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  • 85
    TaKaRa egfp open reading frame orf
    Modulation of rostro-caudal and dorso-ventral axis specification induces the development of PHOX2B -expressing NCCs from hPSCs. ( a ) A diagram of the culture conditions for the modification of rostro-caudal and dorso-ventral axis specification of hPSCs. ( b ) A heat map image showing the percentage of <t>eGFP</t> + cells on day 10 of differentiation using KhES1 PHOX2B::eGFP under various conditions. ( c ) Representative FCM plots of day 10 KhES1 PHOX2B::eGFP-derived aggregates under the indicated conditions (i–iv) of ( b ). ( d ) <t>RT-PCR</t> analyses for PHOX2B , SOX1 , PAX6 , SOX10 , FOXD3 , HOXB1 , HOXB2 , HOXB4 , HOXB6 , HOXB8 and HOXC9 in day 10 aggregates under conditions (i–iv). The right diagram shows the expression pattern of HOX genes in the rhombomere (r1–8) and the spinal cord (cervical and thoracic) region. SB = SB431542, CHIR = CHIR 99021, RA = retinoic acid, Pur = Purmorphamine, BMP = BMP4, NT = neural tube, NCC = neural crest cell, HB = hindbrain, SC = spinal cord.
    Egfp Open Reading Frame Orf, supplied by TaKaRa, used in various techniques. Bioz Stars score: 85/100, based on 42 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/egfp open reading frame orf/product/TaKaRa
    Average 85 stars, based on 42 article reviews
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    egfp open reading frame orf - by Bioz Stars, 2020-08
    85/100 stars
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    92
    OriGene smoc2 open reading frame orf
    Modulation of rostro-caudal and dorso-ventral axis specification induces the development of PHOX2B -expressing NCCs from hPSCs. ( a ) A diagram of the culture conditions for the modification of rostro-caudal and dorso-ventral axis specification of hPSCs. ( b ) A heat map image showing the percentage of <t>eGFP</t> + cells on day 10 of differentiation using KhES1 PHOX2B::eGFP under various conditions. ( c ) Representative FCM plots of day 10 KhES1 PHOX2B::eGFP-derived aggregates under the indicated conditions (i–iv) of ( b ). ( d ) <t>RT-PCR</t> analyses for PHOX2B , SOX1 , PAX6 , SOX10 , FOXD3 , HOXB1 , HOXB2 , HOXB4 , HOXB6 , HOXB8 and HOXC9 in day 10 aggregates under conditions (i–iv). The right diagram shows the expression pattern of HOX genes in the rhombomere (r1–8) and the spinal cord (cervical and thoracic) region. SB = SB431542, CHIR = CHIR 99021, RA = retinoic acid, Pur = Purmorphamine, BMP = BMP4, NT = neural tube, NCC = neural crest cell, HB = hindbrain, SC = spinal cord.
    Smoc2 Open Reading Frame Orf, supplied by OriGene, used in various techniques. Bioz Stars score: 92/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 12 article reviews
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    smoc2 open reading frame orf - by Bioz Stars, 2020-08
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    93
    Thermo Fisher ftt2 open reading frame orf
    Modulation of rostro-caudal and dorso-ventral axis specification induces the development of PHOX2B -expressing NCCs from hPSCs. ( a ) A diagram of the culture conditions for the modification of rostro-caudal and dorso-ventral axis specification of hPSCs. ( b ) A heat map image showing the percentage of <t>eGFP</t> + cells on day 10 of differentiation using KhES1 PHOX2B::eGFP under various conditions. ( c ) Representative FCM plots of day 10 KhES1 PHOX2B::eGFP-derived aggregates under the indicated conditions (i–iv) of ( b ). ( d ) <t>RT-PCR</t> analyses for PHOX2B , SOX1 , PAX6 , SOX10 , FOXD3 , HOXB1 , HOXB2 , HOXB4 , HOXB6 , HOXB8 and HOXC9 in day 10 aggregates under conditions (i–iv). The right diagram shows the expression pattern of HOX genes in the rhombomere (r1–8) and the spinal cord (cervical and thoracic) region. SB = SB431542, CHIR = CHIR 99021, RA = retinoic acid, Pur = Purmorphamine, BMP = BMP4, NT = neural tube, NCC = neural crest cell, HB = hindbrain, SC = spinal cord.
    Ftt2 Open Reading Frame Orf, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ftt2 open reading frame orf - by Bioz Stars, 2020-08
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    85
    Genecopoeia apol1 open reading frame orf
    Modulation of rostro-caudal and dorso-ventral axis specification induces the development of PHOX2B -expressing NCCs from hPSCs. ( a ) A diagram of the culture conditions for the modification of rostro-caudal and dorso-ventral axis specification of hPSCs. ( b ) A heat map image showing the percentage of <t>eGFP</t> + cells on day 10 of differentiation using KhES1 PHOX2B::eGFP under various conditions. ( c ) Representative FCM plots of day 10 KhES1 PHOX2B::eGFP-derived aggregates under the indicated conditions (i–iv) of ( b ). ( d ) <t>RT-PCR</t> analyses for PHOX2B , SOX1 , PAX6 , SOX10 , FOXD3 , HOXB1 , HOXB2 , HOXB4 , HOXB6 , HOXB8 and HOXC9 in day 10 aggregates under conditions (i–iv). The right diagram shows the expression pattern of HOX genes in the rhombomere (r1–8) and the spinal cord (cervical and thoracic) region. SB = SB431542, CHIR = CHIR 99021, RA = retinoic acid, Pur = Purmorphamine, BMP = BMP4, NT = neural tube, NCC = neural crest cell, HB = hindbrain, SC = spinal cord.
    Apol1 Open Reading Frame Orf, supplied by Genecopoeia, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 85 stars, based on 6 article reviews
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    apol1 open reading frame orf - by Bioz Stars, 2020-08
    85/100 stars
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    85
    Thermo Fisher lrk 1 open reading frame orf
    Modulation of rostro-caudal and dorso-ventral axis specification induces the development of PHOX2B -expressing NCCs from hPSCs. ( a ) A diagram of the culture conditions for the modification of rostro-caudal and dorso-ventral axis specification of hPSCs. ( b ) A heat map image showing the percentage of <t>eGFP</t> + cells on day 10 of differentiation using KhES1 PHOX2B::eGFP under various conditions. ( c ) Representative FCM plots of day 10 KhES1 PHOX2B::eGFP-derived aggregates under the indicated conditions (i–iv) of ( b ). ( d ) <t>RT-PCR</t> analyses for PHOX2B , SOX1 , PAX6 , SOX10 , FOXD3 , HOXB1 , HOXB2 , HOXB4 , HOXB6 , HOXB8 and HOXC9 in day 10 aggregates under conditions (i–iv). The right diagram shows the expression pattern of HOX genes in the rhombomere (r1–8) and the spinal cord (cervical and thoracic) region. SB = SB431542, CHIR = CHIR 99021, RA = retinoic acid, Pur = Purmorphamine, BMP = BMP4, NT = neural tube, NCC = neural crest cell, HB = hindbrain, SC = spinal cord.
    Lrk 1 Open Reading Frame Orf, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 85 stars, based on 3 article reviews
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    lrk 1 open reading frame orf - by Bioz Stars, 2020-08
    85/100 stars
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    94
    Pacific Biosciences open reading frame
    Modulation of rostro-caudal and dorso-ventral axis specification induces the development of PHOX2B -expressing NCCs from hPSCs. ( a ) A diagram of the culture conditions for the modification of rostro-caudal and dorso-ventral axis specification of hPSCs. ( b ) A heat map image showing the percentage of <t>eGFP</t> + cells on day 10 of differentiation using KhES1 PHOX2B::eGFP under various conditions. ( c ) Representative FCM plots of day 10 KhES1 PHOX2B::eGFP-derived aggregates under the indicated conditions (i–iv) of ( b ). ( d ) <t>RT-PCR</t> analyses for PHOX2B , SOX1 , PAX6 , SOX10 , FOXD3 , HOXB1 , HOXB2 , HOXB4 , HOXB6 , HOXB8 and HOXC9 in day 10 aggregates under conditions (i–iv). The right diagram shows the expression pattern of HOX genes in the rhombomere (r1–8) and the spinal cord (cervical and thoracic) region. SB = SB431542, CHIR = CHIR 99021, RA = retinoic acid, Pur = Purmorphamine, BMP = BMP4, NT = neural tube, NCC = neural crest cell, HB = hindbrain, SC = spinal cord.
    Open Reading Frame, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 94/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 94 stars, based on 5 article reviews
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    open reading frame - by Bioz Stars, 2020-08
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    85
    Sigma-Genosys open reading frame orfs
    Modulation of rostro-caudal and dorso-ventral axis specification induces the development of PHOX2B -expressing NCCs from hPSCs. ( a ) A diagram of the culture conditions for the modification of rostro-caudal and dorso-ventral axis specification of hPSCs. ( b ) A heat map image showing the percentage of <t>eGFP</t> + cells on day 10 of differentiation using KhES1 PHOX2B::eGFP under various conditions. ( c ) Representative FCM plots of day 10 KhES1 PHOX2B::eGFP-derived aggregates under the indicated conditions (i–iv) of ( b ). ( d ) <t>RT-PCR</t> analyses for PHOX2B , SOX1 , PAX6 , SOX10 , FOXD3 , HOXB1 , HOXB2 , HOXB4 , HOXB6 , HOXB8 and HOXC9 in day 10 aggregates under conditions (i–iv). The right diagram shows the expression pattern of HOX genes in the rhombomere (r1–8) and the spinal cord (cervical and thoracic) region. SB = SB431542, CHIR = CHIR 99021, RA = retinoic acid, Pur = Purmorphamine, BMP = BMP4, NT = neural tube, NCC = neural crest cell, HB = hindbrain, SC = spinal cord.
    Open Reading Frame Orfs, supplied by Sigma-Genosys, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 85 stars, based on 4 article reviews
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    open reading frame orfs - by Bioz Stars, 2020-08
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    85
    OriGene nrac open reading frame
    <t>Nrac</t> localizes to the plasma membrane. A) Predicted transmembrane domains. Fluorescence imaging of HEK293 cells transfected with plasmids encoding B) LCK-tRFP and C) <t>Nrac-GFP</t> and D) Merged picture. E) Immunostaining with a primary antibody against Nrac, visualized by an Alexa Fluor 488-conjugated secondary antibody, F) Hoechst staining for nuclei, and G) merged picture, in paraffin-embedded sections of mouse white adipose tissue.
    Nrac Open Reading Frame, supplied by OriGene, used in various techniques. Bioz Stars score: 85/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 85 stars, based on 9 article reviews
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    nrac open reading frame - by Bioz Stars, 2020-08
    85/100 stars
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    85
    OriGene hkat open reading frame
    <t>Hkat</t> tissue expression pattern and subcellular localization. A) Hkat is expression in both white adipose tissue and brown adipose tissue, but is highest expressed in heart and kidney. B) Hkat is localized to the plasma membrane. Fluorescence imaging of HEK 293 cells transfected with plasmids encoding B) LCK-tRFP and C) <t>Hkat-GFP</t> and D) Merged picture.
    Hkat Open Reading Frame, supplied by OriGene, used in various techniques. Bioz Stars score: 85/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    hkat open reading frame - by Bioz Stars, 2020-08
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    88
    Addgene inc cas9 open reading frame
    Deletion of the Fpr1-3 gene cluster by two sgRNAs spanning 95 kb. ( a ) Schematic overview of the strategy to delete a 95 kb DNA fragment on chromosome 17. The exons Fpr1 and Fpr3 are labeled in blue and purple respectively, and the target sites are indicated by arrowheads. PAM sequences are in red following the target sequence highlighted in blue or purple. After deletion of the DNA fragment, the resulting genomic sequence is composed of the 5′ part of Fpr1 (blue) and the 3′ portion of Fpr3 (purple). The locations of PCR primers (F, Forward; R, reverse) are indicated by arrows. ( b ) (Top) Genotyping of the founders. PCR analysis of F0 mice injected with <t>Cas9</t> protein and sgRNAs listed in ( a ). Arrowheads indicate the founders with deletion of the 95 kb genomic DNA fragment. (Below) Sequencing data of the PCR products from two founders showing the joint Fpr1/Fpr3 genomic sequence. M, DNA marker. ( c ) Genotyping analysis of F1 progenies from two founders showing germ line transmission of the 95 kb deletion. M, DNA marker.
    Cas9 Open Reading Frame, supplied by Addgene inc, used in various techniques. Bioz Stars score: 88/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    cas9 open reading frame - by Bioz Stars, 2020-08
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    92
    Addgene inc open reading frame orf
    Deletion of the Fpr1-3 gene cluster by two sgRNAs spanning 95 kb. ( a ) Schematic overview of the strategy to delete a 95 kb DNA fragment on chromosome 17. The exons Fpr1 and Fpr3 are labeled in blue and purple respectively, and the target sites are indicated by arrowheads. PAM sequences are in red following the target sequence highlighted in blue or purple. After deletion of the DNA fragment, the resulting genomic sequence is composed of the 5′ part of Fpr1 (blue) and the 3′ portion of Fpr3 (purple). The locations of PCR primers (F, Forward; R, reverse) are indicated by arrows. ( b ) (Top) Genotyping of the founders. PCR analysis of F0 mice injected with <t>Cas9</t> protein and sgRNAs listed in ( a ). Arrowheads indicate the founders with deletion of the 95 kb genomic DNA fragment. (Below) Sequencing data of the PCR products from two founders showing the joint Fpr1/Fpr3 genomic sequence. M, DNA marker. ( c ) Genotyping analysis of F1 progenies from two founders showing germ line transmission of the 95 kb deletion. M, DNA marker.
    Open Reading Frame Orf, supplied by Addgene 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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    Average 92 stars, based on 8 article reviews
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    open reading frame orf - by Bioz Stars, 2020-08
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    89
    TaKaRa open reading frame orf
    Analysis of the essential domains of human TSKS required for interaction with <t>TSSK2</t> A: Schematic drawing of TSKS <t>ORF</t> highlighting known motifs and deletion mutants. Two putative coiled-coil domains [C-C1, C-C2], the six amino-acid repeats (Rpt) and the amino terminal nuclear localization signal (NLS) are marked. A total of 7 deletion mutants of TSKS were created and fused with the Gal4 activation domain in the pGAD two hybrid vectors. Fusion proteins of each mutant and the Gal-AD were co-transformed with Gal-DBDTSSK2 into the yeast host strain AH109. B: The expression of the fusion proteins of each mutant was analyzed by Western analysis. C: Culture supernatants of each pair were assayed for alpha-galactosidase activity. The activity shown by each deletion mutant is expressed as the percentage of wild type (WT) TSKS. The corresponding deletion mutant is shown in A. The N-terminus of TSKS is crucial to its interaction with TSSK2. Error bars indicate variation among 3 experiments.
    Open Reading Frame Orf, supplied by TaKaRa, used in various techniques. Bioz Stars score: 89/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    open reading frame orf - by Bioz Stars, 2020-08
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    89
    Promega luciferase open reading frame
