transfected with constructs encoding for FLAG-tagged RIG-I-K207A 2 days after HCV infection. On day 4 after infection, cells were probed with antibodies directed against the FLAG epitope (grey) and either HCV core or NS5A (green). DNA probes (Affymetrix) targeted to either the positive-strand or the negative-strand of the HCV RNA (red) were then hybridized to the viral RNA. DNA was stained with DAPI (blue) and cells were examined by confocal fluorescence microscopy. Boxed regions in the middle row of both panels outline the area of magnification presented in the bottom rows. Scale bars represent 5 μm.

    Journal: PLoS Pathogens

    Article Title: The Hepatitis C Virus-Induced Membranous Web and Associated Nuclear Transport Machinery Limit Access of Pattern Recognition Receptors to Viral Replication Sites

    doi: 10.1371/journal.ppat.1005428

    Figure Lengend Snippet: Exclusion of RIG-I from compartments containing plus-strand and minus-strand HCV RNA. A and B) Uninfected and HCV-infected Huh7.5 cells were transfected with constructs encoding for FLAG-tagged RIG-I-K207A 2 days after HCV infection. On day 4 after infection, cells were probed with antibodies directed against the FLAG epitope (grey) and either HCV core or NS5A (green). DNA probes (Affymetrix) targeted to either the positive-strand or the negative-strand of the HCV RNA (red) were then hybridized to the viral RNA. DNA was stained with DAPI (blue) and cells were examined by confocal fluorescence microscopy. Boxed regions in the middle row of both panels outline the area of magnification presented in the bottom rows. Scale bars represent 5 μm.

    Article Snippet: DNA probes (Affymetrix) complementary to either positive-strand (panel A, red) or negative-strand HCV RNA (panel B, red) were then hybridized to the samples using the manufacturers protocol.

    Techniques: Infection, Transfection, Construct, FLAG-tag, Staining, Fluorescence, Microscopy

    Generation of ISP2 and ISP3 double null mutants. A. Schematic representation of the ISP2–ISP3 locus in WT L. major (upper) and the constructs for gene deletion. ORFs are shown as grey arrows and 5′ FR and 3′ FR boxes represent the FR DNA sequences used for gene targeting. The predicted DNA fragment sizes after restriction digest are shown. HYG , hygromycin-resistance gene; BLE , phleomycin-resistance gene. B. Southern blot of the WT L. major (lanes 1, 3 and 5) and Δ isp2/3 (lanes 2, 4 and 6) digested with AgeI or EcoRI/BamHI and probed with radiolabelled 5′ FR, ISP3 ORF and 3′ FR probes. C. Western blot of cell extracts from 0.5 × 10 7 purified metacyclic promastigotes of WT L. major (lane 1), Δ isp2/3 (lane 2) and Δ isp2/3 : ISP2–ISP3 (lane 3) using antibodies against ISP2, HASPB and EF1α.

    Journal: Cellular Microbiology

    Article Title: Influence of parasite encoded inhibitors of serine peptidases in early infection of macrophages with Leishmania major

    doi: 10.1111/j.1462-5822.2008.01243.x

    Figure Lengend Snippet: Generation of ISP2 and ISP3 double null mutants. A. Schematic representation of the ISP2–ISP3 locus in WT L. major (upper) and the constructs for gene deletion. ORFs are shown as grey arrows and 5′ FR and 3′ FR boxes represent the FR DNA sequences used for gene targeting. The predicted DNA fragment sizes after restriction digest are shown. HYG , hygromycin-resistance gene; BLE , phleomycin-resistance gene. B. Southern blot of the WT L. major (lanes 1, 3 and 5) and Δ isp2/3 (lanes 2, 4 and 6) digested with AgeI or EcoRI/BamHI and probed with radiolabelled 5′ FR, ISP3 ORF and 3′ FR probes. C. Western blot of cell extracts from 0.5 × 10 7 purified metacyclic promastigotes of WT L. major (lane 1), Δ isp2/3 (lane 2) and Δ isp2/3 : ISP2–ISP3 (lane 3) using antibodies against ISP2, HASPB and EF1α.

    Article Snippet: The DNA probes were radiolabelled with a random priming kit (Stratagene) and the blots were hybridized at 65°C overnight.

