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Agilent technologies mouse microarrays
Mouse Microarrays, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 88/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/mouse microarrays/product/Agilent technologies
Average 88 stars, based on 5 article reviews
Price from $9.99 to $1999.99
mouse microarrays - by Bioz Stars, 2020-08
88/100 stars

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In Situ:

Article Title: Circulating exosomes potentiate tumor malignant properties in a mouse model of chronic sleep fragmentation
Article Snippet: .. The labeled miRNAs were hybridized to custom 8 × 60 K mouse microarrays, consisting of 60-mer DNA probes synthesized in situ that represent 2006 miRNA (Version 19.0) and each of them represented by 40 features probes (Agilent), Santa Clara, CA). .. After hybridization and washing, the arrays were scanned with an Agilent microarray scanner using high dynamic range settings as specified by the manufacturer.

Synthesized:

Article Title: Circulating exosomes potentiate tumor malignant properties in a mouse model of chronic sleep fragmentation
Article Snippet: .. The labeled miRNAs were hybridized to custom 8 × 60 K mouse microarrays, consisting of 60-mer DNA probes synthesized in situ that represent 2006 miRNA (Version 19.0) and each of them represented by 40 features probes (Agilent), Santa Clara, CA). .. After hybridization and washing, the arrays were scanned with an Agilent microarray scanner using high dynamic range settings as specified by the manufacturer.

Labeling:

Article Title: Circulating exosomes potentiate tumor malignant properties in a mouse model of chronic sleep fragmentation
Article Snippet: .. The labeled miRNAs were hybridized to custom 8 × 60 K mouse microarrays, consisting of 60-mer DNA probes synthesized in situ that represent 2006 miRNA (Version 19.0) and each of them represented by 40 features probes (Agilent), Santa Clara, CA). .. After hybridization and washing, the arrays were scanned with an Agilent microarray scanner using high dynamic range settings as specified by the manufacturer.

Article Title: Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids
Article Snippet: .. We labeled the samples and applied them to two mouse microarrays (Agilent) differing by a dye-swap ( ) . .. Labeled RNA from A23 cells served as the control channel.

Mouse Assay:

Article Title: Cerebellar Oxidative DNA Damage and Altered DNA Methylation in the BTBR T+tf/J Mouse Model of Autism and Similarities with Human Post Mortem Cerebellum
Article Snippet: .. Gene expression profiles in the cerebellum of BTBR T+tf/J and C57BL/6J mice were determined utilizing Agilent whole genome 8×60 K mouse microarrays (Agilent Technologies, Santa Clara, CA, USA). .. Sample labeling and microarray processing were performed as detailed in the “One-Color Microarray-Based Gene Expression Analysis” Version 5.5 (Agilent Technologies) protocol.

Infection:

Article Title: Role of Interleukin 6 in Innate Immunity to Mycobacterium tuberculosis Infection
Article Snippet: .. A total of 24 hours after infection and silencing, host transcripts extracted from approximately 3 × 105 cells by means of the RNeasy kit (Qiagen) were used to profile the expression of mouse genome, using 4 × 44 mouse microarrays (Agilent) as described elsewhere [ – ]. .. Control samples (ie, samples infected with wild type or Mtb :Δ- sig H and treated with negative-control siRNA) were labeled with Cy3, whereas experimental samples (ie, samples infected with wild type or Mtb :Δ- sig H and treated with siRNA to silence Il-6 expression) were labeled with Cy5; methods are described elsewhere [ – ].

Expressing:

Article Title: Cerebellar Oxidative DNA Damage and Altered DNA Methylation in the BTBR T+tf/J Mouse Model of Autism and Similarities with Human Post Mortem Cerebellum
Article Snippet: .. Gene expression profiles in the cerebellum of BTBR T+tf/J and C57BL/6J mice were determined utilizing Agilent whole genome 8×60 K mouse microarrays (Agilent Technologies, Santa Clara, CA, USA). .. Sample labeling and microarray processing were performed as detailed in the “One-Color Microarray-Based Gene Expression Analysis” Version 5.5 (Agilent Technologies) protocol.

Article Title: Role of Interleukin 6 in Innate Immunity to Mycobacterium tuberculosis Infection
Article Snippet: .. A total of 24 hours after infection and silencing, host transcripts extracted from approximately 3 × 105 cells by means of the RNeasy kit (Qiagen) were used to profile the expression of mouse genome, using 4 × 44 mouse microarrays (Agilent) as described elsewhere [ – ]. .. Control samples (ie, samples infected with wild type or Mtb :Δ- sig H and treated with negative-control siRNA) were labeled with Cy3, whereas experimental samples (ie, samples infected with wild type or Mtb :Δ- sig H and treated with siRNA to silence Il-6 expression) were labeled with Cy5; methods are described elsewhere [ – ].

Hybridization:

Article Title: Transcriptional profiling of the acute pulmonary inflammatory response induced by LPS: role of neutrophils
Article Snippet: .. Dye incorporation rates were used to put appropriate amounts of Cy5 and Cy3 labelled samples (10 pmol each) together for hybridisation on Agilent 4× 44 K Mouse Microarrays (Agilent Technologies). .. After hybridisation, slides were washed and dried with N2 gas before scanning.