    Analysis of the essential domains of human TSKS required for interaction with <t>TSSK2</t> A: Schematic drawing of TSKS <t>ORF</t> highlighting known motifs and deletion mutants. Two putative coiled-coil domains [C-C1, C-C2], the six amino-acid repeats (Rpt) and the amino terminal nuclear localization signal (NLS) are marked. A total of 7 deletion mutants of TSKS were created and fused with the Gal4 activation domain in the pGAD two hybrid vectors. Fusion proteins of each mutant and the Gal-AD were co-transformed with Gal-DBDTSSK2 into the yeast host strain AH109. B: The expression of the fusion proteins of each mutant was analyzed by Western analysis. C: Culture supernatants of each pair were assayed for alpha-galactosidase activity. The activity shown by each deletion mutant is expressed as the percentage of wild type (WT) TSKS. The corresponding deletion mutant is shown in A. The N-terminus of TSKS is crucial to its interaction with TSSK2. Error bars indicate variation among 3 experiments.
    Luciferase Open Reading Frame, supplied by Promega, used in various techniques. Bioz Stars score: 89/100, based on 170 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 89 stars, based on 170 article reviews
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    luciferase open reading frame - by Bioz Stars, 2020-08
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    86
    OriGene ccr5 open reading frame
    Dual-luciferase reporters, frameshifting data from other cell types, and frameshift peptide LC-MS/MS sequencing data a , Schematic of dual-luciferase constructs used to test the <t>CCR5</t> frameshifting signal. Transcription is driven from the SV40 early enhancer/promoter and transcription termination and polyadenylation utilizes the SV40 late poly(A) signal. The in-frame control is p2luci, encoding a firefly/ Renilla luciferase fusion protein. In the out of frame reporter (OOF), firefly luciferase lies in the –1 reading frame with respect to the Renilla open reading frame. In the HIV –1 PRF reporter, the –1 PRF signal of HIV-1 was cloned in between the two luciferase reporters, and the firefly ORF is in the –1 frame with respect to Renilla . The CCR5 –1 PRF reporter is the same, except that it contains the CCR5 –1 PRF signal. In the CCR5 slip site mutant (SSM), the UUUAAAA slippery heptamer of the CCR5 –1 PRF signal was mutated to GCGCGCG. The PTC reporter is based on the CCR5 –1 PRF reporter in which a premature termination codon was inserted following the Renilla open reading frame. b , Efficient –1 PRF promoted by the CCR5 sequence in CHO and Vero cells. Error bars denote standard error. c , d , LC-MS/MS analysis of the CCR5/β-Gal –1 PRF fusion protein. c , Primary amino acid sequence of the predicted fusion protein. Matched peptides are shown in bold red. Leader sequence is highlighted in cyan. CCR5 0-frame sequence is yellow, and CCR5 –1 frame peptide is highlighted in green. Non-highlighted sequence is β-galactosidase. d , Partial list of matching peptides identified by MS/MS analysis. Highlighted sequences show MSMS spectra of TSRIPVVHAVFALKSQ (2–17) and of TSRIPVVHAVFALKSQDGHLWGG (2–24) with N-terminal acetylation.
    Ccr5 Open Reading Frame, supplied by OriGene, used in various techniques. Bioz Stars score: 86/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 86 stars, based on 6 article reviews
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    ccr5 open reading frame - by Bioz Stars, 2020-08
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    90
    Genecopoeia human cbl open reading frame orf
    Dual-luciferase reporters, frameshifting data from other cell types, and frameshift peptide LC-MS/MS sequencing data a , Schematic of dual-luciferase constructs used to test the <t>CCR5</t> frameshifting signal. Transcription is driven from the SV40 early enhancer/promoter and transcription termination and polyadenylation utilizes the SV40 late poly(A) signal. The in-frame control is p2luci, encoding a firefly/ Renilla luciferase fusion protein. In the out of frame reporter (OOF), firefly luciferase lies in the –1 reading frame with respect to the Renilla open reading frame. In the HIV –1 PRF reporter, the –1 PRF signal of HIV-1 was cloned in between the two luciferase reporters, and the firefly ORF is in the –1 frame with respect to Renilla . The CCR5 –1 PRF reporter is the same, except that it contains the CCR5 –1 PRF signal. In the CCR5 slip site mutant (SSM), the UUUAAAA slippery heptamer of the CCR5 –1 PRF signal was mutated to GCGCGCG. The PTC reporter is based on the CCR5 –1 PRF reporter in which a premature termination codon was inserted following the Renilla open reading frame. b , Efficient –1 PRF promoted by the CCR5 sequence in CHO and Vero cells. Error bars denote standard error. c , d , LC-MS/MS analysis of the CCR5/β-Gal –1 PRF fusion protein. c , Primary amino acid sequence of the predicted fusion protein. Matched peptides are shown in bold red. Leader sequence is highlighted in cyan. CCR5 0-frame sequence is yellow, and CCR5 –1 frame peptide is highlighted in green. Non-highlighted sequence is β-galactosidase. d , Partial list of matching peptides identified by MS/MS analysis. Highlighted sequences show MSMS spectra of TSRIPVVHAVFALKSQ (2–17) and of TSRIPVVHAVFALKSQDGHLWGG (2–24) with N-terminal acetylation.
    Human Cbl Open Reading Frame Orf, supplied by Genecopoeia, used in various techniques. Bioz Stars score: 90/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human cbl open reading frame orf/product/Genecopoeia
    Average 90 stars, based on 9 article reviews
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    human cbl open reading frame orf - by Bioz Stars, 2020-08
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    91
    Genechem luciferase open reading frame
    Dual-luciferase reporters, frameshifting data from other cell types, and frameshift peptide LC-MS/MS sequencing data a , Schematic of dual-luciferase constructs used to test the <t>CCR5</t> frameshifting signal. Transcription is driven from the SV40 early enhancer/promoter and transcription termination and polyadenylation utilizes the SV40 late poly(A) signal. The in-frame control is p2luci, encoding a firefly/ Renilla luciferase fusion protein. In the out of frame reporter (OOF), firefly luciferase lies in the –1 reading frame with respect to the Renilla open reading frame. In the HIV –1 PRF reporter, the –1 PRF signal of HIV-1 was cloned in between the two luciferase reporters, and the firefly ORF is in the –1 frame with respect to Renilla . The CCR5 –1 PRF reporter is the same, except that it contains the CCR5 –1 PRF signal. In the CCR5 slip site mutant (SSM), the UUUAAAA slippery heptamer of the CCR5 –1 PRF signal was mutated to GCGCGCG. The PTC reporter is based on the CCR5 –1 PRF reporter in which a premature termination codon was inserted following the Renilla open reading frame. b , Efficient –1 PRF promoted by the CCR5 sequence in CHO and Vero cells. Error bars denote standard error. c , d , LC-MS/MS analysis of the CCR5/β-Gal –1 PRF fusion protein. c , Primary amino acid sequence of the predicted fusion protein. Matched peptides are shown in bold red. Leader sequence is highlighted in cyan. CCR5 0-frame sequence is yellow, and CCR5 –1 frame peptide is highlighted in green. Non-highlighted sequence is β-galactosidase. d , Partial list of matching peptides identified by MS/MS analysis. Highlighted sequences show MSMS spectra of TSRIPVVHAVFALKSQ (2–17) and of TSRIPVVHAVFALKSQDGHLWGG (2–24) with N-terminal acetylation.
    Luciferase Open Reading Frame, supplied by Genechem, used in various techniques. Bioz Stars score: 91/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/luciferase open reading frame/product/Genechem
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    luciferase open reading frame - by Bioz Stars, 2020-08
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    89
    GenScript open reading frame orf
    Dual-luciferase reporters, frameshifting data from other cell types, and frameshift peptide LC-MS/MS sequencing data a , Schematic of dual-luciferase constructs used to test the <t>CCR5</t> frameshifting signal. Transcription is driven from the SV40 early enhancer/promoter and transcription termination and polyadenylation utilizes the SV40 late poly(A) signal. The in-frame control is p2luci, encoding a firefly/ Renilla luciferase fusion protein. In the out of frame reporter (OOF), firefly luciferase lies in the –1 reading frame with respect to the Renilla open reading frame. In the HIV –1 PRF reporter, the –1 PRF signal of HIV-1 was cloned in between the two luciferase reporters, and the firefly ORF is in the –1 frame with respect to Renilla . The CCR5 –1 PRF reporter is the same, except that it contains the CCR5 –1 PRF signal. In the CCR5 slip site mutant (SSM), the UUUAAAA slippery heptamer of the CCR5 –1 PRF signal was mutated to GCGCGCG. The PTC reporter is based on the CCR5 –1 PRF reporter in which a premature termination codon was inserted following the Renilla open reading frame. b , Efficient –1 PRF promoted by the CCR5 sequence in CHO and Vero cells. Error bars denote standard error. c , d , LC-MS/MS analysis of the CCR5/β-Gal –1 PRF fusion protein. c , Primary amino acid sequence of the predicted fusion protein. Matched peptides are shown in bold red. Leader sequence is highlighted in cyan. CCR5 0-frame sequence is yellow, and CCR5 –1 frame peptide is highlighted in green. Non-highlighted sequence is β-galactosidase. d , Partial list of matching peptides identified by MS/MS analysis. Highlighted sequences show MSMS spectra of TSRIPVVHAVFALKSQ (2–17) and of TSRIPVVHAVFALKSQDGHLWGG (2–24) with N-terminal acetylation.
    Open Reading Frame Orf, supplied by GenScript, used in various techniques. Bioz Stars score: 89/100, based on 54 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/open reading frame orf/product/GenScript
    Average 89 stars, based on 54 article reviews
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    open reading frame orf - by Bioz Stars, 2020-08
    89/100 stars
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    89
    OriGene open reading frame orf
    <t>Lpo</t> protein expression detected by Western blotting and activity assay Panel A shows a Western blot of CMT-93 (CMT) cells, a CMT transfectant clone expressing Lpo <t>ORF</t> cDNA, colon of B6 DKO, B6 WT, 129 DKO and 129 WT 22-day-old mice, in this order. The upper panel shows the proteins recognized by anti-LPO antibody, and the lower panel shows β-actin. The open arrow points to ~90 kDa Lpo. Panel B shows the relative levels of Lpo protein in B6 and 129 DKO and WT colons, quantified from Western blots. Arrow bars are SEM from 4 colons in each group. Means that differ are shown with different letter, where a > b. Panel C shows the peroxidase activity in the colon of 10 B6 and five 129 DKO as well as 10 B6 and six 129 non-DKO control (Con) mice with at least 2 WT GPx alleles. The mean of total activity (open column) that differs is shown with different letter, where a > b > c. The mean of resorcinol-resistant activity (shaded column) that differs is shown with different number of asterisk, where *** > ** > *. The mean of NaCl-resistant activity (solid column) that differs is shown with different number of number sign, where ## > #. The error bars are standard deviations of the means.
    Open Reading Frame Orf, supplied by OriGene, used in various techniques. Bioz Stars score: 89/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Biotechnology Information open reading frame orf
    <t>Lpo</t> protein expression detected by Western blotting and activity assay Panel A shows a Western blot of CMT-93 (CMT) cells, a CMT transfectant clone expressing Lpo <t>ORF</t> cDNA, colon of B6 DKO, B6 WT, 129 DKO and 129 WT 22-day-old mice, in this order. The upper panel shows the proteins recognized by anti-LPO antibody, and the lower panel shows β-actin. The open arrow points to ~90 kDa Lpo. Panel B shows the relative levels of Lpo protein in B6 and 129 DKO and WT colons, quantified from Western blots. Arrow bars are SEM from 4 colons in each group. Means that differ are shown with different letter, where a > b. Panel C shows the peroxidase activity in the colon of 10 B6 and five 129 DKO as well as 10 B6 and six 129 non-DKO control (Con) mice with at least 2 WT GPx alleles. The mean of total activity (open column) that differs is shown with different letter, where a > b > c. The mean of resorcinol-resistant activity (shaded column) that differs is shown with different number of asterisk, where *** > ** > *. The mean of NaCl-resistant activity (solid column) that differs is shown with different number of number sign, where ## > #. The error bars are standard deviations of the means.
    Open Reading Frame Orf, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 89/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GenScript sim1a transcript open reading frame
    RA mediates the <t>sim1a</t> domain within the pronephric renal progenitor field
    Sim1a Transcript Open Reading Frame, supplied by GenScript, used in various techniques. Bioz Stars score: 86/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    OriGene pp5c open reading frame orf construct
    RA mediates the <t>sim1a</t> domain within the pronephric renal progenitor field
    Pp5c Open Reading Frame Orf Construct, supplied by OriGene, used in various techniques. Bioz Stars score: 90/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GenScript jafrac1 open reading frame orf
    RA mediates the <t>sim1a</t> domain within the pronephric renal progenitor field
    Jafrac1 Open Reading Frame Orf, supplied by GenScript, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    OriGene srf open reading frame orf
    RA mediates the <t>sim1a</t> domain within the pronephric renal progenitor field
    Srf Open Reading Frame Orf, supplied by OriGene, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    OriGene mcl 1 open reading frame
    The regulation of <t>Mcl-1</t> stability by ERK1/2 and the sensitivity of cells to U0126. (A) The levels of phospho-ERK1/2 (p-ERK1/2) and total ERK1/2 (t-ERK1/2) as determined by Western blot. A representative example of three blots is shown. (B) Drug sensitivity
    Mcl 1 Open Reading Frame, supplied by OriGene, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Modulation of rostro-caudal and dorso-ventral axis specification induces the development of PHOX2B -expressing NCCs from hPSCs. ( a ) A diagram of the culture conditions for the modification of rostro-caudal and dorso-ventral axis specification of hPSCs. ( b ) A heat map image showing the percentage of eGFP + cells on day 10 of differentiation using KhES1 PHOX2B::eGFP under various conditions. ( c ) Representative FCM plots of day 10 KhES1 PHOX2B::eGFP-derived aggregates under the indicated conditions (i–iv) of ( b ). ( d ) RT-PCR analyses for PHOX2B , SOX1 , PAX6 , SOX10 , FOXD3 , HOXB1 , HOXB2 , HOXB4 , HOXB6 , HOXB8 and HOXC9 in day 10 aggregates under conditions (i–iv). The right diagram shows the expression pattern of HOX genes in the rhombomere (r1–8) and the spinal cord (cervical and thoracic) region. SB = SB431542, CHIR = CHIR 99021, RA = retinoic acid, Pur = Purmorphamine, BMP = BMP4, NT = neural tube, NCC = neural crest cell, HB = hindbrain, SC = spinal cord.