    Techniques: Construct, Southern Blot, Western Blot, Purification

    Viral 1.9-kb mRNA is expressed by different BDV strains in cell culture and in vivo. (A) Northern blot analysis of viral mRNA from infected rat brain or Vero, C6 and Oligo cells persistently infected with recombinant BDV strain He/80 (rBDV). Total RNA (20 μg) was used for mRNA enrichment by oligo(dT)-cellulose. Poly(A) + and poly(A) − fractions were analyzed by Northern blotting with a radiolabeled DNA probe corresponding to nucleotides 1 to 1876 of the BDV antigenome. Ethidium bromide-stained 18S RNA was used as control for RNA fractionation and loading. (B) Detection of polyadenylated viral 1.9-kb RNA in Vero cells persistently infected with BDV strains V, He80, and No98. Total RNA (20 μg) was used for mRNA enrichment by oligo(dT)-cellulose. Poly(A) + and poly(A) − fractions were analyzed by Northern blotting as in panel A.

    Journal: Journal of Virology

    Article Title: Polymerase Read-Through at the First Transcription Termination Site Contributes to Regulation of Borna Disease Virus Gene Expression ▿

    doi: 10.1128/JVI.00639-08

    Figure Lengend Snippet: Viral 1.9-kb mRNA is expressed by different BDV strains in cell culture and in vivo. (A) Northern blot analysis of viral mRNA from infected rat brain or Vero, C6 and Oligo cells persistently infected with recombinant BDV strain He/80 (rBDV). Total RNA (20 μg) was used for mRNA enrichment by oligo(dT)-cellulose. Poly(A) + and poly(A) − fractions were analyzed by Northern blotting with a radiolabeled DNA probe corresponding to nucleotides 1 to 1876 of the BDV antigenome. Ethidium bromide-stained 18S RNA was used as control for RNA fractionation and loading. (B) Detection of polyadenylated viral 1.9-kb RNA in Vero cells persistently infected with BDV strains V, He80, and No98. Total RNA (20 μg) was used for mRNA enrichment by oligo(dT)-cellulose. Poly(A) + and poly(A) − fractions were analyzed by Northern blotting as in panel A.

    Article Snippet: A DNA probe for detecting viral RNA was amplified by PCR using the primers 1+ (5′-TGTTGCGTTAACAACAAAC-3′) and 1876− (5′-GCGCTCGAGTTATGGTATGATGTCCCACTC-3′) and radioactively labeled with a Prime-It II random primer labeling kit (Stratagene).

    Techniques: Cell Culture, In Vivo, Northern Blot, Infection, Recombinant, Staining, Fractionation

    Mutations in the noncoding region between the N and X gene of BDV alter viral transcription. (A) Western blot analysis of protein samples (10 μg) derived from uninfected (uninf.) cells or Vero cells persistently infected with the indicated viruses. Viral proteins were detected using a mixture of rabbit antisera specific for BDV proteins N, P, and X. The levels of X and P were quantified, and the X/P ratios were determined. (B) Northern blot analysis of RNA samples (5 μg) of uninfected (uninf.) cells or Vero cells persistently infected with the indicated viruses. Viral RNA was detected by using a radiolabeled DNA probe corresponding to nucleotides 1 to 1876 of the BDV antigenome. Ethidium bromide staining of the 18S RNA was used as loading control. The levels of the 1.9-, 1.2-, and 0.8-kb mRNAs were quantified, and the mRNA ratios were determined.

    Journal: Journal of Virology

    Article Title: Polymerase Read-Through at the First Transcription Termination Site Contributes to Regulation of Borna Disease Virus Gene Expression ▿

    doi: 10.1128/JVI.00639-08

    Figure Lengend Snippet: Mutations in the noncoding region between the N and X gene of BDV alter viral transcription. (A) Western blot analysis of protein samples (10 μg) derived from uninfected (uninf.) cells or Vero cells persistently infected with the indicated viruses. Viral proteins were detected using a mixture of rabbit antisera specific for BDV proteins N, P, and X. The levels of X and P were quantified, and the X/P ratios were determined. (B) Northern blot analysis of RNA samples (5 μg) of uninfected (uninf.) cells or Vero cells persistently infected with the indicated viruses. Viral RNA was detected by using a radiolabeled DNA probe corresponding to nucleotides 1 to 1876 of the BDV antigenome. Ethidium bromide staining of the 18S RNA was used as loading control. The levels of the 1.9-, 1.2-, and 0.8-kb mRNAs were quantified, and the mRNA ratios were determined.