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    Agilent technologies profine
    <t>ProFine</t> affects multiple genes in PCa cells. (A) Heat map of C4-2 transcriptome following the treatment with ProFine (5.8 μg/ml, 6 hours) or control (DMSO). Total RNAs were extracted from triplicate preparations. (B) Hallmark pathway gene set enrichment analysis of C4-2 cells treated with ProFine (5.8 μg/ml, 6 hours). (C) Pathway enrichment plots of androgen-responsive and apoptosis-related genes, respectively, in C4-2 cells treated with ProFine (5.8 μg/ml, 6 hours) or DMSO. (D) Selected target genes of ProFine in C4-2 cells, as validated by quantitative real-time PCR (left) and Western blot analyses (right, ProFine: 11.6 μg/ml; Ctrl: DMSO).
    Profine, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/profine/product/Agilent technologies
    Average 92 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    profine - by Bioz Stars, 2020-08
    92/100 stars
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    93
    Agilent technologies cd8 t cells
    Increased Chop in CD8 +  tumor-infiltrating T lymphocytes (TILs) correlates with poor survival in ovarian cancer.  a Ddit3  mRNA levels in tumor-associated CD45 +  CD8 +  T cells (TILs) sorted from subcutaneous 3LL, EL-4, MCA-38, or B16 tumors and CD8 +  T cells from the spleens of the same tumor-bearing mice (Tumor bearing) or tumor-free mice (Tumor free). Bar graphs show the mean ± s.e.m. ( n  = 5 mice/group).  b  Chop expression in CD8 +  TILs from B16 melanoma tumors (left) and 3LL tumors (right), compared with splenic CD8 +  T cells from the corresponding tumor-bearing mice. Chop was detected by fluorescence-activated cell sorter and levels indicated by mean fluorescence intensity (MFI). Representative findings from four repeats.  c  CHOP in CD8 +  TILs from ovarian carcinoma patients (Ovarian Ca tumor,  n  = 18) compared to peripheral blood CD8 +  T cells from ovarian carcinoma patients (Ovarian Ca blood,  n  = 11) or healthy controls (Healthy blood,  n  = 6).  d  CHOP levels in autologous CD8 +  TILs (Tumor) and peripheral blood CD8 +  T cells (Blood) from ovarian carcinoma patients ( n  = 7).  e  Representative image (scale 10 μm) showing CHOP expression in CD8 +  TILs from ovarian carcinoma patients compared to CD8 +  T cells from healthy ovarian tissues. Isotype (red) or CHOP (red, tested by clone 9C8 (left) or polyclonal antibody R-20 (right)), CD8 (green) and DAPI (blue) were detected by confocal microscopy.  f  Percentage of nuclear CHOP +  cells (clone 9C8) among tumor-associated CD8 +  T lymphocytes in a tissue microarray containing advanced ovarian carcinoma tissues ( n  = 87) vs. normal ovarian tissues ( n  = 12).  g  Overall survival in advanced ovarian tumor patients having increased frequency of nuclear CHOP in CD8 +  TILs (CHOP high ) ( n  = 52) vs. those having low frequency of nuclear CHOP in CD8 +  TILs (CHOP low ) ( n  = 29) (logrank 4.39,  p  = 0.0361 using Gehan–Breslow–Wilcoxon test; cutoff was established as described in the Methods section). Studies were developed using the anti-CHOP antibody clone 9C8.  h  Percentage of CD8 +  TILs having nuclear CHOP (clone 9C8) in ovarian cancer patients that had optimal ( n  = 59) vs. suboptimal ( n  = 23) cytoreductive debulking surgery. Bar graphs represent mean value ± s.e.m., * p
    Cd8 T Cells, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Agilent technologies microarray analysis
    The genomic map of total lncRNAs and deregulated LncRNAs in chromosomes of mouse. The distribution of LncRNAs in chromosomes of mouse is marked in blue. The upregulated LncRNAs are highlighed in red and the downregulated lncRNAs are highlighted in green. The length of the bars represents the folds of LncRNAs expression change. <t>Microarray</t> assays revealed the existence of a total of 20073 LncRNAs in mouse livers. The numbers and symbols represent chromosome numbers.
    Microarray Analysis, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 95/100, based on 1637 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 95 stars, based on 1637 article reviews
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    89
    Agilent technologies arabidopsis host
    <t>Arabidopsis</t> knock-out mutants show altered susceptibility to Myzus persicae and Myzus cerasi . Four-week old plants were exposed to two adult aphids and nymph production was counted after 10 days. Average nymph production was calculated from three independent replicated experiments, with 10 plants per replicate per treatment. Error bars indicate standard error. The two-tailed Student's t -test was used for statistical analyses (*** indicates p-value
    Arabidopsis Host, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    ProFine affects multiple genes in PCa cells. (A) Heat map of C4-2 transcriptome following the treatment with ProFine (5.8 μg/ml, 6 hours) or control (DMSO). Total RNAs were extracted from triplicate preparations. (B) Hallmark pathway gene set enrichment analysis of C4-2 cells treated with ProFine (5.8 μg/ml, 6 hours). (C) Pathway enrichment plots of androgen-responsive and apoptosis-related genes, respectively, in C4-2 cells treated with ProFine (5.8 μg/ml, 6 hours) or DMSO. (D) Selected target genes of ProFine in C4-2 cells, as validated by quantitative real-time PCR (left) and Western blot analyses (right, ProFine: 11.6 μg/ml; Ctrl: DMSO).

    Journal: Neoplasia (New York, N.Y.)

    Article Title: A Novel Flavonoid Composition Targets Androgen Receptor Signaling and Inhibits Prostate Cancer Growth in Preclinical Models

    doi: 10.1016/j.neo.2018.06.003

    Figure Lengend Snippet: ProFine affects multiple genes in PCa cells. (A) Heat map of C4-2 transcriptome following the treatment with ProFine (5.8 μg/ml, 6 hours) or control (DMSO). Total RNAs were extracted from triplicate preparations. (B) Hallmark pathway gene set enrichment analysis of C4-2 cells treated with ProFine (5.8 μg/ml, 6 hours). (C) Pathway enrichment plots of androgen-responsive and apoptosis-related genes, respectively, in C4-2 cells treated with ProFine (5.8 μg/ml, 6 hours) or DMSO. (D) Selected target genes of ProFine in C4-2 cells, as validated by quantitative real-time PCR (left) and Western blot analyses (right, ProFine: 11.6 μg/ml; Ctrl: DMSO).

    Article Snippet: Microarray and Gene Set Enrichment Analysis (GSEA) Total RNAs from triplicate preparations of ProFine- and DMSO-treated C4-2 cells as well as reference total RNA samples were amplified and hybridized to Agilent 44 K whole human genome expression oligonucleotide microarray slides.

    Techniques: Real-time Polymerase Chain Reaction, Western Blot

    In vivo effect of oral ProFine on the subcutaneous growth of C4-2-Luc tumors in athymic nude mice. (A) Tumor size and pairwise comparison of C4-2-Luc xenografts treated with ProFine (100 mg/kg or 200 mg/kg) or vehicle control at the indicated times. (B) Log-rank survival curve and pairwise comparison of C4-2-Luc tumor-bearing animals treated with ProFine or vehicle control. (C) Upper: H E, IHC staining of putative ProFine targets, and TUNEL expression in C4-2-Luc xenograft tissues. Scale bar: 100 μm. Lower: quantitation of IHC and TUNEL expression. Weighted index was calculated as the average (intensity × percentage of positive cells) from three random tissue areas. P values were calculated using Student's t test.

    Journal: Neoplasia (New York, N.Y.)

    Article Title: A Novel Flavonoid Composition Targets Androgen Receptor Signaling and Inhibits Prostate Cancer Growth in Preclinical Models

    doi: 10.1016/j.neo.2018.06.003

    Figure Lengend Snippet: In vivo effect of oral ProFine on the subcutaneous growth of C4-2-Luc tumors in athymic nude mice. (A) Tumor size and pairwise comparison of C4-2-Luc xenografts treated with ProFine (100 mg/kg or 200 mg/kg) or vehicle control at the indicated times. (B) Log-rank survival curve and pairwise comparison of C4-2-Luc tumor-bearing animals treated with ProFine or vehicle control. (C) Upper: H E, IHC staining of putative ProFine targets, and TUNEL expression in C4-2-Luc xenograft tissues. Scale bar: 100 μm. Lower: quantitation of IHC and TUNEL expression. Weighted index was calculated as the average (intensity × percentage of positive cells) from three random tissue areas. P values were calculated using Student's t test.

    Article Snippet: Microarray and Gene Set Enrichment Analysis (GSEA) Total RNAs from triplicate preparations of ProFine- and DMSO-treated C4-2 cells as well as reference total RNA samples were amplified and hybridized to Agilent 44 K whole human genome expression oligonucleotide microarray slides.

    Techniques: In Vivo, Mouse Assay, Immunohistochemistry, Staining, TUNEL Assay, Expressing, Quantitation Assay

    In vivo toxicity and pharmacokinetics of ProFine in rodent models. (A) Average body weights of CD-1 mice treated with ProFine or vehicle control ( n = 5 per group) via oral gavage, daily for the first week, then three times per week for the second week (arrow indicates the time of schedule change). (B) Plasma levels of luteolin, quercetin, and kaempferol at the indicated times in rats administered with ProFine via oral gavage (p.o.) or tail vein injection (i.v.). n = 3 per group.

    Journal: Neoplasia (New York, N.Y.)

    Article Title: A Novel Flavonoid Composition Targets Androgen Receptor Signaling and Inhibits Prostate Cancer Growth in Preclinical Models

    doi: 10.1016/j.neo.2018.06.003

    Figure Lengend Snippet: In vivo toxicity and pharmacokinetics of ProFine in rodent models. (A) Average body weights of CD-1 mice treated with ProFine or vehicle control ( n = 5 per group) via oral gavage, daily for the first week, then three times per week for the second week (arrow indicates the time of schedule change). (B) Plasma levels of luteolin, quercetin, and kaempferol at the indicated times in rats administered with ProFine via oral gavage (p.o.) or tail vein injection (i.v.). n = 3 per group.