    Journal: Scientific Reports

    Article Title: Efficient derivation of sympathetic neurons from human pluripotent stem cells with a defined condition

    doi: 10.1038/s41598-018-31256-1

    Figure Lengend Snippet: Modulation of rostro-caudal and dorso-ventral axis specification induces the development of PHOX2B -expressing NCCs from hPSCs. ( a ) A diagram of the culture conditions for the modification of rostro-caudal and dorso-ventral axis specification of hPSCs. ( b ) A heat map image showing the percentage of eGFP + cells on day 10 of differentiation using KhES1 PHOX2B::eGFP under various conditions. ( c ) Representative FCM plots of day 10 KhES1 PHOX2B::eGFP-derived aggregates under the indicated conditions (i–iv) of ( b ). ( d ) RT-PCR analyses for PHOX2B , SOX1 , PAX6 , SOX10 , FOXD3 , HOXB1 , HOXB2 , HOXB4 , HOXB6 , HOXB8 and HOXC9 in day 10 aggregates under conditions (i–iv). The right diagram shows the expression pattern of HOX genes in the rhombomere (r1–8) and the spinal cord (cervical and thoracic) region. SB = SB431542, CHIR = CHIR 99021, RA = retinoic acid, Pur = Purmorphamine, BMP = BMP4, NT = neural tube, NCC = neural crest cell, HB = hindbrain, SC = spinal cord.