    Article Snippet: A DNA probe for detecting viral RNA was amplified by PCR using the primers 1+ (5′-TGTTGCGTTAACAACAAAC-3′) and 1876− (5′-GCGCTCGAGTTATGGTATGATGTCCCACTC-3′) and radioactively labeled with a Prime-It II random primer labeling kit (Stratagene).

    Techniques: Western Blot, Derivative Assay, Infection, Northern Blot, Staining

    Viral 1.9-kb RNA in infected cells is capped and polyadenylated. (A) Specific detection of capped viral mRNA. Total RNA (20 μg) isolated from Vero cells persistently infected with wild-type BDV or rBDV-08gc-26 was treated with a specific antibody for mRNA cap structures (anti-cap) and precipitated with protein G-Sepharose. Bound (+) and unbound (−) fractions were analyzed by Northern blotting. Viral RNA was detected by using a radiolabeled DNA probe corresponding to nucleotides 1 to 1876 of the BDV antigenome. Ethidium bromide-stained 18S RNA and GAPDH mRNA were used as controls. (B) Specific detection of polyadenylated viral mRNA. Total RNA (20 μg) isolated from Vero cells persistently infected with wild-type BDV or rBDV-08gc-26 was used for mRNA enrichment by oligo(dT)-cellulose. Poly(A) + and poly(A) − fractions were analyzed as in panel A. (C) Determination of the 5′ and 3′ end sequences the viral 1.9-kb mRNA. Oligo(dT)-cellulose-fractionated RNA from either wild-type or mutant virus was circularized by RNA self-ligation before the fragment containing the joining regions was amplified by RT-PCR as described in Materials and Methods. The fragment was sequenced from both ends, and the sequence was assembled. The analysis demonstrated that 1.9-kb transcripts of wild-type and mutant BDV start at the S1 site (genome position 44) and end at the T2 site (genome position 1879) after which a poly(A) tail of variable length is added.

    Journal: Journal of Virology

    Article Title: Polymerase Read-Through at the First Transcription Termination Site Contributes to Regulation of Borna Disease Virus Gene Expression ▿

    doi: 10.1128/JVI.00639-08

    Figure Lengend Snippet: Viral 1.9-kb RNA in infected cells is capped and polyadenylated. (A) Specific detection of capped viral mRNA. Total RNA (20 μg) isolated from Vero cells persistently infected with wild-type BDV or rBDV-08gc-26 was treated with a specific antibody for mRNA cap structures (anti-cap) and precipitated with protein G-Sepharose. Bound (+) and unbound (−) fractions were analyzed by Northern blotting. Viral RNA was detected by using a radiolabeled DNA probe corresponding to nucleotides 1 to 1876 of the BDV antigenome. Ethidium bromide-stained 18S RNA and GAPDH mRNA were used as controls. (B) Specific detection of polyadenylated viral mRNA. Total RNA (20 μg) isolated from Vero cells persistently infected with wild-type BDV or rBDV-08gc-26 was used for mRNA enrichment by oligo(dT)-cellulose. Poly(A) + and poly(A) − fractions were analyzed as in panel A. (C) Determination of the 5′ and 3′ end sequences the viral 1.9-kb mRNA. Oligo(dT)-cellulose-fractionated RNA from either wild-type or mutant virus was circularized by RNA self-ligation before the fragment containing the joining regions was amplified by RT-PCR as described in Materials and Methods. The fragment was sequenced from both ends, and the sequence was assembled. The analysis demonstrated that 1.9-kb transcripts of wild-type and mutant BDV start at the S1 site (genome position 44) and end at the T2 site (genome position 1879) after which a poly(A) tail of variable length is added.

    Article Snippet: A DNA probe for detecting viral RNA was amplified by PCR using the primers 1+ (5′-TGTTGCGTTAACAACAAAC-3′) and 1876− (5′-GCGCTCGAGTTATGGTATGATGTCCCACTC-3′) and radioactively labeled with a Prime-It II random primer labeling kit (Stratagene).