    Article Snippet: Microarray and Gene Set Enrichment Analysis (GSEA) Total RNAs from triplicate preparations of ProFine- and DMSO-treated C4-2 cells as well as reference total RNA samples were amplified and hybridized to Agilent 44 K whole human genome expression oligonucleotide microarray slides.

    Techniques: In Vivo, Mouse Assay, Injection

    In vitro cytotoxicity of ProFine in PCa cells. (A) Left: MTS cell proliferation assay of the in vitro cytotoxicity of luteolin, quercetin, and kaempferol in C4-2 cells (72 hours); right: MTS assay of the in vitro cytotoxicity of ProFine in C4-2 cells (72 hours). (B) CompuSyn analysis of the synergistic effect among the ingredients of ProFine. Left: Dose-effect curve of ProFine and the three individual ingredients in C4-2 cells; right: combination index plot of ProFine in C4-2 cells. Fa: fraction affected; CI: combination index. (C) Fluorescence-activated cell sorting analysis of Annexin V expression in C4-2 cells treated with varying concentrations of ProFine (48 hours). (D) MTS assay of the in vitro cytotoxicity of ProFine in PCa cell lines (72 hours); (E) left: MTS assay of the in vitro cytotoxicity of docetaxel in the presence of varying concentrations of ProFine in C4-2 cells (72 hours); right: MTS assay of the in vitro cytotoxicity of enzalutamide in the presence of varying concentrations of ProFine in C4-2 cells (72 hours).

    Journal: Neoplasia (New York, N.Y.)

    Article Title: A Novel Flavonoid Composition Targets Androgen Receptor Signaling and Inhibits Prostate Cancer Growth in Preclinical Models

    doi: 10.1016/j.neo.2018.06.003

    Figure Lengend Snippet: In vitro cytotoxicity of ProFine in PCa cells. (A) Left: MTS cell proliferation assay of the in vitro cytotoxicity of luteolin, quercetin, and kaempferol in C4-2 cells (72 hours); right: MTS assay of the in vitro cytotoxicity of ProFine in C4-2 cells (72 hours). (B) CompuSyn analysis of the synergistic effect among the ingredients of ProFine. Left: Dose-effect curve of ProFine and the three individual ingredients in C4-2 cells; right: combination index plot of ProFine in C4-2 cells. Fa: fraction affected; CI: combination index. (C) Fluorescence-activated cell sorting analysis of Annexin V expression in C4-2 cells treated with varying concentrations of ProFine (48 hours). (D) MTS assay of the in vitro cytotoxicity of ProFine in PCa cell lines (72 hours); (E) left: MTS assay of the in vitro cytotoxicity of docetaxel in the presence of varying concentrations of ProFine in C4-2 cells (72 hours); right: MTS assay of the in vitro cytotoxicity of enzalutamide in the presence of varying concentrations of ProFine in C4-2 cells (72 hours).

    Article Snippet: Microarray and Gene Set Enrichment Analysis (GSEA) Total RNAs from triplicate preparations of ProFine- and DMSO-treated C4-2 cells as well as reference total RNA samples were amplified and hybridized to Agilent 44 K whole human genome expression oligonucleotide microarray slides.

    Techniques: In Vitro, Proliferation Assay, MTS Assay, Fluorescence, FACS, Expressing

    In vivo effect of oral ProFine on the intratibial growth of C4-2-Luc tumors in athymic nude mice. (A) Serum PSA levels in C4-2-Luc tumor-bearing mice treated with ProFine (100 mg/kg) or vehicle control. (B) Log-rank survival curve of C4-2-Luc tumor-bearing animals treated with ProFine or vehicle control. (C) X-ray radiography of C4-2-Luc tumor-bearing tibias of mice treated with ProFine or vehicle control, collected at end points. Red arrows: osteolytic lesions. (D) Upper: H E and IHC staining of AR and survivin expression in C4-2-Luc bone tumors. Scale bar: 100 μm. Lower: Quantitation of IHC expression of AR and survivin in bone tumors. P values were calculated using Student's t test.

    Journal: Neoplasia (New York, N.Y.)

    Article Title: A Novel Flavonoid Composition Targets Androgen Receptor Signaling and Inhibits Prostate Cancer Growth in Preclinical Models

    doi: 10.1016/j.neo.2018.06.003

    Figure Lengend Snippet: In vivo effect of oral ProFine on the intratibial growth of C4-2-Luc tumors in athymic nude mice. (A) Serum PSA levels in C4-2-Luc tumor-bearing mice treated with ProFine (100 mg/kg) or vehicle control. (B) Log-rank survival curve of C4-2-Luc tumor-bearing animals treated with ProFine or vehicle control. (C) X-ray radiography of C4-2-Luc tumor-bearing tibias of mice treated with ProFine or vehicle control, collected at end points. Red arrows: osteolytic lesions. (D) Upper: H E and IHC staining of AR and survivin expression in C4-2-Luc bone tumors. Scale bar: 100 μm. Lower: Quantitation of IHC expression of AR and survivin in bone tumors. P values were calculated using Student's t test.

    Article Snippet: Microarray and Gene Set Enrichment Analysis (GSEA) Total RNAs from triplicate preparations of ProFine- and DMSO-treated C4-2 cells as well as reference total RNA samples were amplified and hybridized to Agilent 44 K whole human genome expression oligonucleotide microarray slides.

    Techniques: In Vivo, Mouse Assay, Immunohistochemistry, Staining, Expressing, Quantitation Assay

    ProFine inhibits AR and survivin signaling in PCa cells. (A) RT-PCR (upper, 24 hours treatment) and Western blot analyses (bottom, 11.6 μg/ml) of AR expression in C4-2 cells treated with ProFine. (B) Upper: Western blot analysis of AR protein expression in C4-2 cells pretreated with CHX (50 μg/ml, 1 hour) and further treated with ProFine (11.6 μg/ml) or DMSO for the indicated times. Lower: Plot of AR protein degradation in C4-2 cells treated with ProFine or DMSO. (C) Western blot analysis of AR protein expression in HSP90 immunoprecipitates from C4-2 cells treated with ProFine (11.6 μg/ml, 24 hours) or DMSO. (D) RT-PCR analysis of survivin expression in C4-2 cells treated with ProFine (24 hours); (E) Western blot analysis of p-Stat3, Stat3, survivin, and PARP in C4-2 cells treated with ProFine (11.6 μg/ml) at indicated times. (F) Upper: Schematic diagram of the Stat3 cis -elements in human survivin promoter; lower: luciferase activity of human survivin promoters in C4-2 cells treated with ProFine (11.6 μg/ml). (G) Western blot analysis of protein expression of AR, HIF-1α, and VEGF in C4-2 cells treated with ProFine (11.6 μg/ml). (H) In vitro tube formation of HUVECs treated with varying concentrations of ProFine (72 hours).

    Journal: Neoplasia (New York, N.Y.)

    Article Title: A Novel Flavonoid Composition Targets Androgen Receptor Signaling and Inhibits Prostate Cancer Growth in Preclinical Models

    doi: 10.1016/j.neo.2018.06.003

    Figure Lengend Snippet: ProFine inhibits AR and survivin signaling in PCa cells. (A) RT-PCR (upper, 24 hours treatment) and Western blot analyses (bottom, 11.6 μg/ml) of AR expression in C4-2 cells treated with ProFine. (B) Upper: Western blot analysis of AR protein expression in C4-2 cells pretreated with CHX (50 μg/ml, 1 hour) and further treated with ProFine (11.6 μg/ml) or DMSO for the indicated times. Lower: Plot of AR protein degradation in C4-2 cells treated with ProFine or DMSO. (C) Western blot analysis of AR protein expression in HSP90 immunoprecipitates from C4-2 cells treated with ProFine (11.6 μg/ml, 24 hours) or DMSO. (D) RT-PCR analysis of survivin expression in C4-2 cells treated with ProFine (24 hours); (E) Western blot analysis of p-Stat3, Stat3, survivin, and PARP in C4-2 cells treated with ProFine (11.6 μg/ml) at indicated times. (F) Upper: Schematic diagram of the Stat3 cis -elements in human survivin promoter; lower: luciferase activity of human survivin promoters in C4-2 cells treated with ProFine (11.6 μg/ml). (G) Western blot analysis of protein expression of AR, HIF-1α, and VEGF in C4-2 cells treated with ProFine (11.6 μg/ml). (H) In vitro tube formation of HUVECs treated with varying concentrations of ProFine (72 hours).

