programs dna protein software version 7.0 Search Results


recombinant proteins ms 222  (Thermo Fisher)
99
Thermo Fisher recombinant proteins ms 222
Recombinant Proteins Ms 222, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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e coli σ 70 rna polymerase holoenzyme  (New England Biolabs)
95
New England Biolabs e coli σ 70 rna polymerase holoenzyme
( A ) Sequence of the torS-adjacent HK022 integration site ( attL HK022 ) in an HK022 lysogen. B, O, and P’ indicate the bacterial, overlap, and phage segments of the integration site, respectively ( ; ). The location of the Ω element terminator insertion in strain JNC175 is indicated. In this strain, transcription reading toward torS from within the HK022 prophage is blocked by the Ω element. The transcription start site, TSS HK022 , was mapped by in vitro transcription and primer extension, shown in ( C ) and ( D ). The previously inferred torS GTG start codon is outlined, and the experimentally confirmed ATG start codon is indicated as the start of the torS coding sequence. ( B ) Aerobic and anaerobic transcription of torS was measured by β-galactosidase assays in strains carrying a torS-lacZ operon fusion. Strains contained the wild-type HK022 prophage (JNC169), the prophage with an Ω element (JNC175), or had no prophage at the integration site (JNC166). Each circle represents a measurement obtained from an independent experiment, and the horizontal lines indicate average values. ( C ) In vitro transcription from plasmids containing sequence upstream of torS from the HK022 lysogen (‘HK022+’, pPK13256) or the non-lysogen (‘no phage’, pPK12669) shows that different transcripts are produced when the prophage is present or absent. Transcription using non-lysogen sequence produces two distinct transcripts, suggesting two transcription start sites for torS . <t>RNA-1</t> is a control transcript for in vitro transcription and gel loading that is generated from a <t>σ</t> <t>70</t> -regulated promoter in pPK13256 or pPK12669. ( D ) Primer extension was performed to map the transcription start site of the in vitro ‘HK022+’ transcript shown in ( C ). The position of the start site is indicated in ( A ). ( E ) Primer extension was performed to map the transcription start sites of the in vitro ‘no phage’ transcripts shown in ( C ). The positions of the start sites are indicated in ( F ). ( F ) Sequence upstream of torS in a non-lysogen, with the torS transcription start sites depicted. Transcripts originating from TSS2 can begin at the underlined G or A position, as indicated by the adjacent bands in ( E ). 10.7554/eLife.49081.012 Figure 3—source data 1. β-Galactosidase measurements for .
E Coli σ 70 Rna Polymerase Holoenzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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replication protein a rpa antibody  (Santa Cruz Biotechnology)
93
Santa Cruz Biotechnology replication protein a rpa antibody
( A ) Sequence of the torS-adjacent HK022 integration site ( attL HK022 ) in an HK022 lysogen. B, O, and P’ indicate the bacterial, overlap, and phage segments of the integration site, respectively ( ; ). The location of the Ω element terminator insertion in strain JNC175 is indicated. In this strain, transcription reading toward torS from within the HK022 prophage is blocked by the Ω element. The transcription start site, TSS HK022 , was mapped by in vitro transcription and primer extension, shown in ( C ) and ( D ). The previously inferred torS GTG start codon is outlined, and the experimentally confirmed ATG start codon is indicated as the start of the torS coding sequence. ( B ) Aerobic and anaerobic transcription of torS was measured by β-galactosidase assays in strains carrying a torS-lacZ operon fusion. Strains contained the wild-type HK022 prophage (JNC169), the prophage with an Ω element (JNC175), or had no prophage at the integration site (JNC166). Each circle represents a measurement obtained from an independent experiment, and the horizontal lines indicate average values. ( C ) In vitro transcription from plasmids containing sequence upstream of torS from the HK022 lysogen (‘HK022+’, pPK13256) or the non-lysogen (‘no phage’, pPK12669) shows that different transcripts are produced when the prophage is present or absent. Transcription using non-lysogen sequence produces two distinct transcripts, suggesting two transcription start sites for torS . <t>RNA-1</t> is a control transcript for in vitro transcription and gel loading that is generated from a <t>σ</t> <t>70</t> -regulated promoter in pPK13256 or pPK12669. ( D ) Primer extension was performed to map the transcription start site of the in vitro ‘HK022+’ transcript shown in ( C ). The position of the start site is indicated in ( A ). ( E ) Primer extension was performed to map the transcription start sites of the in vitro ‘no phage’ transcripts shown in ( C ). The positions of the start sites are indicated in ( F ). ( F ) Sequence upstream of torS in a non-lysogen, with the torS transcription start sites depicted. Transcripts originating from TSS2 can begin at the underlined G or A position, as indicated by the adjacent bands in ( E ). 10.7554/eLife.49081.012 Figure 3—source data 1. β-Galactosidase measurements for .
Replication Protein A Rpa Antibody, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rabbit polyclonal proteintech 10723 1 ap  (Proteintech)