    Techniques: Infection, Isolation, Northern Blot, Staining, Mutagenesis, Ligation, Amplification, Reverse Transcription Polymerase Chain Reaction, Sequencing

    Replicon localization of mob DNAs in cosmids pRmOR69 and pRmOR65. Blots of Eco RI-digested genomic DNAs were hybridized against digoxigenin-labeled cosmid probes. Lanes: M, digoxigenin-labeled molecular weight marker; 1, R. meliloti 2011 (wild-type); 2, A. tumefaciens C58; 3, A. tumefaciens C58(pRme2011a); 4, R. meliloti GR4 (wild type); 5, R. meliloti GRM6 (cured of plasmid pRmeGR4b); 6, R. meliloti GRM10 (cured of plasmid pRmeGR4a); 7, R. meliloti GRM8 (cured of pRmeGR4a and pRmeGR4b); 8, R. meliloti GRT3 (carrying pSym1 deletion); 9, Eco RI-digested cosmid DNA.

    Journal: Journal of Bacteriology

    Article Title: Cloning and Identification of Conjugative Transfer Origins in the Rhizobium meliloti Genome

    doi:

    Figure Lengend Snippet: Replicon localization of mob DNAs in cosmids pRmOR69 and pRmOR65. Blots of Eco RI-digested genomic DNAs were hybridized against digoxigenin-labeled cosmid probes. Lanes: M, digoxigenin-labeled molecular weight marker; 1, R. meliloti 2011 (wild-type); 2, A. tumefaciens C58; 3, A. tumefaciens C58(pRme2011a); 4, R. meliloti GR4 (wild type); 5, R. meliloti GRM6 (cured of plasmid pRmeGR4b); 6, R. meliloti GRM10 (cured of plasmid pRmeGR4a); 7, R. meliloti GRM8 (cured of pRmeGR4a and pRmeGR4b); 8, R. meliloti GRT3 (carrying pSym1 deletion); 9, Eco RI-digested cosmid DNA.

    Article Snippet: DNA hybridization probes were digoxigenin-labeled according to standard protocols (Boehringer, Mannheim, Germany).

    Techniques: Labeling, Molecular Weight, Marker, Plasmid Preparation, Cosmid DNA

    Replicon localization of mob DNAs in cosmids pRmOR106, -1012, -1026, -1034, and -1030. Blots of Eco RI-digested genomic DNAs were hybridized against digoxigenin-labeled cosmid probes. Lanes: M, digoxigenin-labeled molecular weight marker; 1, R. meliloti 2011 (wild type); 2, A. tumefaciens C58; 3, A. tumefaciens C58(pRme2011a); 4, R. meliloti GR4 (wild type); 5, R. meliloti GRM6 (cured of plasmid pRmeGR4b); 6, R. meliloti GRM10 (cured of plasmid pRmeGR4a); 7, R. meliloti GRM8 (cured of pRmeGR4a and pRmeGR4b); 8, R. meliloti GRT3 (carrying pSym1 deletion); 9, Eco RI-digested cosmid DNA.

    Journal: Journal of Bacteriology

    Article Title: Cloning and Identification of Conjugative Transfer Origins in the Rhizobium meliloti Genome

    doi:

    Figure Lengend Snippet: Replicon localization of mob DNAs in cosmids pRmOR106, -1012, -1026, -1034, and -1030. Blots of Eco RI-digested genomic DNAs were hybridized against digoxigenin-labeled cosmid probes. Lanes: M, digoxigenin-labeled molecular weight marker; 1, R. meliloti 2011 (wild type); 2, A. tumefaciens C58; 3, A. tumefaciens C58(pRme2011a); 4, R. meliloti GR4 (wild type); 5, R. meliloti GRM6 (cured of plasmid pRmeGR4b); 6, R. meliloti GRM10 (cured of plasmid pRmeGR4a); 7, R. meliloti GRM8 (cured of pRmeGR4a and pRmeGR4b); 8, R. meliloti GRT3 (carrying pSym1 deletion); 9, Eco RI-digested cosmid DNA.