    Article Snippet: Microarray and Gene Set Enrichment Analysis (GSEA) Total RNAs from triplicate preparations of ProFine- and DMSO-treated C4-2 cells as well as reference total RNA samples were amplified and hybridized to Agilent 44 K whole human genome expression oligonucleotide microarray slides.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Western Blot, Expressing, Luciferase, Activity Assay, In Vitro

    Increased Chop in CD8 +  tumor-infiltrating T lymphocytes (TILs) correlates with poor survival in ovarian cancer.  a Ddit3  mRNA levels in tumor-associated CD45 +  CD8 +  T cells (TILs) sorted from subcutaneous 3LL, EL-4, MCA-38, or B16 tumors and CD8 +  T cells from the spleens of the same tumor-bearing mice (Tumor bearing) or tumor-free mice (Tumor free). Bar graphs show the mean ± s.e.m. ( n  = 5 mice/group).  b  Chop expression in CD8 +  TILs from B16 melanoma tumors (left) and 3LL tumors (right), compared with splenic CD8 +  T cells from the corresponding tumor-bearing mice. Chop was detected by fluorescence-activated cell sorter and levels indicated by mean fluorescence intensity (MFI). Representative findings from four repeats.  c  CHOP in CD8 +  TILs from ovarian carcinoma patients (Ovarian Ca tumor,  n  = 18) compared to peripheral blood CD8 +  T cells from ovarian carcinoma patients (Ovarian Ca blood,  n  = 11) or healthy controls (Healthy blood,  n  = 6).  d  CHOP levels in autologous CD8 +  TILs (Tumor) and peripheral blood CD8 +  T cells (Blood) from ovarian carcinoma patients ( n  = 7).  e  Representative image (scale 10 μm) showing CHOP expression in CD8 +  TILs from ovarian carcinoma patients compared to CD8 +  T cells from healthy ovarian tissues. Isotype (red) or CHOP (red, tested by clone 9C8 (left) or polyclonal antibody R-20 (right)), CD8 (green) and DAPI (blue) were detected by confocal microscopy.  f  Percentage of nuclear CHOP +  cells (clone 9C8) among tumor-associated CD8 +  T lymphocytes in a tissue microarray containing advanced ovarian carcinoma tissues ( n  = 87) vs. normal ovarian tissues ( n  = 12).  g  Overall survival in advanced ovarian tumor patients having increased frequency of nuclear CHOP in CD8 +  TILs (CHOP high ) ( n  = 52) vs. those having low frequency of nuclear CHOP in CD8 +  TILs (CHOP low ) ( n  = 29) (logrank 4.39,  p  = 0.0361 using Gehan–Breslow–Wilcoxon test; cutoff was established as described in the Methods section). Studies were developed using the anti-CHOP antibody clone 9C8.  h  Percentage of CD8 +  TILs having nuclear CHOP (clone 9C8) in ovarian cancer patients that had optimal ( n  = 59) vs. suboptimal ( n  = 23) cytoreductive debulking surgery. Bar graphs represent mean value ± s.e.m., * p

    Journal: Nature Communications

    Article Title: ER stress-induced mediator C/EBP homologous protein thwarts effector T cell activity in tumors through T-bet repression

    doi: 10.1038/s41467-019-09263-1

    Figure Lengend Snippet: Increased Chop in CD8 + tumor-infiltrating T lymphocytes (TILs) correlates with poor survival in ovarian cancer. a Ddit3 mRNA levels in tumor-associated CD45 + CD8 + T cells (TILs) sorted from subcutaneous 3LL, EL-4, MCA-38, or B16 tumors and CD8 + T cells from the spleens of the same tumor-bearing mice (Tumor bearing) or tumor-free mice (Tumor free). Bar graphs show the mean ± s.e.m. ( n  = 5 mice/group). b Chop expression in CD8 + TILs from B16 melanoma tumors (left) and 3LL tumors (right), compared with splenic CD8 + T cells from the corresponding tumor-bearing mice. Chop was detected by fluorescence-activated cell sorter and levels indicated by mean fluorescence intensity (MFI). Representative findings from four repeats. c CHOP in CD8 + TILs from ovarian carcinoma patients (Ovarian Ca tumor, n  = 18) compared to peripheral blood CD8 + T cells from ovarian carcinoma patients (Ovarian Ca blood, n  = 11) or healthy controls (Healthy blood, n  = 6). d CHOP levels in autologous CD8 + TILs (Tumor) and peripheral blood CD8 + T cells (Blood) from ovarian carcinoma patients ( n  = 7). e Representative image (scale 10 μm) showing CHOP expression in CD8 + TILs from ovarian carcinoma patients compared to CD8 + T cells from healthy ovarian tissues. Isotype (red) or CHOP (red, tested by clone 9C8 (left) or polyclonal antibody R-20 (right)), CD8 (green) and DAPI (blue) were detected by confocal microscopy. f Percentage of nuclear CHOP + cells (clone 9C8) among tumor-associated CD8 + T lymphocytes in a tissue microarray containing advanced ovarian carcinoma tissues ( n  = 87) vs. normal ovarian tissues ( n  = 12). g Overall survival in advanced ovarian tumor patients having increased frequency of nuclear CHOP in CD8 + TILs (CHOP high ) ( n  = 52) vs. those having low frequency of nuclear CHOP in CD8 + TILs (CHOP low ) ( n  = 29) (logrank 4.39, p  = 0.0361 using Gehan–Breslow–Wilcoxon test; cutoff was established as described in the Methods section). Studies were developed using the anti-CHOP antibody clone 9C8. h Percentage of CD8 + TILs having nuclear CHOP (clone 9C8) in ovarian cancer patients that had optimal ( n  = 59) vs. suboptimal ( n  = 23) cytoreductive debulking surgery. Bar graphs represent mean value ± s.e.m., * p

    Article Snippet: Purified wild-type or Ddit3 −/− CD8+ T cells were activated with anti-CD3/CD28 for 72 h. Then, T cells were collected, washed, plated onto CellTak pre-coated wells (1 × 105 T cells/well), and subjected to Seahorse XF Cell Mito Stress Test or Seahorse XF Glycolysis Stress Test (both from Agilent) using specific non-buffered XF base mediums.