    Article Snippet: Then, the 1 kbp 5′ homology arm (PCR amplified), T2A peptide sequence (annealed oligonucleotide pair) and eGFP open reading frame (ORF; without first ATG; PCR amplified) were cloned into the 5′ side of the loxP-neo-loxP cassette vector using the In-Fusion HD cloning kit (Clontech) in a seamless manner.

    Techniques: Expressing, Modification, Derivative Assay, Reverse Transcription Polymerase Chain Reaction

    Nrac localizes to the plasma membrane. A) Predicted transmembrane domains. Fluorescence imaging of HEK293 cells transfected with plasmids encoding B) LCK-tRFP and C) Nrac-GFP and D) Merged picture. E) Immunostaining with a primary antibody against Nrac, visualized by an Alexa Fluor 488-conjugated secondary antibody, F) Hoechst staining for nuclei, and G) merged picture, in paraffin-embedded sections of mouse white adipose tissue.

    Journal: PLoS ONE

    Article Title: Nrac, a Novel Nutritionally-Regulated Adipose and Cardiac-Enriched Gene

    doi: 10.1371/journal.pone.0046254

    Figure Lengend Snippet: Nrac localizes to the plasma membrane. A) Predicted transmembrane domains. Fluorescence imaging of HEK293 cells transfected with plasmids encoding B) LCK-tRFP and C) Nrac-GFP and D) Merged picture. E) Immunostaining with a primary antibody against Nrac, visualized by an Alexa Fluor 488-conjugated secondary antibody, F) Hoechst staining for nuclei, and G) merged picture, in paraffin-embedded sections of mouse white adipose tissue.

    Article Snippet: To examine Nrac subcellular localization, fusion protein of Nrac-GFP was made by cloning the Nrac open reading frame (Origene, MD) into the pCMV6-AC-GFP vector.

    Techniques: Fluorescence, Imaging, Transfection, Immunostaining, Staining

    Hkat tissue expression pattern and subcellular localization. A) Hkat is expression in both white adipose tissue and brown adipose tissue, but is highest expressed in heart and kidney. B) Hkat is localized to the plasma membrane. Fluorescence imaging of HEK 293 cells transfected with plasmids encoding B) LCK-tRFP and C) Hkat-GFP and D) Merged picture.

    Journal: Scientific Reports

    Article Title: Hkat, a novel nutritionally regulated transmembrane protein in adipose tissues

    doi: 10.1038/srep00825

    Figure Lengend Snippet: Hkat tissue expression pattern and subcellular localization. A) Hkat is expression in both white adipose tissue and brown adipose tissue, but is highest expressed in heart and kidney. B) Hkat is localized to the plasma membrane. Fluorescence imaging of HEK 293 cells transfected with plasmids encoding B) LCK-tRFP and C) Hkat-GFP and D) Merged picture.

    Article Snippet: Imaging To examine Hkat subcellular localization, fusion protein of Hkat-GFP was made by cloning the Hkat open reading frame (Origene, MD) into the pCMV6-AC-GFP vector.

    Techniques: Expressing, Fluorescence, Imaging, Transfection

    Deletion of the Fpr1-3 gene cluster by two sgRNAs spanning 95 kb. ( a ) Schematic overview of the strategy to delete a 95 kb DNA fragment on chromosome 17. The exons Fpr1 and Fpr3 are labeled in blue and purple respectively, and the target sites are indicated by arrowheads. PAM sequences are in red following the target sequence highlighted in blue or purple. After deletion of the DNA fragment, the resulting genomic sequence is composed of the 5′ part of Fpr1 (blue) and the 3′ portion of Fpr3 (purple). The locations of PCR primers (F, Forward; R, reverse) are indicated by arrows. ( b ) (Top) Genotyping of the founders. PCR analysis of F0 mice injected with Cas9 protein and sgRNAs listed in ( a ). Arrowheads indicate the founders with deletion of the 95 kb genomic DNA fragment. (Below) Sequencing data of the PCR products from two founders showing the joint Fpr1/Fpr3 genomic sequence. M, DNA marker. ( c ) Genotyping analysis of F1 progenies from two founders showing germ line transmission of the 95 kb deletion. M, DNA marker.

    Journal: Scientific Reports

    Article Title: Large genomic fragment deletion and functional gene cassette knock-in via Cas9 protein mediated genome editing in one-cell rodent embryos

    doi: 10.1038/srep17517

    Figure Lengend Snippet: Deletion of the Fpr1-3 gene cluster by two sgRNAs spanning 95 kb. ( a ) Schematic overview of the strategy to delete a 95 kb DNA fragment on chromosome 17. The exons Fpr1 and Fpr3 are labeled in blue and purple respectively, and the target sites are indicated by arrowheads. PAM sequences are in red following the target sequence highlighted in blue or purple. After deletion of the DNA fragment, the resulting genomic sequence is composed of the 5′ part of Fpr1 (blue) and the 3′ portion of Fpr3 (purple). The locations of PCR primers (F, Forward; R, reverse) are indicated by arrows. ( b ) (Top) Genotyping of the founders. PCR analysis of F0 mice injected with Cas9 protein and sgRNAs listed in ( a ). Arrowheads indicate the founders with deletion of the 95 kb genomic DNA fragment. (Below) Sequencing data of the PCR products from two founders showing the joint Fpr1/Fpr3 genomic sequence. M, DNA marker. ( c ) Genotyping analysis of F1 progenies from two founders showing germ line transmission of the 95 kb deletion. M, DNA marker.

    Article Snippet: Recombinant Cas9 expression and purification The Cas9 open reading frame was amplified from pX330 (Addgene #42230) and cloned into pET28a in frame with an N-terminal His-6 tag for in vitro expression.

    Techniques: Labeling, Sequencing, Polymerase Chain Reaction, Mouse Assay, Injection, Marker, Transmission Assay

    Comparison of the knock-in efficiency between injection of Cas9 protein and Cas9 mRNA. ( a ) Schematic overview of the strategy to introduce specific mutations in the Sirt3 locus. PAM sequence is labeled in red, designed mutations are blue. ( b ) The sequence of F0 pups generated from Cas9 mRNA (left) or protein (right) injection are listed. Founders with the desired mutation are labeled with a red asterisk. PAM sequence is red, designed mutations are blue, random mutations are green.

    Journal: Scientific Reports

    Article Title: Large genomic fragment deletion and functional gene cassette knock-in via Cas9 protein mediated genome editing in one-cell rodent embryos

    doi: 10.1038/srep17517

    Figure Lengend Snippet: Comparison of the knock-in efficiency between injection of Cas9 protein and Cas9 mRNA. ( a ) Schematic overview of the strategy to introduce specific mutations in the Sirt3 locus. PAM sequence is labeled in red, designed mutations are blue. ( b ) The sequence of F0 pups generated from Cas9 mRNA (left) or protein (right) injection are listed. Founders with the desired mutation are labeled with a red asterisk. PAM sequence is red, designed mutations are blue, random mutations are green.

    Article Snippet: Recombinant Cas9 expression and purification The Cas9 open reading frame was amplified from pX330 (Addgene #42230) and cloned into pET28a in frame with an N-terminal His-6 tag for in vitro expression.

    Techniques: Knock-In, Injection, Introduce, Sequencing, Labeling, Generated, Mutagenesis

    Site-specific insertion of IRES-Cre ERT2 -pA into the mouse Nfatc1 locus . ( a ) Schematic of the strategy for insertion of the CreERT2 cassette into the mouse Nfatc1 locus. Cas9/sgRNA targeted the 3′UTR of the Nfatc1 gene in Exon 9. The HDR donor sequence consists of IRES-CreERT2-polyA (2.7 kb) flanked by two homologous arms 650 bp (left-arm) and 600 bp (right-arm) in length. Positions of genotyping primers are indicated by arrows. ( b ) Genotyping of Nfatc1-CreERT2 mice. Upper, T7E1 assay to check the indels created by CRISPR/Cas. Middle, identification of founder (F0) and F1 Nfatc1-CreERT2 mice by primer pairs: F1 + R1 and F2 + R2. Arrowheads: desired bands of site-specific inserted pups. M, DNA marker. ( c ) Lineage tracing of skin Nfatc1 stem cells in Nfatc1-CreERT2 +/− :Rosa26-LacZ +/− mouse via X-gal staining. Lineage tracing began at the age of 4 weeks by intraperitoneal injection of tamoxifen. Mice dorsal skin tissue was stained 2 days (middle) or 4 weeks (right) after induction. Scale bar, 100 μm.

    Journal: Scientific Reports

    Article Title: Large genomic fragment deletion and functional gene cassette knock-in via Cas9 protein mediated genome editing in one-cell rodent embryos

    doi: 10.1038/srep17517

    Figure Lengend Snippet: Site-specific insertion of IRES-Cre ERT2 -pA into the mouse Nfatc1 locus . ( a ) Schematic of the strategy for insertion of the CreERT2 cassette into the mouse Nfatc1 locus. Cas9/sgRNA targeted the 3′UTR of the Nfatc1 gene in Exon 9. The HDR donor sequence consists of IRES-CreERT2-polyA (2.7 kb) flanked by two homologous arms 650 bp (left-arm) and 600 bp (right-arm) in length. Positions of genotyping primers are indicated by arrows. ( b ) Genotyping of Nfatc1-CreERT2 mice. Upper, T7E1 assay to check the indels created by CRISPR/Cas. Middle, identification of founder (F0) and F1 Nfatc1-CreERT2 mice by primer pairs: F1 + R1 and F2 + R2. Arrowheads: desired bands of site-specific inserted pups. M, DNA marker. ( c ) Lineage tracing of skin Nfatc1 stem cells in Nfatc1-CreERT2 +/− :Rosa26-LacZ +/− mouse via X-gal staining. Lineage tracing began at the age of 4 weeks by intraperitoneal injection of tamoxifen. Mice dorsal skin tissue was stained 2 days (middle) or 4 weeks (right) after induction. Scale bar, 100 μm.