95
Proteintech rabbit polyclonal proteintech 10723 1 ap
( A ) Sequence of the torS-adjacent HK022 integration site ( attL HK022 ) in an HK022 lysogen. B, O, and P’ indicate the bacterial, overlap, and phage segments of the integration site, respectively ( ; ). The location of the Ω element terminator insertion in strain JNC175 is indicated. In this strain, transcription reading toward torS from within the HK022 prophage is blocked by the Ω element. The transcription start site, TSS HK022 , was mapped by in vitro transcription and primer extension, shown in ( C ) and ( D ). The previously inferred torS GTG start codon is outlined, and the experimentally confirmed ATG start codon is indicated as the start of the torS coding sequence. ( B ) Aerobic and anaerobic transcription of torS was measured by β-galactosidase assays in strains carrying a torS-lacZ operon fusion. Strains contained the wild-type HK022 prophage (JNC169), the prophage with an Ω element (JNC175), or had no prophage at the integration site (JNC166). Each circle represents a measurement obtained from an independent experiment, and the horizontal lines indicate average values. ( C ) In vitro transcription from plasmids containing sequence upstream of torS from the HK022 lysogen (‘HK022+’, pPK13256) or the non-lysogen (‘no phage’, pPK12669) shows that different transcripts are produced when the prophage is present or absent. Transcription using non-lysogen sequence produces two distinct transcripts, suggesting two transcription start sites for torS . <t>RNA-1</t> is a control transcript for in vitro transcription and gel loading that is generated from a <t>σ</t> <t>70</t> -regulated promoter in pPK13256 or pPK12669. ( D ) Primer extension was performed to map the transcription start site of the in vitro ‘HK022+’ transcript shown in ( C ). The position of the start site is indicated in ( A ). ( E ) Primer extension was performed to map the transcription start sites of the in vitro ‘no phage’ transcripts shown in ( C ). The positions of the start sites are indicated in ( F ). ( F ) Sequence upstream of torS in a non-lysogen, with the torS transcription start sites depicted. Transcripts originating from TSS2 can begin at the underlined G or A position, as indicated by the adjacent bands in ( E ). 10.7554/eLife.49081.012 Figure 3—source data 1. β-Galactosidase measurements for .
Rabbit Polyclonal Proteintech 10723 1 Ap, supplied by Proteintech, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/rabbit polyclonal proteintech 10723 1 ap/product/Proteintech
Average 95 stars, based on 1 article reviews
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salmon sperm dna/protein a/g agarose beads  (Millipore)
90
Millipore salmon sperm dna/protein a/g agarose beads
( A ) Sequence of the torS-adjacent HK022 integration site ( attL HK022 ) in an HK022 lysogen. B, O, and P’ indicate the bacterial, overlap, and phage segments of the integration site, respectively ( ; ). The location of the Ω element terminator insertion in strain JNC175 is indicated. In this strain, transcription reading toward torS from within the HK022 prophage is blocked by the Ω element. The transcription start site, TSS HK022 , was mapped by in vitro transcription and primer extension, shown in ( C ) and ( D ). The previously inferred torS GTG start codon is outlined, and the experimentally confirmed ATG start codon is indicated as the start of the torS coding sequence. ( B ) Aerobic and anaerobic transcription of torS was measured by β-galactosidase assays in strains carrying a torS-lacZ operon fusion. Strains contained the wild-type HK022 prophage (JNC169), the prophage with an Ω element (JNC175), or had no prophage at the integration site (JNC166). Each circle represents a measurement obtained from an independent experiment, and the horizontal lines indicate average values. ( C ) In vitro transcription from plasmids containing sequence upstream of torS from the HK022 lysogen (‘HK022+’, pPK13256) or the non-lysogen (‘no phage’, pPK12669) shows that different transcripts are produced when the prophage is present or absent. Transcription using non-lysogen sequence produces two distinct transcripts, suggesting two transcription start sites for torS . <t>RNA-1</t> is a control transcript for in vitro transcription and gel loading that is generated from a <t>σ</t> <t>70</t> -regulated promoter in pPK13256 or pPK12669. ( D ) Primer extension was performed to map the transcription start site of the in vitro ‘HK022+’ transcript shown in ( C ). The position of the start site is indicated in ( A ). ( E ) Primer extension was performed to map the transcription start sites of the in vitro ‘no phage’ transcripts shown in ( C ). The positions of the start sites are indicated in ( F ). ( F ) Sequence upstream of torS in a non-lysogen, with the torS transcription start sites depicted. Transcripts originating from TSS2 can begin at the underlined G or A position, as indicated by the adjacent bands in ( E ). 10.7554/eLife.49081.012 Figure 3—source data 1. β-Galactosidase measurements for .
Salmon Sperm Dna/Protein A/G Agarose Beads, supplied by Millipore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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4-hydroxytamoxifen (≥70% z isomer, remainder primarily e-isomer)  (Millipore)
90