    Techniques: Mouse Assay, Expressing, Fluorescence, Confocal Microscopy, Microarray

    Perk regulates Chop expression in primed CD8 +  T cells and CD8 +  TILs.  a  Upper panel: Time-dependent induction of Chop in murine (left) and human (right) T cells primed in vitro. T cells were stimulated with anti-CD3/CD28 and collected at the indicated time points (0–72 h). Lower panel: Densitometry quantitation of immunoblots ( n  = 3).  b  Carboxyfluorescein succinimidyl ester-labeled Pmel CD8 +  T cells (CD90.1 + ) were transferred into wild-type mice (CD90.2 + ), followed or not by vaccination with gp100 25–33  plus IFA. On day 4, Chop levels by mean fluorescence intensity (MFI) (left) and percentage of Chop +  cells (right) were established by fluorescence-activated cell sorter (FACS) in gated CD8 +  CD90.1 +  T cells from lymph nodes of vaccinated vs. non-vaccinated mice ( n  = 3).  c  Left: Tauroursodeoxycholic acid (0.5 mM, at time 0) or Thapsigargin (100 nM, after 48 h) were added to CD8 +  T cells stimulated with plate-bond anti-CD3/CD28. Protein extracts were collected 72 h post-activation. Right: Quantitation of immunoblots ( n  = 3).  d  Unfolded protein response mediators Perk, Ire-1α, and Atf4 in stimulated murine (left) and human (right) T cells (0–72 h). Representative Immunoblot from  n  = 3.  e  CD8 +  T cells from  Eif2ak3 flox  or  Eif2ak3 T cell-KO  mice were primed with anti-CD3/CD28 for 0–72 h. Upper panel: Chop and Perk detected by immunoblotting; lower panel: Densitometry quantitation of immunoblots ( n  = 3).  f  Chop MFI levels in CD8 +  TILs from B16-bearing  Eif2ak3 flox  and  Eif2ak3 T cell-KO  mice ( n  = 3). Chop was detected in viable CD45 + CD8 +  TILs by FACS (left) and MFI values compiled (right).  g  Representative reactive oxygen species levels in murine and human DHE-labeled CD8 +  T cells activated with anti-CD3/CD28 and treated for 24 h with 5% cell-free ovarian ascites obtained from mice bearing ID8- Defb29 / Vegf-a  ovarian tumors or 5% primary ascites from patients with ovarian cancer, respectively ( n  = 4).  h  Murine CD8 +  T cells were primed with anti-CD3/CD28 for 48 h and then cultured with or without ID8- Defb29 / Vegf-a  cell-free ovarian tumors ascites for 24 h ( n  = 3).  i  CD8 +  T cells treated as in  h  were cultured in the presence or the absence of 2 mM L-NAC during the ascites treatment ( n  = 3). Bar graphs represent mean ± s.e.m., * p

    Journal: Nature Communications

    Article Title: ER stress-induced mediator C/EBP homologous protein thwarts effector T cell activity in tumors through T-bet repression

    doi: 10.1038/s41467-019-09263-1

    Figure Lengend Snippet: Perk regulates Chop expression in primed CD8 + T cells and CD8 + TILs. a Upper panel: Time-dependent induction of Chop in murine (left) and human (right) T cells primed in vitro. T cells were stimulated with anti-CD3/CD28 and collected at the indicated time points (0–72 h). Lower panel: Densitometry quantitation of immunoblots ( n  = 3). b Carboxyfluorescein succinimidyl ester-labeled Pmel CD8 + T cells (CD90.1 + ) were transferred into wild-type mice (CD90.2 + ), followed or not by vaccination with gp100 25–33 plus IFA. On day 4, Chop levels by mean fluorescence intensity (MFI) (left) and percentage of Chop + cells (right) were established by fluorescence-activated cell sorter (FACS) in gated CD8 + CD90.1 + T cells from lymph nodes of vaccinated vs. non-vaccinated mice ( n  = 3). c Left: Tauroursodeoxycholic acid (0.5 mM, at time 0) or Thapsigargin (100 nM, after 48 h) were added to CD8 + T cells stimulated with plate-bond anti-CD3/CD28. Protein extracts were collected 72 h post-activation. Right: Quantitation of immunoblots ( n  = 3). d Unfolded protein response mediators Perk, Ire-1α, and Atf4 in stimulated murine (left) and human (right) T cells (0–72 h). Representative Immunoblot from n  = 3. e CD8 + T cells from Eif2ak3 flox or Eif2ak3 T cell-KO mice were primed with anti-CD3/CD28 for 0–72 h. Upper panel: Chop and Perk detected by immunoblotting; lower panel: Densitometry quantitation of immunoblots ( n  = 3). f Chop MFI levels in CD8 + TILs from B16-bearing Eif2ak3 flox and Eif2ak3 T cell-KO mice ( n  = 3). Chop was detected in viable CD45 + CD8 + TILs by FACS (left) and MFI values compiled (right). g Representative reactive oxygen species levels in murine and human DHE-labeled CD8 + T cells activated with anti-CD3/CD28 and treated for 24 h with 5% cell-free ovarian ascites obtained from mice bearing ID8- Defb29 / Vegf-a ovarian tumors or 5% primary ascites from patients with ovarian cancer, respectively ( n  = 4). h Murine CD8 + T cells were primed with anti-CD3/CD28 for 48 h and then cultured with or without ID8- Defb29 / Vegf-a cell-free ovarian tumors ascites for 24 h ( n  = 3). i CD8 + T cells treated as in h were cultured in the presence or the absence of 2 mM L-NAC during the ascites treatment ( n  = 3). Bar graphs represent mean ± s.e.m., * p

    Article Snippet: Purified wild-type or Ddit3 −/− CD8+ T cells were activated with anti-CD3/CD28 for 72 h. Then, T cells were collected, washed, plated onto CellTak pre-coated wells (1 × 105 T cells/well), and subjected to Seahorse XF Cell Mito Stress Test or Seahorse XF Glycolysis Stress Test (both from Agilent) using specific non-buffered XF base mediums.

    Techniques: Expressing, In Vitro, Quantitation Assay, Western Blot, Labeling, Mouse Assay, Immunofluorescence, Fluorescence, FACS, Activation Assay, Cell Culture

    Chop negatively regulates T-bet expression.  a  Time-dependent expression (upper panel) and corresponding densitometry quantitation (lower panel) of T-bet in primed wild-type and  Ddit3 −/− CD8 +  T cells. Left: protein level (0–72 h); right:  Tbx21  mRNA levels 48 h post-activation. CD8 +  T cells were stimulated with plate-bound anti-CD3/CD28 ( n  = 3).  b Tbx21  and  Ifng  mRNA expression in activated CD8 +  T cells infected with control retrovirus (Retro-Ctrl) or  Ddit3 -expressing retrovirus (Retro-Chop). Cells were primed for 48 h and then infected for additional 48 h in the presence of the stimulating anti-CD3/CD28 antibodies ( n  = 4).  c Ifng ,  Il12b2 ,  Cbfa3 , and  Cxcr3  mRNA levels in control vs.  Ddit3 −/− CD8 +  T cells primed as in  a  ( n  = 5).  d  Predicted Chop-binding site in the  Tbx21  promoter region (GGGTGCAATCTTC).  e  Chromatin immunoprecipitation assay for the endogenous binding of Chop to  Tbx21  promoter in primed wild-type or  Ddit3 −/− CD8 +  T cells. Chop-binding activity was measured by real-time quantitative PCR, compared with IgG binding activity after normalizing to the activity of anti-H3 ( n  = 4).  f  A dual luciferase system composed of 2x-CRE containing Firefly luciferase reporter and the control Renilla luciferase reporter was transfected into 293T cells in combination with  Ddit3 -expressing or control vectors.  n  = 4 experimental repeats.  g  Expression of Chop (left) and T-bet (right) by fluorescence-activated cell sorter (FACS) upon transduction of primed CD8 +  T cells with green fluorescent protein (GFP)-coding retroviruses containing control or 8x-CRE sequences. Cells were primed for 48 h and then infected for another 48 h in the presence of the stimulating anti-CD3/CD28 antibodies plus interleukin (IL)-2 (50 U/ml).  n  = 3 independent repeats.  h  Interferon-γ (IFNγ) levels in primed CD8 +  T cells transduced with: (1) GFP/CD90.1-expressing control virus (Ctrl); (2) Chop/CD90.1-expressing virus and GFP-expressing control virus (Chop); (3) CD90.1-expressing control virus and T-bet/GFP-expressing virus (T-bet); or (4) Chop/CD90.1-expressing virus and T-bet/GFP-expressing virus (Chop/T-bet). Cells were primed for 24 h and then transduced for additional 72 h in the presence of stimulating antibodies plus IL-2 (50 U/ml). Then IFNγ levels were detected by FACS in gated CD90.1 + GFP +  cells. Right: Representative FACS result; left: Merged results from three independent experiments. In the bar graphs showing mean ± s.e.m., * p