    Article Snippet: Recombinant Cas9 expression and purification The Cas9 open reading frame was amplified from pX330 (Addgene #42230) and cloned into pET28a in frame with an N-terminal His-6 tag for in vitro expression.

    Techniques: Sequencing, Mouse Assay, CRISPR, Marker, Staining, Injection

    Analysis of the essential domains of human TSKS required for interaction with TSSK2 A: Schematic drawing of TSKS ORF highlighting known motifs and deletion mutants. Two putative coiled-coil domains [C-C1, C-C2], the six amino-acid repeats (Rpt) and the amino terminal nuclear localization signal (NLS) are marked. A total of 7 deletion mutants of TSKS were created and fused with the Gal4 activation domain in the pGAD two hybrid vectors. Fusion proteins of each mutant and the Gal-AD were co-transformed with Gal-DBDTSSK2 into the yeast host strain AH109. B: The expression of the fusion proteins of each mutant was analyzed by Western analysis. C: Culture supernatants of each pair were assayed for alpha-galactosidase activity. The activity shown by each deletion mutant is expressed as the percentage of wild type (WT) TSKS. The corresponding deletion mutant is shown in A. The N-terminus of TSKS is crucial to its interaction with TSSK2. Error bars indicate variation among 3 experiments.

    Journal: Developmental biology

    Article Title: Targeted Deletion of Tssk1 2 Causes Male Infertility Due to Haploinsufficiency

    doi: 10.1016/j.ydbio.2008.03.047

    Figure Lengend Snippet: Analysis of the essential domains of human TSKS required for interaction with TSSK2 A: Schematic drawing of TSKS ORF highlighting known motifs and deletion mutants. Two putative coiled-coil domains [C-C1, C-C2], the six amino-acid repeats (Rpt) and the amino terminal nuclear localization signal (NLS) are marked. A total of 7 deletion mutants of TSKS were created and fused with the Gal4 activation domain in the pGAD two hybrid vectors. Fusion proteins of each mutant and the Gal-AD were co-transformed with Gal-DBDTSSK2 into the yeast host strain AH109. B: The expression of the fusion proteins of each mutant was analyzed by Western analysis. C: Culture supernatants of each pair were assayed for alpha-galactosidase activity. The activity shown by each deletion mutant is expressed as the percentage of wild type (WT) TSKS. The corresponding deletion mutant is shown in A. The N-terminus of TSKS is crucial to its interaction with TSSK2. Error bars indicate variation among 3 experiments.

    Article Snippet: The entire open-reading frame (ORF) of human TSSK2 was fused with the GAL4 DNA binding domain (DBD) and a myc tag in frame in the pGBKT7 two-hybrid vector (Match-Maker yeast two-hybrid reaction kit, Clonetech).

    Techniques: Activation Assay, Mutagenesis, Transformation Assay, Expressing, Western Blot, Activity Assay

    Dual-luciferase reporters, frameshifting data from other cell types, and frameshift peptide LC-MS/MS sequencing data a , Schematic of dual-luciferase constructs used to test the CCR5 frameshifting signal. Transcription is driven from the SV40 early enhancer/promoter and transcription termination and polyadenylation utilizes the SV40 late poly(A) signal. The in-frame control is p2luci, encoding a firefly/ Renilla luciferase fusion protein. In the out of frame reporter (OOF), firefly luciferase lies in the –1 reading frame with respect to the Renilla open reading frame. In the HIV –1 PRF reporter, the –1 PRF signal of HIV-1 was cloned in between the two luciferase reporters, and the firefly ORF is in the –1 frame with respect to Renilla . The CCR5 –1 PRF reporter is the same, except that it contains the CCR5 –1 PRF signal. In the CCR5 slip site mutant (SSM), the UUUAAAA slippery heptamer of the CCR5 –1 PRF signal was mutated to GCGCGCG. The PTC reporter is based on the CCR5 –1 PRF reporter in which a premature termination codon was inserted following the Renilla open reading frame. b , Efficient –1 PRF promoted by the CCR5 sequence in CHO and Vero cells. Error bars denote standard error. c , d , LC-MS/MS analysis of the CCR5/β-Gal –1 PRF fusion protein. c , Primary amino acid sequence of the predicted fusion protein. Matched peptides are shown in bold red. Leader sequence is highlighted in cyan. CCR5 0-frame sequence is yellow, and CCR5 –1 frame peptide is highlighted in green. Non-highlighted sequence is β-galactosidase. d , Partial list of matching peptides identified by MS/MS analysis. Highlighted sequences show MSMS spectra of TSRIPVVHAVFALKSQ (2–17) and of TSRIPVVHAVFALKSQDGHLWGG (2–24) with N-terminal acetylation.

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: Dual-luciferase reporters, frameshifting data from other cell types, and frameshift peptide LC-MS/MS sequencing data a , Schematic of dual-luciferase constructs used to test the CCR5 frameshifting signal. Transcription is driven from the SV40 early enhancer/promoter and transcription termination and polyadenylation utilizes the SV40 late poly(A) signal. The in-frame control is p2luci, encoding a firefly/ Renilla luciferase fusion protein. In the out of frame reporter (OOF), firefly luciferase lies in the –1 reading frame with respect to the Renilla open reading frame. In the HIV –1 PRF reporter, the –1 PRF signal of HIV-1 was cloned in between the two luciferase reporters, and the firefly ORF is in the –1 frame with respect to Renilla . The CCR5 –1 PRF reporter is the same, except that it contains the CCR5 –1 PRF signal. In the CCR5 slip site mutant (SSM), the UUUAAAA slippery heptamer of the CCR5 –1 PRF signal was mutated to GCGCGCG. The PTC reporter is based on the CCR5 –1 PRF reporter in which a premature termination codon was inserted following the Renilla open reading frame. b , Efficient –1 PRF promoted by the CCR5 sequence in CHO and Vero cells. Error bars denote standard error. c , d , LC-MS/MS analysis of the CCR5/β-Gal –1 PRF fusion protein. c , Primary amino acid sequence of the predicted fusion protein. Matched peptides are shown in bold red. Leader sequence is highlighted in cyan. CCR5 0-frame sequence is yellow, and CCR5 –1 frame peptide is highlighted in green. Non-highlighted sequence is β-galactosidase. d , Partial list of matching peptides identified by MS/MS analysis. Highlighted sequences show MSMS spectra of TSRIPVVHAVFALKSQ (2–17) and of TSRIPVVHAVFALKSQDGHLWGG (2–24) with N-terminal acetylation.

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: Luciferase, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Sequencing, Construct, Clone Assay, Mutagenesis

    Specific stimulation of CCR5-mediated –1 PRF by miR-1224 a , HeLa cells were transfected with 0–30 nmol of miR-1224 miRNA expressing constructs and with HIV-1 or CCR5 –1 PRF reporters. b , PRF assays of HeLa cells mock-transfected (0), or transfected with scrambled miRNA (Scr), a miR-1224 antagomir (anti-1224), miR-1224, miR1224 + anti-miR-1224, or miR-1224 plus an siRNA directed against argonaute 1. c , Ablation of the miRNA processing machinery affects –1 PRF promoted by the HIV-1 and CCR5 frameshift signals. –1 PRF assays were performed using cells transfected with siRNAs targeting Argonaute 1 ( AGO1 ), Argonaute 2 ( AGO2 ), DGCR8 , exportin 5 ( XPO5 ) or scrambled sequences (Scr). Error bars denote standard error. * P

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: Specific stimulation of CCR5-mediated –1 PRF by miR-1224 a , HeLa cells were transfected with 0–30 nmol of miR-1224 miRNA expressing constructs and with HIV-1 or CCR5 –1 PRF reporters. b , PRF assays of HeLa cells mock-transfected (0), or transfected with scrambled miRNA (Scr), a miR-1224 antagomir (anti-1224), miR-1224, miR1224 + anti-miR-1224, or miR-1224 plus an siRNA directed against argonaute 1. c , Ablation of the miRNA processing machinery affects –1 PRF promoted by the HIV-1 and CCR5 frameshift signals. –1 PRF assays were performed using cells transfected with siRNAs targeting Argonaute 1 ( AGO1 ), Argonaute 2 ( AGO2 ), DGCR8 , exportin 5 ( XPO5 ) or scrambled sequences (Scr). Error bars denote standard error. * P

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: Transfection, Expressing, Construct

    Close relationship of CCR5 sequences among simians a , Phylogenetic trees. The larger tree uses Danio rerio CCR5 as an outgroup while the smaller inset tree uses two Lemur species. Bootstrap support is included at each node; branch lengths are provided where appropriate. The low bootstrap values between some clades are indicative of the very small number of phylogenetically informative bases and high propensity of invariant bases. b , Sequence alignment of CCR5 coding sequences. The portion of the CCR5 coding sequence alignment containing the –1 PRF signal is shown from the seaview sequence editor. In total, these 45 species were trimmed to 7,000 bases each and comprise 827 complete sites, of which 241 are invariant and 586 were informative for phylogenetic analyses. Danio rerio (at bottom) provides an outgroup; when considering the conservation of the region surrounding the –1 PRF signal at position 408, it was removed. This results in 170 sites, of which 69 are invariant, and 58 informative. With the exception of the Lemur, the –1 PRF region is strikingly conserved among primates.