    Article Snippet: DNA hybridization probes were digoxigenin-labeled according to standard protocols (Boehringer, Mannheim, Germany).

    Techniques: Labeling, Molecular Weight, Marker, Plasmid Preparation, Cosmid DNA

    Genome localization of mob DNAs in cosmids pRmOR1035, -1033, -1041, and -1042. Blots of Eco RI-digested genomic DNAs were hybridized against digoxigenin-labeled cosmid probes. Lanes: M, digoxigenin-labeled molecular weight marker; 1, R. meliloti 2011 (wild type); 2, A. tumefaciens C58; 3, A. tumefaciens 104 (C58 carrying pRmeSU47b); 4, A. tumefaciens 117 (C58 carrying pRmeSU47a); 5, R. meliloti GR4 (wild type); 6, Eco RI-digested cosmid DNA.

    Journal: Journal of Bacteriology

    Article Title: Cloning and Identification of Conjugative Transfer Origins in the Rhizobium meliloti Genome

    doi:

    Figure Lengend Snippet: Genome localization of mob DNAs in cosmids pRmOR1035, -1033, -1041, and -1042. Blots of Eco RI-digested genomic DNAs were hybridized against digoxigenin-labeled cosmid probes. Lanes: M, digoxigenin-labeled molecular weight marker; 1, R. meliloti 2011 (wild type); 2, A. tumefaciens C58; 3, A. tumefaciens 104 (C58 carrying pRmeSU47b); 4, A. tumefaciens 117 (C58 carrying pRmeSU47a); 5, R. meliloti GR4 (wild type); 6, Eco RI-digested cosmid DNA.

    Article Snippet: DNA hybridization probes were digoxigenin-labeled according to standard protocols (Boehringer, Mannheim, Germany).

    Techniques: Labeling, Molecular Weight, Marker, Cosmid DNA

    RNA Gel Blot Analysis of the Orchid DOH1 Sense and Antisense Transgenic Plants. (A) Expression of DOH1 in orchid 35S :: DOH1se transformants. Total RNA was isolated from mature CLLs from wild-type plants (wt) and the independent 35S :: DOH1se transgenic lines (lines se1, se7, se17, se28, and se33). The gel blot, containing 10 μg of total RNA in each lane, was hybridized with the digoxigenin-labeled full-length DOH1 DNA probe. (B) Expression of the DOH1 sense and antisense genes in 35S :: DOH1as transformants. Total RNA was isolated from 6-week-old VSAMs (length, 1.5 mm) from wild-type plants (wt) and independent 35S :: DOH1as transformants (lines as4, as10, as15, as23, as27, as31, and as38). The gel blot, containing 20 μg of total RNA in each lane, was hybridized with the digoxigenin-labeled full-length DOH1 RNA sense probe (SP) or antisense probe (AP). The rRNAs, stained by methylene blue, indicate the amount of total RNA in each lane.

    Journal: The Plant Cell

    Article Title: DOH1, a Class 1 knox Gene, Is Required for Maintenance of the Basic Plant Architecture and Floral Transition in Orchid

    doi:

    Figure Lengend Snippet: RNA Gel Blot Analysis of the Orchid DOH1 Sense and Antisense Transgenic Plants. (A) Expression of DOH1 in orchid 35S :: DOH1se transformants. Total RNA was isolated from mature CLLs from wild-type plants (wt) and the independent 35S :: DOH1se transgenic lines (lines se1, se7, se17, se28, and se33). The gel blot, containing 10 μg of total RNA in each lane, was hybridized with the digoxigenin-labeled full-length DOH1 DNA probe. (B) Expression of the DOH1 sense and antisense genes in 35S :: DOH1as transformants. Total RNA was isolated from 6-week-old VSAMs (length, 1.5 mm) from wild-type plants (wt) and independent 35S :: DOH1as transformants (lines as4, as10, as15, as23, as27, as31, and as38). The gel blot, containing 20 μg of total RNA in each lane, was hybridized with the digoxigenin-labeled full-length DOH1 RNA sense probe (SP) or antisense probe (AP). The rRNAs, stained by methylene blue, indicate the amount of total RNA in each lane.