    Journal: Nature Communications

    Article Title: ER stress-induced mediator C/EBP homologous protein thwarts effector T cell activity in tumors through T-bet repression

    doi: 10.1038/s41467-019-09263-1

    Figure Lengend Snippet: Chop negatively regulates T-bet expression. a Time-dependent expression (upper panel) and corresponding densitometry quantitation (lower panel) of T-bet in primed wild-type and Ddit3 −/− CD8 + T cells. Left: protein level (0–72 h); right: Tbx21 mRNA levels 48 h post-activation. CD8 + T cells were stimulated with plate-bound anti-CD3/CD28 ( n  = 3). b Tbx21 and Ifng mRNA expression in activated CD8 + T cells infected with control retrovirus (Retro-Ctrl) or Ddit3 -expressing retrovirus (Retro-Chop). Cells were primed for 48 h and then infected for additional 48 h in the presence of the stimulating anti-CD3/CD28 antibodies ( n  = 4). c Ifng , Il12b2 , Cbfa3 , and Cxcr3 mRNA levels in control vs. Ddit3 −/− CD8 + T cells primed as in a ( n  = 5). d Predicted Chop-binding site in the Tbx21 promoter region (GGGTGCAATCTTC). e Chromatin immunoprecipitation assay for the endogenous binding of Chop to Tbx21 promoter in primed wild-type or Ddit3 −/− CD8 + T cells. Chop-binding activity was measured by real-time quantitative PCR, compared with IgG binding activity after normalizing to the activity of anti-H3 ( n  = 4). f A dual luciferase system composed of 2x-CRE containing Firefly luciferase reporter and the control Renilla luciferase reporter was transfected into 293T cells in combination with Ddit3 -expressing or control vectors. n  = 4 experimental repeats. g Expression of Chop (left) and T-bet (right) by fluorescence-activated cell sorter (FACS) upon transduction of primed CD8 + T cells with green fluorescent protein (GFP)-coding retroviruses containing control or 8x-CRE sequences. Cells were primed for 48 h and then infected for another 48 h in the presence of the stimulating anti-CD3/CD28 antibodies plus interleukin (IL)-2 (50 U/ml). n  = 3 independent repeats. h Interferon-γ (IFNγ) levels in primed CD8 + T cells transduced with: (1) GFP/CD90.1-expressing control virus (Ctrl); (2) Chop/CD90.1-expressing virus and GFP-expressing control virus (Chop); (3) CD90.1-expressing control virus and T-bet/GFP-expressing virus (T-bet); or (4) Chop/CD90.1-expressing virus and T-bet/GFP-expressing virus (Chop/T-bet). Cells were primed for 24 h and then transduced for additional 72 h in the presence of stimulating antibodies plus IL-2 (50 U/ml). Then IFNγ levels were detected by FACS in gated CD90.1 + GFP + cells. Right: Representative FACS result; left: Merged results from three independent experiments. In the bar graphs showing mean ± s.e.m., * p

    Article Snippet: Purified wild-type or Ddit3 −/− CD8+ T cells were activated with anti-CD3/CD28 for 72 h. Then, T cells were collected, washed, plated onto CellTak pre-coated wells (1 × 105 T cells/well), and subjected to Seahorse XF Cell Mito Stress Test or Seahorse XF Glycolysis Stress Test (both from Agilent) using specific non-buffered XF base mediums.

    Techniques: Expressing, Quantitation Assay, Activation Assay, Infection, Binding Assay, Chromatin Immunoprecipitation, Activity Assay, Real-time Polymerase Chain Reaction, Luciferase, Transfection, Fluorescence, FACS, Transduction

    Chop negatively regulates effector CD8 +  T cell activity.  a  Gene set enrichment analysis was performed to determine the specific enrichment in effector CD8 +  T cell gene signature in primed wild-type or  Ddit3 −/− Pmel CD8 +  T cells.  b  Heatmap showing the expression of selective effector function-related transcripts in primed wild-type vs.  Ddit3 −/− Pmel CD8 +  T cells, as described in the Methods section.  c  Carboxyfluorescein succinimidyl ester (CFSE)-labeled wild-type or  Ddit3 −/− CD8 +  T cells were stimulated with anti-CD3/CD28 and proliferation tested after 72 h by fluorescence-activated cell sorter (FACS). Left: representative histogram of T cell proliferation (n = 6); right: T cell proliferation rates under different concentrations of anti-CD3/CD28 (µg/ml) ( n  = 6).  d  Granzyme B protein (upper panel, long- and short-time exposure) and  Gzmb  mRNA levels (lower panel) in wild-type or  Ddit3 −/− CD8 +  T cells primed with anti-CD3/CD28 for 72 h ( n  = 5).  e  Percentage of IFNγ +  cells in wild-type or  Ddit3 −/− CD8 +  T cells primed as in ( d ). Right: representative FACS findings; left: merged percentage values from  n  = 4.  f  Extracellular acidification rate (ECAR) of wild-type or  Ddit3 −/− CD8 +  T cells primed as in  d  upon glycolysis stress analysis ( n  = 3).  g  Oxygen consumption rate (OCR) of wild-type or  Ddit3 −/− CD8 +  T cells activated as in  d  after mitochondrial stress analysis ( n  = 3).  h ,  i  Percentage of IFNγ +  cells in CD8 +  T cells primed in the presence of Tauroursodeoxycholic acid ( n  = 4) ( h ) or from  Eif2ak3 flox  or  Eif2ak3 T cell-KO  mice ( n  = 5) ( i ).  j  In vitro cytotoxicity of wild-type and  Ddit3 −/− CD8 +  Tcells was assessed by measuring EL-4 cell proportion after co-culturing gp100 25–33  pre-activated wild-type or  Ddit3 −/− Pmel CD8 +  T cells with EL-4 cells loaded with gp100 25–33  or control peptide (high or low CFSE, respectively). Cytotoxicity was evaluated after 24 h of co-culture by FACS. Right: representative FACS result; left: merged results from  n  = 5.  k  Representative result of CD44 high  CD62L −  effector memory cells in wild-type or  Ddit3 -null CD8 +  T cells primed as in  d  ( n  = 10). Bar graphs represent mean ± s.e.m., * p

    Journal: Nature Communications

    Article Title: ER stress-induced mediator C/EBP homologous protein thwarts effector T cell activity in tumors through T-bet repression