Millipore 4-hydroxytamoxifen (≥70% z isomer, remainder primarily e-isomer)
( A ) Sequence of the torS-adjacent HK022 integration site ( attL HK022 ) in an HK022 lysogen. B, O, and P’ indicate the bacterial, overlap, and phage segments of the integration site, respectively ( ; ). The location of the Ω element terminator insertion in strain JNC175 is indicated. In this strain, transcription reading toward torS from within the HK022 prophage is blocked by the Ω element. The transcription start site, TSS HK022 , was mapped by in vitro transcription and primer extension, shown in ( C ) and ( D ). The previously inferred torS GTG start codon is outlined, and the experimentally confirmed ATG start codon is indicated as the start of the torS coding sequence. ( B ) Aerobic and anaerobic transcription of torS was measured by β-galactosidase assays in strains carrying a torS-lacZ operon fusion. Strains contained the wild-type HK022 prophage (JNC169), the prophage with an Ω element (JNC175), or had no prophage at the integration site (JNC166). Each circle represents a measurement obtained from an independent experiment, and the horizontal lines indicate average values. ( C ) In vitro transcription from plasmids containing sequence upstream of torS from the HK022 lysogen (‘HK022+’, pPK13256) or the non-lysogen (‘no phage’, pPK12669) shows that different transcripts are produced when the prophage is present or absent. Transcription using non-lysogen sequence produces two distinct transcripts, suggesting two transcription start sites for torS . <t>RNA-1</t> is a control transcript for in vitro transcription and gel loading that is generated from a <t>σ</t> <t>70</t> -regulated promoter in pPK13256 or pPK12669. ( D ) Primer extension was performed to map the transcription start site of the in vitro ‘HK022+’ transcript shown in ( C ). The position of the start site is indicated in ( A ). ( E ) Primer extension was performed to map the transcription start sites of the in vitro ‘no phage’ transcripts shown in ( C ). The positions of the start sites are indicated in ( F ). ( F ) Sequence upstream of torS in a non-lysogen, with the torS transcription start sites depicted. Transcripts originating from TSS2 can begin at the underlined G or A position, as indicated by the adjacent bands in ( E ). 10.7554/eLife.49081.012 Figure 3—source data 1. β-Galactosidase measurements for .
4 Hydroxytamoxifen (≥70% Z Isomer, Remainder Primarily E Isomer), supplied by Millipore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/4-hydroxytamoxifen (≥70% z isomer, remainder primarily e-isomer)/product/Millipore
Average 90 stars, based on 1 article reviews
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qiaamp ucp dna micro kit  (Qiagen)
95
Qiagen qiaamp ucp dna micro kit
( A ) Sequence of the torS-adjacent HK022 integration site ( attL HK022 ) in an HK022 lysogen. B, O, and P’ indicate the bacterial, overlap, and phage segments of the integration site, respectively ( ; ). The location of the Ω element terminator insertion in strain JNC175 is indicated. In this strain, transcription reading toward torS from within the HK022 prophage is blocked by the Ω element. The transcription start site, TSS HK022 , was mapped by in vitro transcription and primer extension, shown in ( C ) and ( D ). The previously inferred torS GTG start codon is outlined, and the experimentally confirmed ATG start codon is indicated as the start of the torS coding sequence. ( B ) Aerobic and anaerobic transcription of torS was measured by β-galactosidase assays in strains carrying a torS-lacZ operon fusion. Strains contained the wild-type HK022 prophage (JNC169), the prophage with an Ω element (JNC175), or had no prophage at the integration site (JNC166). Each circle represents a measurement obtained from an independent experiment, and the horizontal lines indicate average values. ( C ) In vitro transcription from plasmids containing sequence upstream of torS from the HK022 lysogen (‘HK022+’, pPK13256) or the non-lysogen (‘no phage’, pPK12669) shows that different transcripts are produced when the prophage is present or absent. Transcription using non-lysogen sequence produces two distinct transcripts, suggesting two transcription start sites for torS . <t>RNA-1</t> is a control transcript for in vitro transcription and gel loading that is generated from a <t>σ</t> <t>70</t> -regulated promoter in pPK13256 or pPK12669. ( D ) Primer extension was performed to map the transcription start site of the in vitro ‘HK022+’ transcript shown in ( C ). The position of the start site is indicated in ( A ). ( E ) Primer extension was performed to map the transcription start sites of the in vitro ‘no phage’ transcripts shown in ( C ). The positions of the start sites are indicated in ( F ). ( F ) Sequence upstream of torS in a non-lysogen, with the torS transcription start sites depicted. Transcripts originating from TSS2 can begin at the underlined G or A position, as indicated by the adjacent bands in ( E ). 10.7554/eLife.49081.012 Figure 3—source data 1. β-Galactosidase measurements for .
Qiaamp Ucp Dna Micro Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/qiaamp ucp dna micro kit/product/Qiagen
Average 95 stars, based on 1 article reviews
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domain protein 2 mbd2 h 70 antibody  (Santa Cruz Biotechnology)
94
Santa Cruz Biotechnology domain protein 2 mbd2 h 70 antibody