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: Close relationship of CCR5 sequences among simians a , Phylogenetic trees. The larger tree uses Danio rerio CCR5 as an outgroup while the smaller inset tree uses two Lemur species. Bootstrap support is included at each node; branch lengths are provided where appropriate. The low bootstrap values between some clades are indicative of the very small number of phylogenetically informative bases and high propensity of invariant bases. b , Sequence alignment of CCR5 coding sequences. The portion of the CCR5 coding sequence alignment containing the –1 PRF signal is shown from the seaview sequence editor. In total, these 45 species were trimmed to 7,000 bases each and comprise 827 complete sites, of which 241 are invariant and 586 were informative for phylogenetic analyses. Danio rerio (at bottom) provides an outgroup; when considering the conservation of the region surrounding the –1 PRF signal at position 408, it was removed. This results in 170 sites, of which 69 are invariant, and 58 informative. With the exception of the Lemur, the –1 PRF region is strikingly conserved among primates.

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: Sequencing

    Specific stimulation of CCR5-mediated –1 PRF by miR-1224 a , Sequence of the CCR5 –1 PRF signal is shown. The UUUAAAA slippery site is italicized, stems 1 and 2 of the mRNA pseudoknot are coloured blue and red, respectively, and unpaired bases are black. Sequences of miR-1224, miR-711, and miR-1413, and their potential hybridization patterns with CCR5 sequence are indicated. b , Stimulation of –1 PRF by miR-1224 in HeLa cells. Cells were transfected with 5 nM of the indicated miRNA expressing constructs, or mock transfected. After 24 h incubation, cells were transfected with the indicated –1 PRF dual-luciferase reporters, and frameshift assays were performed 24–36 h. later. c , miR-141 stimulates CCR5 mediated –1 PRF in CHO cells. CHO and Vero cells were transfected with 5 nM of the indicated miRNA expressing constructs, with scrambled miRNA sequences, or mock transfected. After 24 h incubation, cells were transfected with the indicated –1 PRF dual-luciferase reporters, and frameshift assays were performed 24–36 h later. Error bars denote standard error. * P

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: Specific stimulation of CCR5-mediated –1 PRF by miR-1224 a , Sequence of the CCR5 –1 PRF signal is shown. The UUUAAAA slippery site is italicized, stems 1 and 2 of the mRNA pseudoknot are coloured blue and red, respectively, and unpaired bases are black. Sequences of miR-1224, miR-711, and miR-1413, and their potential hybridization patterns with CCR5 sequence are indicated. b , Stimulation of –1 PRF by miR-1224 in HeLa cells. Cells were transfected with 5 nM of the indicated miRNA expressing constructs, or mock transfected. After 24 h incubation, cells were transfected with the indicated –1 PRF dual-luciferase reporters, and frameshift assays were performed 24–36 h. later. c , miR-141 stimulates CCR5 mediated –1 PRF in CHO cells. CHO and Vero cells were transfected with 5 nM of the indicated miRNA expressing constructs, with scrambled miRNA sequences, or mock transfected. After 24 h incubation, cells were transfected with the indicated –1 PRF dual-luciferase reporters, and frameshift assays were performed 24–36 h later. Error bars denote standard error. * P

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: Sequencing, Hybridization, Transfection, Expressing, Construct, Incubation, Luciferase

    Mapping the CCR5/miR-1224 interaction: miR-1224 stimulates CCR5 –1 PRF by stabilizing Stem 2 through a proposed triple helical interaction a , Putative miR-1224 binding sites were changed to their complements (green). b , Gel-shift assays using miR1224 and M1, M2 and M3 variants of the CCR5 signal (described in ) using native conditions. n = 6 for each sample (three times each of two technical replicates). c , Models diagramming experimental results. The CCR5 pseudoknot is cartooned with wild-type sequences shown as black lines, mutant sequences shown as green lines, and miR-1224 in red. Proposed triple helical interactions between the CCR5 –1 PRF promoting pseudoknot and miR-1224 are shown in the Native and M2 models. Extended Data Fig. 5

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: Mapping the CCR5/miR-1224 interaction: miR-1224 stimulates CCR5 –1 PRF by stabilizing Stem 2 through a proposed triple helical interaction a , Putative miR-1224 binding sites were changed to their complements (green). b , Gel-shift assays using miR1224 and M1, M2 and M3 variants of the CCR5 signal (described in ) using native conditions. n = 6 for each sample (three times each of two technical replicates). c , Models diagramming experimental results. The CCR5 pseudoknot is cartooned with wild-type sequences shown as black lines, mutant sequences shown as green lines, and miR-1224 in red. Proposed triple helical interactions between the CCR5 –1 PRF promoting pseudoknot and miR-1224 are shown in the Native and M2 models. Extended Data Fig. 5

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: Binding Assay, Electrophoretic Mobility Shift Assay, Mutagenesis

    Models of the CCR5 –1 PRF stimulating mRNA pseudoknot a , Best-fit two-dimensional model based on chemical modification analyses. b , Three-dimensional model, two views. Slippery site is green, stem 1 is dark blue, unpaired bases and the loop within stem 1 are light blue, paired bases in stem 2 are red, and unpaired bases in stem 2 are yellow.

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: Models of the CCR5 –1 PRF stimulating mRNA pseudoknot a , Best-fit two-dimensional model based on chemical modification analyses. b , Three-dimensional model, two views. Slippery site is green, stem 1 is dark blue, unpaired bases and the loop within stem 1 are light blue, paired bases in stem 2 are red, and unpaired bases in stem 2 are yellow.

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: Modification

    mRNA stability studies a , Rabbit β-globin reporter containing a doxycycline repressible promoter and SV40 derived polyA signal is shown. The native CCR5 –1 PRF signal was cloned into exon 1. Controls included insertion of the CCR5 SSM –1 PRF signal, PTCs in all three reading frames at this position, or insertion of the 27 nucleotide TNF-α-derived A-U rich element (ARE) immediately following the rabbit β-globin open reading frame. b , Time course measurements of rabbit β-globin reporter abundances transcriptionally arrested with doxycycline. c , Time course measurements of native CCR5 mRNA reporter abundances from HeLa-TZM BL cells transcriptionally arrested with actinomycin D. Cells were transfected with SMG1 miRNA or scrambled miRNA control. d , Effects of various RNAs on CCR5 mRNA steady-state abundance. HeLa-TZM BL cells expressing CCR5 were transfected as follows: scrambled siRNA control (scr), human SMG1 siRNA (Smg), miR-1224 (1224), a mIR-1224 antagomir (anti), and combinations thereof. b – d , n = 9 (three times on three independent biological replicates). Error bars denote standard error. * P

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: mRNA stability studies a , Rabbit β-globin reporter containing a doxycycline repressible promoter and SV40 derived polyA signal is shown. The native CCR5 –1 PRF signal was cloned into exon 1. Controls included insertion of the CCR5 SSM –1 PRF signal, PTCs in all three reading frames at this position, or insertion of the 27 nucleotide TNF-α-derived A-U rich element (ARE) immediately following the rabbit β-globin open reading frame. b , Time course measurements of rabbit β-globin reporter abundances transcriptionally arrested with doxycycline. c , Time course measurements of native CCR5 mRNA reporter abundances from HeLa-TZM BL cells transcriptionally arrested with actinomycin D. Cells were transfected with SMG1 miRNA or scrambled miRNA control. d , Effects of various RNAs on CCR5 mRNA steady-state abundance. HeLa-TZM BL cells expressing CCR5 were transfected as follows: scrambled siRNA control (scr), human SMG1 siRNA (Smg), miR-1224 (1224), a mIR-1224 antagomir (anti), and combinations thereof. b – d , n = 9 (three times on three independent biological replicates). Error bars denote standard error. * P

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: Derivative Assay, Clone Assay, Transfection, Expressing

    Mapping and modelling the interactions of miR-1224 with the CCR5 –1 PRF signal in vitro and in live cells a , Dilutions of CCR5 –1 PRF signal (R5) transcript were mixed with [ 32 P]-labelled miR-1224 RNA (miR), and incubated at 30 °C (Native), or denatured at 90 °C and slowly cooled (Refolded). Samples separated through native PAGE were quantified and data plotted onto single site binding isotherms. K D values and standard deviations are indicated. b , In vivo pull-down of native CCR5 mRNA in live cells. Biotinylated miR-1224 precursor or a scrambled biotinylated control (Scr) were transfected into HeLa TZM BL cells expressing CCR5. Fold enrichment of affinity purified mRNAs were analysed by quantitative PCR with reverse transcription (qRT–PCR) using CCR5 - or GAPDH -specific primer sets. c , HeLa cells were co-transfected with dual-luciferase plasmids containing either the CCR5 or HIV-1 –1 PRF signal sequences and affinity-purified mRNAs were analysed as in b. d , EMSA assays were performed using miR1224 and M1, M2 and M3 variants of the CCR5 signal using native conditions. Single site binding isotherms generated from these data are plotted. K D values are indicated. For a and d , n = 6 for each sample (three times each of two technical replicates). For b and c , n = 9 for each sample (three times each for three biological replicates. Error bars denote standard deviation. * P

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: Mapping and modelling the interactions of miR-1224 with the CCR5 –1 PRF signal in vitro and in live cells a , Dilutions of CCR5 –1 PRF signal (R5) transcript were mixed with [ 32 P]-labelled miR-1224 RNA (miR), and incubated at 30 °C (Native), or denatured at 90 °C and slowly cooled (Refolded). Samples separated through native PAGE were quantified and data plotted onto single site binding isotherms. K D values and standard deviations are indicated. b , In vivo pull-down of native CCR5 mRNA in live cells. Biotinylated miR-1224 precursor or a scrambled biotinylated control (Scr) were transfected into HeLa TZM BL cells expressing CCR5. Fold enrichment of affinity purified mRNAs were analysed by quantitative PCR with reverse transcription (qRT–PCR) using CCR5 - or GAPDH -specific primer sets. c , HeLa cells were co-transfected with dual-luciferase plasmids containing either the CCR5 or HIV-1 –1 PRF signal sequences and affinity-purified mRNAs were analysed as in b. d , EMSA assays were performed using miR1224 and M1, M2 and M3 variants of the CCR5 signal using native conditions. Single site binding isotherms generated from these data are plotted. K D values are indicated. For a and d , n = 6 for each sample (three times each of two technical replicates). For b and c , n = 9 for each sample (three times each for three biological replicates. Error bars denote standard deviation. * P

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: In Vitro, Incubation, Clear Native PAGE, Binding Assay, In Vivo, Transfection, Expressing, Affinity Purification, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Luciferase, Generated, Standard Deviation

    Gel shifts and SHAPE analysis of CCR5 + miR-1224 a , b , In vitro binding of mIR-1224 with the CCR5 –1 PRF signal. Serial dilutions from 30 nM to 0.25 nM of a CCR5 –1 PRF signal (R5) containing transcript were mixed with equal volumes of 1.0 nM [ 32 P]-labelled synthetic miR-1224 RNA (miR), and incubated for 30 °C for 30 min ( a , Native), or at 90 °C for 5 s, cooled quickly to 60° and then slowly to 37° ( b , Refolded). Samples were separated through 10% native PAGE, dried, and intensities of retarded bands were quantified using phosphorimager and BioRad Quantity One software. c , d , miR-1224 does not bind to the HIV-1 –1 PRF signal in vitro . c , ‘Native’ annealing conditions. d , ‘Refolded’ annealing conditions. For a – d , n = 6 for each sample (three times each of two technical replicates). e , SHAPE analysis of the CCR5 –1 PRF signal in the absence (lane 7) or presence (lane 8) of miR-1224.