    doi: 10.1038/s41467-019-09263-1

    Figure Lengend Snippet: Chop negatively regulates effector CD8 + T cell activity. a Gene set enrichment analysis was performed to determine the specific enrichment in effector CD8 + T cell gene signature in primed wild-type or Ddit3 −/− Pmel CD8 + T cells. b Heatmap showing the expression of selective effector function-related transcripts in primed wild-type vs. Ddit3 −/− Pmel CD8 + T cells, as described in the Methods section. c Carboxyfluorescein succinimidyl ester (CFSE)-labeled wild-type or Ddit3 −/− CD8 + T cells were stimulated with anti-CD3/CD28 and proliferation tested after 72 h by fluorescence-activated cell sorter (FACS). Left: representative histogram of T cell proliferation (n = 6); right: T cell proliferation rates under different concentrations of anti-CD3/CD28 (µg/ml) ( n  = 6). d Granzyme B protein (upper panel, long- and short-time exposure) and Gzmb mRNA levels (lower panel) in wild-type or Ddit3 −/− CD8 + T cells primed with anti-CD3/CD28 for 72 h ( n  = 5). e Percentage of IFNγ + cells in wild-type or Ddit3 −/− CD8 + T cells primed as in ( d ). Right: representative FACS findings; left: merged percentage values from n  = 4. f Extracellular acidification rate (ECAR) of wild-type or Ddit3 −/− CD8 + T cells primed as in d upon glycolysis stress analysis ( n  = 3). g Oxygen consumption rate (OCR) of wild-type or Ddit3 −/− CD8 + T cells activated as in d after mitochondrial stress analysis ( n  = 3). h , i Percentage of IFNγ + cells in CD8 + T cells primed in the presence of Tauroursodeoxycholic acid ( n  = 4) ( h ) or from Eif2ak3 flox or Eif2ak3 T cell-KO mice ( n  = 5) ( i ). j In vitro cytotoxicity of wild-type and Ddit3 −/− CD8 + Tcells was assessed by measuring EL-4 cell proportion after co-culturing gp100 25–33 pre-activated wild-type or Ddit3 −/− Pmel CD8 + T cells with EL-4 cells loaded with gp100 25–33 or control peptide (high or low CFSE, respectively). Cytotoxicity was evaluated after 24 h of co-culture by FACS. Right: representative FACS result; left: merged results from n  = 5. k Representative result of CD44 high CD62L − effector memory cells in wild-type or Ddit3 -null CD8 + T cells primed as in d ( n  = 10). Bar graphs represent mean ± s.e.m., * p

    Article Snippet: Purified wild-type or Ddit3 −/− CD8+ T cells were activated with anti-CD3/CD28 for 72 h. Then, T cells were collected, washed, plated onto CellTak pre-coated wells (1 × 105 T cells/well), and subjected to Seahorse XF Cell Mito Stress Test or Seahorse XF Glycolysis Stress Test (both from Agilent) using specific non-buffered XF base mediums.

    Techniques: Activity Assay, Expressing, Labeling, Fluorescence, FACS, Mouse Assay, In Vitro, Co-Culture Assay

    The genomic map of total lncRNAs and deregulated LncRNAs in chromosomes of mouse. The distribution of LncRNAs in chromosomes of mouse is marked in blue. The upregulated LncRNAs are highlighed in red and the downregulated lncRNAs are highlighted in green. The length of the bars represents the folds of LncRNAs expression change. Microarray assays revealed the existence of a total of 20073 LncRNAs in mouse livers. The numbers and symbols represent chromosome numbers.

    Journal: PLoS ONE

    Article Title: Silencing of Long Noncoding RNA AK139328 Attenuates Ischemia/Reperfusion Injury in Mouse Livers

    doi: 10.1371/journal.pone.0080817

    Figure Lengend Snippet: The genomic map of total lncRNAs and deregulated LncRNAs in chromosomes of mouse. The distribution of LncRNAs in chromosomes of mouse is marked in blue. The upregulated LncRNAs are highlighed in red and the downregulated lncRNAs are highlighted in green. The length of the bars represents the folds of LncRNAs expression change. Microarray assays revealed the existence of a total of 20073 LncRNAs in mouse livers. The numbers and symbols represent chromosome numbers.

    Article Snippet: Overall, real time PCR assays validated the accuracy of LncRNA profile determined by microarray analysis.

    Techniques: Expressing, Microarray

    Arabidopsis knock-out mutants show altered susceptibility to Myzus persicae and Myzus cerasi . Four-week old plants were exposed to two adult aphids and nymph production was counted after 10 days. Average nymph production was calculated from three independent replicated experiments, with 10 plants per replicate per treatment. Error bars indicate standard error. The two-tailed Student's t -test was used for statistical analyses (*** indicates p-value

    Journal: PLoS Pathogens

    Article Title: Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance

    doi: 10.1371/journal.ppat.1004918

    Figure Lengend Snippet: Arabidopsis knock-out mutants show altered susceptibility to Myzus persicae and Myzus cerasi . Four-week old plants were exposed to two adult aphids and nymph production was counted after 10 days. Average nymph production was calculated from three independent replicated experiments, with 10 plants per replicate per treatment. Error bars indicate standard error. The two-tailed Student's t -test was used for statistical analyses (*** indicates p-value

    Article Snippet: Arabidopsis transcriptome analyses reveal an enhanced response to interaction with M . persicae versus interaction with M . cerasi and R . padi To further investigate Arabidopsis host, poor-host, and non-host responses to M . persicae , M . cerasi and R . padi , respectively, we performed microarray analyses using Agilent Arabidopsis 4×44K arrays.

    Techniques: Knock-Out, Two Tailed Test

    Overlap of Arabidopsis differentially expressed genes across different aphid interactions. Venn diagram analyses of 874 differentially expressed as determined by one-way ANOVA (Bonferroni correction, p-value ≤ 0.05) across different aphid interactions and timepoints. (A) Venn diagrams showing the numbers of genes that are down-regulated during different aphid interactions at 3h, 6h and 24h post aphid exposure. (B) Venn diagrams showing the numbers of genes that are up-regulated during different aphid interactions at 3h, 6h and 24h post aphid exposure. Mc indicates Myzus cerasi , Mp indicates M . persicae and Rp indicates Rhopalosiphum padi .

    Journal: PLoS Pathogens

    Article Title: Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance

    doi: 10.1371/journal.ppat.1004918

    Figure Lengend Snippet: Overlap of Arabidopsis differentially expressed genes across different aphid interactions. Venn diagram analyses of 874 differentially expressed as determined by one-way ANOVA (Bonferroni correction, p-value ≤ 0.05) across different aphid interactions and timepoints. (A) Venn diagrams showing the numbers of genes that are down-regulated during different aphid interactions at 3h, 6h and 24h post aphid exposure. (B) Venn diagrams showing the numbers of genes that are up-regulated during different aphid interactions at 3h, 6h and 24h post aphid exposure. Mc indicates Myzus cerasi , Mp indicates M . persicae and Rp indicates Rhopalosiphum padi .

    Article Snippet: Arabidopsis transcriptome analyses reveal an enhanced response to interaction with M . persicae versus interaction with M . cerasi and R . padi To further investigate Arabidopsis host, poor-host, and non-host responses to M . persicae , M . cerasi and R . padi , respectively, we performed microarray analyses using Agilent Arabidopsis 4×44K arrays.

    Techniques:

    Expression profile of Arabidopsis genes showing opposite gene expression changes during aphid host and non-host interactions. Using volcano plot analyses (fold change ≥ 2.0, p-value ≤ 0.05) in GeneSpring, we identified 11 genes with statistically significant opposite gene expression changes during different aphid interactions. Hierarchical gene tree cluster analysis in GeneSpring generated an overview of the expression changes of these 11 genes 3h, 6h and 24h after aphid exposure. Low gene expression levels are indicated by blue color and high gene expression levels are indicated by red color.

    Journal: PLoS Pathogens

    Article Title: Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance

    doi: 10.1371/journal.ppat.1004918

    Figure Lengend Snippet: Expression profile of Arabidopsis genes showing opposite gene expression changes during aphid host and non-host interactions. Using volcano plot analyses (fold change ≥ 2.0, p-value ≤ 0.05) in GeneSpring, we identified 11 genes with statistically significant opposite gene expression changes during different aphid interactions. Hierarchical gene tree cluster analysis in GeneSpring generated an overview of the expression changes of these 11 genes 3h, 6h and 24h after aphid exposure. Low gene expression levels are indicated by blue color and high gene expression levels are indicated by red color.

    Article Snippet: Arabidopsis transcriptome analyses reveal an enhanced response to interaction with M . persicae versus interaction with M . cerasi and R . padi To further investigate Arabidopsis host, poor-host, and non-host responses to M . persicae , M . cerasi and R . padi , respectively, we performed microarray analyses using Agilent Arabidopsis 4×44K arrays.