Figure 2. B[a]P treatment results in global loss of DNA methylation in 16HBE cells. A and B, Confocal microscopy analysis of 5-mC-positive cells using a 5-mC-specific antibody; DAPI was used as control. C and D, Total protein of 16HBE cells was subjected to SDS-PAGE and probed with DNMT1, DNMT3b, or <t>MBD2-specific</t> antibodies. Data are presented in terms of percentage versus the results using non-B[a]P-treated controls, which was assigned a value of 100%, and as means + standard deviations. Significant difference versus non-B[a]P-treated control, *P < 0.05. B[a]P indicates benzo[a]pyrene; 16HBE, human bronchial epithelial cells; DAPI, 40,6-diamidino-2-phenylindole; SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis; DNMT, DNA methyltransferases; MBD2, methyl-CpG-binding protein 2.
Domain Protein 2 Mbd2 H 70 Antibody, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/domain protein 2 mbd2 h 70 antibody/product/Santa Cruz Biotechnology
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xrcc6  (Proteintech)
92
Proteintech xrcc6
Fig. 7. O6-methylguanine (O6-MG)-DNA methyltransferase (MGMT) interacts with <t>XRCC6</t> involved in the nonhomologous end joining. (A, B) Co-immunoprecipitation (Co-IP) of MGMT and XRCC6 in HCT116 (A) and SW480 (B) cells. (C, D) Reverse verification of the interaction between XRCC6 and MGMT in HCT116 (C) and SW480 (D) cells. (E) XRCC6 knockdown in HCT116 cells with or without MGMT overexpression. (F) Phospho-H2A.X (S139) (g-H2AX) staining for HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after cisplatin (DDP) treatment. (G) Percentage of g-H2AX positive cells in HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after DDP treatment. Data were statistically analyzed using Student's t-test. *P < 0.05. ns: no significance. IB: immunoblotting; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; sh: short hairpin; DAPI: 4,6-diamino-2-phenyl indole; OE: overexpression.
Xrcc6, supplied by Proteintech, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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quantum st5 gel imaging system  (VILBER GmbH)
98
VILBER GmbH quantum st5 gel imaging system
Fig. 7. O6-methylguanine (O6-MG)-DNA methyltransferase (MGMT) interacts with <t>XRCC6</t> involved in the nonhomologous end joining. (A, B) Co-immunoprecipitation (Co-IP) of MGMT and XRCC6 in HCT116 (A) and SW480 (B) cells. (C, D) Reverse verification of the interaction between XRCC6 and MGMT in HCT116 (C) and SW480 (D) cells. (E) XRCC6 knockdown in HCT116 cells with or without MGMT overexpression. (F) Phospho-H2A.X (S139) (g-H2AX) staining for HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after cisplatin (DDP) treatment. (G) Percentage of g-H2AX positive cells in HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after DDP treatment. Data were statistically analyzed using Student's t-test. *P < 0.05. ns: no significance. IB: immunoblotting; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; sh: short hairpin; DAPI: 4,6-diamino-2-phenyl indole; OE: overexpression.
Quantum St5 Gel Imaging System, supplied by VILBER GmbH, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/quantum st5 gel imaging system/product/VILBER GmbH
Average 98 stars, based on 1 article reviews
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2bscientific  (Addgene inc)
93
Addgene inc 2bscientific
Fig. 7. O6-methylguanine (O6-MG)-DNA methyltransferase (MGMT) interacts with <t>XRCC6</t> involved in the nonhomologous end joining. (A, B) Co-immunoprecipitation (Co-IP) of MGMT and XRCC6 in HCT116 (A) and SW480 (B) cells. (C, D) Reverse verification of the interaction between XRCC6 and MGMT in HCT116 (C) and SW480 (D) cells. (E) XRCC6 knockdown in HCT116 cells with or without MGMT overexpression. (F) Phospho-H2A.X (S139) (g-H2AX) staining for HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after cisplatin (DDP) treatment. (G) Percentage of g-H2AX positive cells in HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after DDP treatment. Data were statistically analyzed using Student's t-test. *P < 0.05. ns: no significance. IB: immunoblotting; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; sh: short hairpin; DAPI: 4,6-diamino-2-phenyl indole; OE: overexpression.
2bscientific, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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dna lobind  (Eppendorf AG)
94
Eppendorf AG dna lobind
Fig. 7. O6-methylguanine (O6-MG)-DNA methyltransferase (MGMT) interacts with <t>XRCC6</t> involved in the nonhomologous end joining. (A, B) Co-immunoprecipitation (Co-IP) of MGMT and XRCC6 in HCT116 (A) and SW480 (B) cells. (C, D) Reverse verification of the interaction between XRCC6 and MGMT in HCT116 (C) and SW480 (D) cells. (E) XRCC6 knockdown in HCT116 cells with or without MGMT overexpression. (F) Phospho-H2A.X (S139) (g-H2AX) staining for HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after cisplatin (DDP) treatment. (G) Percentage of g-H2AX positive cells in HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after DDP treatment. Data were statistically analyzed using Student's t-test. *P < 0.05. ns: no significance. IB: immunoblotting; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; sh: short hairpin; DAPI: 4,6-diamino-2-phenyl indole; OE: overexpression.
Dna Lobind, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