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: Gel shifts and SHAPE analysis of CCR5 + miR-1224 a , b , In vitro binding of mIR-1224 with the CCR5 –1 PRF signal. Serial dilutions from 30 nM to 0.25 nM of a CCR5 –1 PRF signal (R5) containing transcript were mixed with equal volumes of 1.0 nM [ 32 P]-labelled synthetic miR-1224 RNA (miR), and incubated for 30 °C for 30 min ( a , Native), or at 90 °C for 5 s, cooled quickly to 60° and then slowly to 37° ( b , Refolded). Samples were separated through 10% native PAGE, dried, and intensities of retarded bands were quantified using phosphorimager and BioRad Quantity One software. c , d , miR-1224 does not bind to the HIV-1 –1 PRF signal in vitro . c , ‘Native’ annealing conditions. d , ‘Refolded’ annealing conditions. For a – d , n = 6 for each sample (three times each of two technical replicates). e , SHAPE analysis of the CCR5 –1 PRF signal in the absence (lane 7) or presence (lane 8) of miR-1224.

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: In Vitro, Binding Assay, Incubation, Clear Native PAGE, Software

    Structural analysis of the CCR5 –1 PRF signal a , Computationally predicted and best fit 2-dimensional mRNA structures with chemical modification data. Stems 1, 2, and the loop are indicated as S1, S2 and L. The five different segments of stem 2 are labelled a–e. Nucleotide bases showing low levels of reactivity with DMS, CMCT, and kethoxal, and ribose sugars whose 2′-OH groups with NMIA were similarly non-reactive are noted as open circles. Moderately reactive sugars and bases are denoted by grey filled circles. Strongly modified (strongly reactive) sugars and bases are represented as black filled circles. Circles proximal to the bases denote reactivity of the bases, while circles distal to the bases denote reactivity of the ribose sugars. From left to right: mRNA pseudoknot best fit to data; mRNA pseudoknot predicted by Pknots; mRNA pseudoknot predicted by NUPAK; tandem stem-loops predicted by mFold. Red bases represent chemical modification patterns inconsistent with computational predictions. b , c , Chemical modification experiments. Autoradiograms of reverse transcriptase primer extensions performed on RNA transcribed by T7 RNA Pol from template PCR amplified from CCR5 –1 PRF signal containing plasmid. Bands correspond to strong readthrough control (RT) stops 1 nucleotide 5′ of bases modified by chemical reagents. b , The CCR5 mRNA was either left unmodified (un), or modified with 3 increasing concentrations of dimethyl sulphate (DMS, reacts with A and C), 1-cyclohexyl-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate (CMCT, reacts with U), or 1,1-dihydroxy-3-ethoxy-2-butanone (kethoxal, reacts with G) respectively. c , Primer extension reactions were performed on unmodified samples and samples incubated with 30, 65, and 110 nM NMIA (N-methyl isatoic anhydride). These are labelled 1, 2 and 3, respectively, beneath each sample, and ‘un’ denotes untreated RNA. d , The all atom r.m.s.d. plot of the 80 ns-long molecular dynamics simulation states against the reference structure (the starting state of the simulation) at the end of a 2 ns-long equilibration. All measures exclude most mobile, single-stranded, first 7 nucleotides. The full structure r.m.s.d. values are shown in black, SL1 data are plotted in cyan, and the SL2 data are plotted in red. Mean r.m.s.d. values with standard deviations are given in the box. Overall, after approximately 21 ns the structure stabilizes. e , Two views (opposite sides) of an average minimized structure based on the last 12 ns of the simulation (indicated with red arrow in d ) where all the r.m.s.d. measures converge and are most stable.

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: Structural analysis of the CCR5 –1 PRF signal a , Computationally predicted and best fit 2-dimensional mRNA structures with chemical modification data. Stems 1, 2, and the loop are indicated as S1, S2 and L. The five different segments of stem 2 are labelled a–e. Nucleotide bases showing low levels of reactivity with DMS, CMCT, and kethoxal, and ribose sugars whose 2′-OH groups with NMIA were similarly non-reactive are noted as open circles. Moderately reactive sugars and bases are denoted by grey filled circles. Strongly modified (strongly reactive) sugars and bases are represented as black filled circles. Circles proximal to the bases denote reactivity of the bases, while circles distal to the bases denote reactivity of the ribose sugars. From left to right: mRNA pseudoknot best fit to data; mRNA pseudoknot predicted by Pknots; mRNA pseudoknot predicted by NUPAK; tandem stem-loops predicted by mFold. Red bases represent chemical modification patterns inconsistent with computational predictions. b , c , Chemical modification experiments. Autoradiograms of reverse transcriptase primer extensions performed on RNA transcribed by T7 RNA Pol from template PCR amplified from CCR5 –1 PRF signal containing plasmid. Bands correspond to strong readthrough control (RT) stops 1 nucleotide 5′ of bases modified by chemical reagents. b , The CCR5 mRNA was either left unmodified (un), or modified with 3 increasing concentrations of dimethyl sulphate (DMS, reacts with A and C), 1-cyclohexyl-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate (CMCT, reacts with U), or 1,1-dihydroxy-3-ethoxy-2-butanone (kethoxal, reacts with G) respectively. c , Primer extension reactions were performed on unmodified samples and samples incubated with 30, 65, and 110 nM NMIA (N-methyl isatoic anhydride). These are labelled 1, 2 and 3, respectively, beneath each sample, and ‘un’ denotes untreated RNA. d , The all atom r.m.s.d. plot of the 80 ns-long molecular dynamics simulation states against the reference structure (the starting state of the simulation) at the end of a 2 ns-long equilibration. All measures exclude most mobile, single-stranded, first 7 nucleotides. The full structure r.m.s.d. values are shown in black, SL1 data are plotted in cyan, and the SL2 data are plotted in red. Mean r.m.s.d. values with standard deviations are given in the box. Overall, after approximately 21 ns the structure stabilizes. e , Two views (opposite sides) of an average minimized structure based on the last 12 ns of the simulation (indicated with red arrow in d ) where all the r.m.s.d. measures converge and are most stable.

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: Modification, Polymerase Chain Reaction, Amplification, Plasmid Preparation, Incubation

    The CCR5 sequence promotes efficient frameshifting a , Measurement of –1 PRF in HeLa cells. –1 PRF efficiency was monitored in HeLa cells using dual luciferase reporters. Error bars denote an approximation of standard errors. *** P

    Journal: Nature

    Article Title: Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

    doi: 10.1038/nature13429

    Figure Lengend Snippet: The CCR5 sequence promotes efficient frameshifting a , Measurement of –1 PRF in HeLa cells. –1 PRF efficiency was monitored in HeLa cells using dual luciferase reporters. Error bars denote an approximation of standard errors. *** P

    Article Snippet: The PRF signal from Homo sapiens CCR5 was amplified from pCMV-XL4 (pJD819) containing the CCR5 open reading frame (Origene) using oligonucleotides with BamHI and SalI restriction sites.

    Techniques: Sequencing, Luciferase

    Lpo protein expression detected by Western blotting and activity assay Panel A shows a Western blot of CMT-93 (CMT) cells, a CMT transfectant clone expressing Lpo ORF cDNA, colon of B6 DKO, B6 WT, 129 DKO and 129 WT 22-day-old mice, in this order. The upper panel shows the proteins recognized by anti-LPO antibody, and the lower panel shows β-actin. The open arrow points to ~90 kDa Lpo. Panel B shows the relative levels of Lpo protein in B6 and 129 DKO and WT colons, quantified from Western blots. Arrow bars are SEM from 4 colons in each group. Means that differ are shown with different letter, where a > b. Panel C shows the peroxidase activity in the colon of 10 B6 and five 129 DKO as well as 10 B6 and six 129 non-DKO control (Con) mice with at least 2 WT GPx alleles. The mean of total activity (open column) that differs is shown with different letter, where a > b > c. The mean of resorcinol-resistant activity (shaded column) that differs is shown with different number of asterisk, where *** > ** > *. The mean of NaCl-resistant activity (solid column) that differs is shown with different number of number sign, where ## > #. The error bars are standard deviations of the means.