    Techniques: Expressing, Generated

    Aphid probing during host and non-host interactions. (A) Autofluorescence around aphid probe sites, indicated by white arrows, was visualized using laser confocal microscopy. Scale bars 100μm. (B) Aphid colonization of Arabidopsis by Myzus persicae , M . cerasi and Rhopalosiphum padi . Graph shows the mean number of nymphs produced after two weeks on wild type Col-0 plants. Error bars indicate standard error. A Student’s t -test was used for statistical analysis of M . persicae versus M . cerasi progeny (*** indicates p-value

    Journal: PLoS Pathogens

    Article Title: Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance

    doi: 10.1371/journal.ppat.1004918

    Figure Lengend Snippet: Aphid probing during host and non-host interactions. (A) Autofluorescence around aphid probe sites, indicated by white arrows, was visualized using laser confocal microscopy. Scale bars 100μm. (B) Aphid colonization of Arabidopsis by Myzus persicae , M . cerasi and Rhopalosiphum padi . Graph shows the mean number of nymphs produced after two weeks on wild type Col-0 plants. Error bars indicate standard error. A Student’s t -test was used for statistical analysis of M . persicae versus M . cerasi progeny (*** indicates p-value

    Article Snippet: Arabidopsis transcriptome analyses reveal an enhanced response to interaction with M . persicae versus interaction with M . cerasi and R . padi To further investigate Arabidopsis host, poor-host, and non-host responses to M . persicae , M . cerasi and R . padi , respectively, we performed microarray analyses using Agilent Arabidopsis 4×44K arrays.

    Techniques: Confocal Microscopy, Produced

    Arabidopsis knock-out mutants show altered susceptibility to Myzus persicae , Myzus cerasi and Rhopalosiphum padi . (A) Graph showing R . padi aphid survival on the control (Col-0) and a vsp1 mutant line over 6 days. Five adult aphids were placed on four-week old plants and survival was monitored the following 6 days. Three independent biological replicates were carried out, with 10 plants per replicate. Error bars indicate standard error. (B) Graph shows the percentage of R . padi survival between day 3 and 4 on a vsp1 mutant line and Col-0 wild-type plants. Data is from the same experiment as described in (A). The two-tailed Student's t -test was used for statistical analyses (*** indicates p-value

    Journal: PLoS Pathogens

    Article Title: Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance

    doi: 10.1371/journal.ppat.1004918

    Figure Lengend Snippet: Arabidopsis knock-out mutants show altered susceptibility to Myzus persicae , Myzus cerasi and Rhopalosiphum padi . (A) Graph showing R . padi aphid survival on the control (Col-0) and a vsp1 mutant line over 6 days. Five adult aphids were placed on four-week old plants and survival was monitored the following 6 days. Three independent biological replicates were carried out, with 10 plants per replicate. Error bars indicate standard error. (B) Graph shows the percentage of R . padi survival between day 3 and 4 on a vsp1 mutant line and Col-0 wild-type plants. Data is from the same experiment as described in (A). The two-tailed Student's t -test was used for statistical analyses (*** indicates p-value

    Article Snippet: Arabidopsis transcriptome analyses reveal an enhanced response to interaction with M . persicae versus interaction with M . cerasi and R . padi To further investigate Arabidopsis host, poor-host, and non-host responses to M . persicae , M . cerasi and R . padi , respectively, we performed microarray analyses using Agilent Arabidopsis 4×44K arrays.

    Techniques: Knock-Out, Mutagenesis, Two Tailed Test

    Clustering of 874 differentially expressed Arabidopsis genes during host and non-host interactions with aphids. Using one-way ANOVA in GeneSpring (Bonferroni correction, p-value ≤ 0.05), we identified 874 genes that display significant differential expression across different aphid treatments and timepoints. Hierarchical gene tree cluster analysis of these 874 genes using GeneSpring software identified three main clusters of genes (A, B and C) according to their expression profiles across all treatments and timepoints. Low gene expression levels are indicated by blue colour and high gene expression levels are indicated by red colour. Mc indicates Myzus cerasi , Mp indicates M . persicae and Rp indicates Rhopalosiphum padi .

    Journal: PLoS Pathogens

    Article Title: Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance

    doi: 10.1371/journal.ppat.1004918

    Figure Lengend Snippet: Clustering of 874 differentially expressed Arabidopsis genes during host and non-host interactions with aphids. Using one-way ANOVA in GeneSpring (Bonferroni correction, p-value ≤ 0.05), we identified 874 genes that display significant differential expression across different aphid treatments and timepoints. Hierarchical gene tree cluster analysis of these 874 genes using GeneSpring software identified three main clusters of genes (A, B and C) according to their expression profiles across all treatments and timepoints. Low gene expression levels are indicated by blue colour and high gene expression levels are indicated by red colour. Mc indicates Myzus cerasi , Mp indicates M . persicae and Rp indicates Rhopalosiphum padi .

    Article Snippet: Arabidopsis transcriptome analyses reveal an enhanced response to interaction with M . persicae versus interaction with M . cerasi and R . padi To further investigate Arabidopsis host, poor-host, and non-host responses to M . persicae , M . cerasi and R . padi , respectively, we performed microarray analyses using Agilent Arabidopsis 4×44K arrays.

    Techniques: Expressing, Software

    Arabidopsis atrbohD-3 and atrbohF-3 knock-out mutants show reduced non-host resistance and enhanced susceptibility to aphids. (A) Myzus persicae (Mp) and M . cerasi (Mc) performance on Arabidopsis atrbohD-3 and atrbohF-3 knock-out lines. Four-week old plants were exposed to two adult aphids and nymph production was counted after 10 days. Average nymph production for M . persicae and M . cerasi was calculated from three independent replicated experiments, with 10 plants per replicate per treatment. (B) Graph shows R . padi aphid survival on control (Col-0) and Arabidopsis atrbohD-3 and atrbohF-3 knock-out lines over 6 days. Three independent biological replicates were carried out, with 10 plants per replicate. Error bars indicate standard error. (C) Rhopalosiphum padi (Rp) survival on Arabidopsis atrbohD-3 and atrbohF-3 mutants and Col-0 wild-type plants between 3 and 4 days of the experiment. The two-tailed Student's t -test was used for statistical analyses (*** indicates p-value

    Journal: PLoS Pathogens

    Article Title: Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance

    doi: 10.1371/journal.ppat.1004918

    Figure Lengend Snippet: Arabidopsis atrbohD-3 and atrbohF-3 knock-out mutants show reduced non-host resistance and enhanced susceptibility to aphids. (A) Myzus persicae (Mp) and M . cerasi (Mc) performance on Arabidopsis atrbohD-3 and atrbohF-3 knock-out lines. Four-week old plants were exposed to two adult aphids and nymph production was counted after 10 days. Average nymph production for M . persicae and M . cerasi was calculated from three independent replicated experiments, with 10 plants per replicate per treatment. (B) Graph shows R . padi aphid survival on control (Col-0) and Arabidopsis atrbohD-3 and atrbohF-3 knock-out lines over 6 days. Three independent biological replicates were carried out, with 10 plants per replicate. Error bars indicate standard error. (C) Rhopalosiphum padi (Rp) survival on Arabidopsis atrbohD-3 and atrbohF-3 mutants and Col-0 wild-type plants between 3 and 4 days of the experiment. The two-tailed Student's t -test was used for statistical analyses (*** indicates p-value

    Article Snippet: Arabidopsis transcriptome analyses reveal an enhanced response to interaction with M . persicae versus interaction with M . cerasi and R . padi To further investigate Arabidopsis host, poor-host, and non-host responses to M . persicae , M . cerasi and R . padi , respectively, we performed microarray analyses using Agilent Arabidopsis 4×44K arrays.

    Techniques: Knock-Out, Two Tailed Test