( A ) Sequence of the torS-adjacent HK022 integration site ( attL HK022 ) in an HK022 lysogen. B, O, and P’ indicate the bacterial, overlap, and phage segments of the integration site, respectively ( ; ). The location of the Ω element terminator insertion in strain JNC175 is indicated. In this strain, transcription reading toward torS from within the HK022 prophage is blocked by the Ω element. The transcription start site, TSS HK022 , was mapped by in vitro transcription and primer extension, shown in ( C ) and ( D ). The previously inferred torS GTG start codon is outlined, and the experimentally confirmed ATG start codon is indicated as the start of the torS coding sequence. ( B ) Aerobic and anaerobic transcription of torS was measured by β-galactosidase assays in strains carrying a torS-lacZ operon fusion. Strains contained the wild-type HK022 prophage (JNC169), the prophage with an Ω element (JNC175), or had no prophage at the integration site (JNC166). Each circle represents a measurement obtained from an independent experiment, and the horizontal lines indicate average values. ( C ) In vitro transcription from plasmids containing sequence upstream of torS from the HK022 lysogen (‘HK022+’, pPK13256) or the non-lysogen (‘no phage’, pPK12669) shows that different transcripts are produced when the prophage is present or absent. Transcription using non-lysogen sequence produces two distinct transcripts, suggesting two transcription start sites for torS . RNA-1 is a control transcript for in vitro transcription and gel loading that is generated from a σ 70 -regulated promoter in pPK13256 or pPK12669. ( D ) Primer extension was performed to map the transcription start site of the in vitro ‘HK022+’ transcript shown in ( C ). The position of the start site is indicated in ( A ). ( E ) Primer extension was performed to map the transcription start sites of the in vitro ‘no phage’ transcripts shown in ( C ). The positions of the start sites are indicated in ( F ). ( F ) Sequence upstream of torS in a non-lysogen, with the torS transcription start sites depicted. Transcripts originating from TSS2 can begin at the underlined G or A position, as indicated by the adjacent bands in ( E ). 10.7554/eLife.49081.012 Figure 3—source data 1. β-Galactosidase measurements for .