    Article Snippet: Blots were hybridized overnight with the digoxigenin-labeled DNA probes at 42°C in DIG Easy Hyb buffer (Boehringer Mannheim).

    Techniques: Western Blot, Transgenic Assay, Expressing, Isolation, Labeling, Staining

    Genomic DNA Gel Blot Analysis of the DOH1 Gene in Wild-Type Plants. A DNA gel blot containing 20 μg of orchid genomic DNA digested with various restriction enzymes was hybridized at low stringency with the digoxigenin-labeled DOH1 DNA probe. The sizes of the DNA markers are given at right in kilobases. A, ApaI; E, EcoRV; P, PstI; Sa, SmaI; Sp, SspI; Su, StuI; X, XbaI.

    Journal: The Plant Cell

    Article Title: DOH1, a Class 1 knox Gene, Is Required for Maintenance of the Basic Plant Architecture and Floral Transition in Orchid

    doi:

    Figure Lengend Snippet: Genomic DNA Gel Blot Analysis of the DOH1 Gene in Wild-Type Plants. A DNA gel blot containing 20 μg of orchid genomic DNA digested with various restriction enzymes was hybridized at low stringency with the digoxigenin-labeled DOH1 DNA probe. The sizes of the DNA markers are given at right in kilobases. A, ApaI; E, EcoRV; P, PstI; Sa, SmaI; Sp, SspI; Su, StuI; X, XbaI.

    Article Snippet: Blots were hybridized overnight with the digoxigenin-labeled DNA probes at 42°C in DIG Easy Hyb buffer (Boehringer Mannheim).

    Techniques: Western Blot, Labeling

    DNA Gel Blot Analysis of the Orchid DOH1 Sense and Antisense Transgenic Plants. A gel blot containing genomic DNA from independent transgenic lines (10 μg per lane) digested with SmaI was hybridized with the digoxigenin-labeled full-length DOH1 DNA probe. DNA was isolated successively from 35S :: DOH1se transformants (lines se1, se7, and se17), 35S :: DOH1as transformants (lines as4 and as10), and wild-type plants (wt). The endogenous DOH1 gene band present in all of the plants is indicated with an arrow. The sizes of the DNA markers are given at right in kilobases.

    Journal: The Plant Cell

    Article Title: DOH1, a Class 1 knox Gene, Is Required for Maintenance of the Basic Plant Architecture and Floral Transition in Orchid

    doi:

    Figure Lengend Snippet: DNA Gel Blot Analysis of the Orchid DOH1 Sense and Antisense Transgenic Plants. A gel blot containing genomic DNA from independent transgenic lines (10 μg per lane) digested with SmaI was hybridized with the digoxigenin-labeled full-length DOH1 DNA probe. DNA was isolated successively from 35S :: DOH1se transformants (lines se1, se7, and se17), 35S :: DOH1as transformants (lines as4 and as10), and wild-type plants (wt). The endogenous DOH1 gene band present in all of the plants is indicated with an arrow. The sizes of the DNA markers are given at right in kilobases.

    Article Snippet: Blots were hybridized overnight with the digoxigenin-labeled DNA probes at 42°C in DIG Easy Hyb buffer (Boehringer Mannheim).

    Techniques: Western Blot, Transgenic Assay, Labeling, Isolation

    RNA Gel Blot Analysis of the DOH1 Gene in Wild-Type Plants. (A) RNA gel blot analysis of the DOH1 gene in different orchid tissues. An RNA gel blot containing 10 μg of total RNA in each lane was hybridized with the digoxigenin-labeled full-length DOH1 DNA probe. RNA was isolated from roots (R; length, 1 cm), vegetative stems (VS; length, 0.4 cm), transitional stems (TS; length, 0.4 cm), young leaves (YL; length, 0.5 cm), old leaves (OL; length, 2 cm), VSAMs (V; 6 weeks old; length, 1.5 mm), TSAMs (T; 12 weeks old; length, 2 mm), and flowers (F; length, 1.5 cm). (B) Time course of DOH1 expression in orchid development. Lanes are labeled according to the age (in weeks) of tissues. From left to right, total RNA (25 μg per lane) was successively extracted from thin sections of protocorms (P; 0 weeks old; length, 1 mm), PLBs (PLB; 2 weeks old; length, 4 to 5 mm), VSAMs (VSAM; 4, 6, and 8 weeks old; ength, 1.5 mm), TSAMs (TSAM; 9 and 12 weeks old; length, 2 mm), and inflorescence meristems (IM; 14 weeks old; length, 3 to 5 mm). Hybridization was performed as in (A) . The rRNAs, stained by methylene blue, indicate the amount of total RNA loaded in each lane.