    Journal: Free radical biology & medicine

    Article Title: Expression of lactoperoxidase in differentiated mouse colon epithelial cells

    doi: 10.1016/j.freeradbiomed.2012.02.009

    Figure Lengend Snippet: Lpo protein expression detected by Western blotting and activity assay Panel A shows a Western blot of CMT-93 (CMT) cells, a CMT transfectant clone expressing Lpo ORF cDNA, colon of B6 DKO, B6 WT, 129 DKO and 129 WT 22-day-old mice, in this order. The upper panel shows the proteins recognized by anti-LPO antibody, and the lower panel shows β-actin. The open arrow points to ~90 kDa Lpo. Panel B shows the relative levels of Lpo protein in B6 and 129 DKO and WT colons, quantified from Western blots. Arrow bars are SEM from 4 colons in each group. Means that differ are shown with different letter, where a > b. Panel C shows the peroxidase activity in the colon of 10 B6 and five 129 DKO as well as 10 B6 and six 129 non-DKO control (Con) mice with at least 2 WT GPx alleles. The mean of total activity (open column) that differs is shown with different letter, where a > b > c. The mean of resorcinol-resistant activity (shaded column) that differs is shown with different number of asterisk, where *** > ** > *. The mean of NaCl-resistant activity (solid column) that differs is shown with different number of number sign, where ## > #. The error bars are standard deviations of the means.

    Article Snippet: Since these cells expressed extremely low levels of endogenous Lpo mRNA, we generated stable Lpo transfectant clones in CMT-93 cells from an open-reading frame (ORF) of Lpo cDNA subcloned from a full-length cDNA in pCMV6-Kan/Neo plasmid (MC201302, Origene Technologies, Inc., Rockville, MD).

    Techniques: Expressing, Western Blot, Activity Assay, Transfection, Mouse Assay

    RA mediates the sim1a domain within the pronephric renal progenitor field

    Journal: Developmental biology

    Article Title: Nephron proximal tubule patterning and corpuscles of Stannius formation are regulated by the sim1a transcription factor and retinoic acid in zebrafish

    doi: 10.1016/j.ydbio.2014.12.020

    Figure Lengend Snippet: RA mediates the sim1a domain within the pronephric renal progenitor field

    Article Snippet: A pUC57 plasmid containing the sim1a transcript open reading frame was obtained from GenScript USA Inc. (Piscataway Township, NJ).

    Techniques:

    The inhibition of RA biosynthesis by DEAB induces distal fates but fails to rescue CS formation in sim1a morphants

    Journal: Developmental biology

    Article Title: Nephron proximal tubule patterning and corpuscles of Stannius formation are regulated by the sim1a transcription factor and retinoic acid in zebrafish

    doi: 10.1016/j.ydbio.2014.12.020

    Figure Lengend Snippet: The inhibition of RA biosynthesis by DEAB induces distal fates but fails to rescue CS formation in sim1a morphants

    Article Snippet: A pUC57 plasmid containing the sim1a transcript open reading frame was obtained from GenScript USA Inc. (Piscataway Township, NJ).

    Techniques: Inhibition

    sim1a morphants display drastic developmental defects and abnormal kidney function

    Journal: Developmental biology

    Article Title: Nephron proximal tubule patterning and corpuscles of Stannius formation are regulated by the sim1a transcription factor and retinoic acid in zebrafish

    doi: 10.1016/j.ydbio.2014.12.020

    Figure Lengend Snippet: sim1a morphants display drastic developmental defects and abnormal kidney function

    Article Snippet: A pUC57 plasmid containing the sim1a transcript open reading frame was obtained from GenScript USA Inc. (Piscataway Township, NJ).

    Techniques:

    The loss of sim1a results in the abrogation of the PST segment and the CS

    Journal: Developmental biology

    Article Title: Nephron proximal tubule patterning and corpuscles of Stannius formation are regulated by the sim1a transcription factor and retinoic acid in zebrafish

    doi: 10.1016/j.ydbio.2014.12.020

    Figure Lengend Snippet: The loss of sim1a results in the abrogation of the PST segment and the CS

    Article Snippet: A pUC57 plasmid containing the sim1a transcript open reading frame was obtained from GenScript USA Inc. (Piscataway Township, NJ).

    Techniques:

    sim1a overexpression is partially sufficient to promote the PST and CS while inhibiting PCT fate

    Journal: Developmental biology

    Article Title: Nephron proximal tubule patterning and corpuscles of Stannius formation are regulated by the sim1a transcription factor and retinoic acid in zebrafish

    doi: 10.1016/j.ydbio.2014.12.020

    Figure Lengend Snippet: sim1a overexpression is partially sufficient to promote the PST and CS while inhibiting PCT fate

    Article Snippet: A pUC57 plasmid containing the sim1a transcript open reading frame was obtained from GenScript USA Inc. (Piscataway Township, NJ).

    Techniques: Over Expression

    Increased RA levels promote the proximalization of the nephron but are not sufficient to rescue PST formation in sim1a morphants

    Journal: Developmental biology

    Article Title: Nephron proximal tubule patterning and corpuscles of Stannius formation are regulated by the sim1a transcription factor and retinoic acid in zebrafish

    doi: 10.1016/j.ydbio.2014.12.020

    Figure Lengend Snippet: Increased RA levels promote the proximalization of the nephron but are not sufficient to rescue PST formation in sim1a morphants

    Article Snippet: A pUC57 plasmid containing the sim1a transcript open reading frame was obtained from GenScript USA Inc. (Piscataway Township, NJ).

    Techniques:

    sim1a expression is dynamic during nephrogenesis

    Journal: Developmental biology

    Article Title: Nephron proximal tubule patterning and corpuscles of Stannius formation are regulated by the sim1a transcription factor and retinoic acid in zebrafish

    doi: 10.1016/j.ydbio.2014.12.020

    Figure Lengend Snippet: sim1a expression is dynamic during nephrogenesis

    Article Snippet: A pUC57 plasmid containing the sim1a transcript open reading frame was obtained from GenScript USA Inc. (Piscataway Township, NJ).

    Techniques: Expressing

    The regulation of Mcl-1 stability by ERK1/2 and the sensitivity of cells to U0126. (A) The levels of phospho-ERK1/2 (p-ERK1/2) and total ERK1/2 (t-ERK1/2) as determined by Western blot. A representative example of three blots is shown. (B) Drug sensitivity

    Journal: Molecular Pharmacology

    Article Title: Overexpression of Mcl-1 Confers Multidrug Resistance, Whereas Topoisomerase IIβ Downregulation Introduces Mitoxantrone-Specific Drug Resistance in Acute Myeloid Leukemia

    doi: 10.1124/mol.113.086140

    Figure Lengend Snippet: The regulation of Mcl-1 stability by ERK1/2 and the sensitivity of cells to U0126. (A) The levels of phospho-ERK1/2 (p-ERK1/2) and total ERK1/2 (t-ERK1/2) as determined by Western blot. A representative example of three blots is shown. (B) Drug sensitivity

    Article Snippet: Cells were either transfected with 12.5 nM small interfering (siRNA) (based on 2.5 ml resuspension volume) from Life Technologies or 5 µ g plasmid containing the Mcl-1 open reading frame (SC315538) from OriGene (Rockville, MD).

    Techniques: Western Blot

    The levels of Mcl-1 among HL60, HL60/MX2, and HL60/MX2/CXL017 cells and the impact of Mcl-1 downregulation on cell survival. (A) Western blot of protein levels of Mcl-1 in various cell lines. Densitometry was performed and normalized to β -actin

    Journal: Molecular Pharmacology

    Article Title: Overexpression of Mcl-1 Confers Multidrug Resistance, Whereas Topoisomerase IIβ Downregulation Introduces Mitoxantrone-Specific Drug Resistance in Acute Myeloid Leukemia

    doi: 10.1124/mol.113.086140

    Figure Lengend Snippet: The levels of Mcl-1 among HL60, HL60/MX2, and HL60/MX2/CXL017 cells and the impact of Mcl-1 downregulation on cell survival. (A) Western blot of protein levels of Mcl-1 in various cell lines. Densitometry was performed and normalized to β -actin

    Article Snippet: Cells were either transfected with 12.5 nM small interfering (siRNA) (based on 2.5 ml resuspension volume) from Life Technologies or 5 µ g plasmid containing the Mcl-1 open reading frame (SC315538) from OriGene (Rockville, MD).

    Techniques: Western Blot

    The impact of Mcl-1 upregulation on drug sensitivity. (A) Western blot of Mcl-1 levels in HL60 cells 24 hours after transfection with Mcl-1 open reading frame. (B–D) Drug sensitivity of HL60/Mcl-1 (♦) cells to mitoxantrone (B), ABT-737

    Journal: Molecular Pharmacology

    Article Title: Overexpression of Mcl-1 Confers Multidrug Resistance, Whereas Topoisomerase IIβ Downregulation Introduces Mitoxantrone-Specific Drug Resistance in Acute Myeloid Leukemia

    doi: 10.1124/mol.113.086140

    Figure Lengend Snippet: The impact of Mcl-1 upregulation on drug sensitivity. (A) Western blot of Mcl-1 levels in HL60 cells 24 hours after transfection with Mcl-1 open reading frame. (B–D) Drug sensitivity of HL60/Mcl-1 (♦) cells to mitoxantrone (B), ABT-737

    Article Snippet: Cells were either transfected with 12.5 nM small interfering (siRNA) (based on 2.5 ml resuspension volume) from Life Technologies or 5 µ g plasmid containing the Mcl-1 open reading frame (SC315538) from OriGene (Rockville, MD).

    Techniques: Western Blot, Transfection

    The regulation of Mcl-1 protein among HL60, HL60/MX2, and HL60/MX2/CXL017 cells. (A) Western Blot of Mcl-1 translation after addition of the proteasome inhibitor MG-132 for the indicated time points. Densitometry was performed and normalized to β

    Journal: Molecular Pharmacology

    Article Title: Overexpression of Mcl-1 Confers Multidrug Resistance, Whereas Topoisomerase IIβ Downregulation Introduces Mitoxantrone-Specific Drug Resistance in Acute Myeloid Leukemia

    doi: 10.1124/mol.113.086140

    Figure Lengend Snippet: The regulation of Mcl-1 protein among HL60, HL60/MX2, and HL60/MX2/CXL017 cells. (A) Western Blot of Mcl-1 translation after addition of the proteasome inhibitor MG-132 for the indicated time points. Densitometry was performed and normalized to β

    Article Snippet: Cells were either transfected with 12.5 nM small interfering (siRNA) (based on 2.5 ml resuspension volume) from Life Technologies or 5 µ g plasmid containing the Mcl-1 open reading frame (SC315538) from OriGene (Rockville, MD).

    Techniques: Western Blot