    Journal: The Plant Cell

    Article Title: DOH1, a Class 1 knox Gene, Is Required for Maintenance of the Basic Plant Architecture and Floral Transition in Orchid

    doi:

    Figure Lengend Snippet: RNA Gel Blot Analysis of the DOH1 Gene in Wild-Type Plants. (A) RNA gel blot analysis of the DOH1 gene in different orchid tissues. An RNA gel blot containing 10 μg of total RNA in each lane was hybridized with the digoxigenin-labeled full-length DOH1 DNA probe. RNA was isolated from roots (R; length, 1 cm), vegetative stems (VS; length, 0.4 cm), transitional stems (TS; length, 0.4 cm), young leaves (YL; length, 0.5 cm), old leaves (OL; length, 2 cm), VSAMs (V; 6 weeks old; length, 1.5 mm), TSAMs (T; 12 weeks old; length, 2 mm), and flowers (F; length, 1.5 cm). (B) Time course of DOH1 expression in orchid development. Lanes are labeled according to the age (in weeks) of tissues. From left to right, total RNA (25 μg per lane) was successively extracted from thin sections of protocorms (P; 0 weeks old; length, 1 mm), PLBs (PLB; 2 weeks old; length, 4 to 5 mm), VSAMs (VSAM; 4, 6, and 8 weeks old; ength, 1.5 mm), TSAMs (TSAM; 9 and 12 weeks old; length, 2 mm), and inflorescence meristems (IM; 14 weeks old; length, 3 to 5 mm). Hybridization was performed as in (A) . The rRNAs, stained by methylene blue, indicate the amount of total RNA loaded in each lane.

    Article Snippet: Blots were hybridized overnight with the digoxigenin-labeled DNA probes at 42°C in DIG Easy Hyb buffer (Boehringer Mannheim).

    Techniques: Western Blot, Labeling, Isolation, Expressing, Hybridization, Staining

    Calcineurin enhances AP-1 binding to the endogenous cytoglobin promoter. A–C , utilizing EMSA, AP-1 was demonstrated to bind to the endogenous Cygb promoter. The binding affinity of AP-1 to DNA was enhanced in the presence of CnA* and in response

    Journal: The Journal of Biological Chemistry

    Article Title: Calcineurin Activates Cytoglobin Transcription in Hypoxic Myocytes

    doi: 10.1074/jbc.M809572200

    Figure Lengend Snippet: Calcineurin enhances AP-1 binding to the endogenous cytoglobin promoter. A–C , utilizing EMSA, AP-1 was demonstrated to bind to the endogenous Cygb promoter. The binding affinity of AP-1 to DNA was enhanced in the presence of CnA* and in response

    Article Snippet: Northern Blot Analysis —The Strip-EZ DNA probe synthesis kit (Ambion) was utilized to construct the Cygb radioactive probe.

    Techniques: Binding Assay

    Induction of cytoglobin transcriptional activity by AP-1. A , illustration depicting the location of the 0.1-kb Cygb promoter fragment within the 0.6-kb Cygb promoter region. This smaller DNA fragment contains the evolutionarily conserved motif for

    Journal: The Journal of Biological Chemistry

    Article Title: Calcineurin Activates Cytoglobin Transcription in Hypoxic Myocytes

    doi: 10.1074/jbc.M809572200

    Figure Lengend Snippet: Induction of cytoglobin transcriptional activity by AP-1. A , illustration depicting the location of the 0.1-kb Cygb promoter fragment within the 0.6-kb Cygb promoter region. This smaller DNA fragment contains the evolutionarily conserved motif for

    Article Snippet: Northern Blot Analysis —The Strip-EZ DNA probe synthesis kit (Ambion) was utilized to construct the Cygb radioactive probe.

    Techniques: Activity Assay