Journal: eLife

Article Title: Phage integration alters the respiratory strategy of its host

doi: 10.7554/eLife.49081

Figure Lengend Snippet: ( A ) Sequence of the torS-adjacent HK022 integration site ( attL HK022 ) in an HK022 lysogen. B, O, and P’ indicate the bacterial, overlap, and phage segments of the integration site, respectively ( ; ). The location of the Ω element terminator insertion in strain JNC175 is indicated. In this strain, transcription reading toward torS from within the HK022 prophage is blocked by the Ω element. The transcription start site, TSS HK022 , was mapped by in vitro transcription and primer extension, shown in ( C ) and ( D ). The previously inferred torS GTG start codon is outlined, and the experimentally confirmed ATG start codon is indicated as the start of the torS coding sequence. ( B ) Aerobic and anaerobic transcription of torS was measured by β-galactosidase assays in strains carrying a torS-lacZ operon fusion. Strains contained the wild-type HK022 prophage (JNC169), the prophage with an Ω element (JNC175), or had no prophage at the integration site (JNC166). Each circle represents a measurement obtained from an independent experiment, and the horizontal lines indicate average values. ( C ) In vitro transcription from plasmids containing sequence upstream of torS from the HK022 lysogen (‘HK022+’, pPK13256) or the non-lysogen (‘no phage’, pPK12669) shows that different transcripts are produced when the prophage is present or absent. Transcription using non-lysogen sequence produces two distinct transcripts, suggesting two transcription start sites for torS . RNA-1 is a control transcript for in vitro transcription and gel loading that is generated from a σ 70 -regulated promoter in pPK13256 or pPK12669. ( D ) Primer extension was performed to map the transcription start site of the in vitro ‘HK022+’ transcript shown in ( C ). The position of the start site is indicated in ( A ). ( E ) Primer extension was performed to map the transcription start sites of the in vitro ‘no phage’ transcripts shown in ( C ). The positions of the start sites are indicated in ( F ). ( F ) Sequence upstream of torS in a non-lysogen, with the torS transcription start sites depicted. Transcripts originating from TSS2 can begin at the underlined G or A position, as indicated by the adjacent bands in ( E ). 10.7554/eLife.49081.012 Figure 3—source data 1. β-Galactosidase measurements for .

Article Snippet: Peptide, recombinant protein , E. coli σ 70 RNA polymerase holoenzyme , New England Biolabs , NEB:M0551S , .

Techniques: Sequencing, In Vitro, Produced, Generated

Journal: eLife

Article Title: Phage integration alters the respiratory strategy of its host

doi: 10.7554/eLife.49081

Figure Lengend Snippet:

Article Snippet: Peptide, recombinant protein , E. coli σ 70 RNA polymerase holoenzyme , New England Biolabs , NEB:M0551S , .

Techniques: Recombinant, Sequencing, Plasmid Preparation, DNA Sequencing, Software

Figure 2. B[a]P treatment results in global loss of DNA methylation in 16HBE cells. A and B, Confocal microscopy analysis of 5-mC-positive cells using a 5-mC-specific antibody; DAPI was used as control. C and D, Total protein of 16HBE cells was subjected to SDS-PAGE and probed with DNMT1, DNMT3b, or MBD2-specific antibodies. Data are presented in terms of percentage versus the results using non-B[a]P-treated controls, which was assigned a value of 100%, and as means + standard deviations. Significant difference versus non-B[a]P-treated control, *P < 0.05. B[a]P indicates benzo[a]pyrene; 16HBE, human bronchial epithelial cells; DAPI, 40,6-diamidino-2-phenylindole; SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis; DNMT, DNA methyltransferases; MBD2, methyl-CpG-binding protein 2.

Journal: International journal of toxicology

Article Title: Repression of Biotin-Related Proteins by Benzo[a]Pyrene-Induced Epigenetic Modifications in Human Bronchial Epithelial Cells.

doi: 10.1177/1091581816637071

Figure Lengend Snippet: Figure 2. B[a]P treatment results in global loss of DNA methylation in 16HBE cells. A and B, Confocal microscopy analysis of 5-mC-positive cells using a 5-mC-specific antibody; DAPI was used as control. C and D, Total protein of 16HBE cells was subjected to SDS-PAGE and probed with DNMT1, DNMT3b, or MBD2-specific antibodies. Data are presented in terms of percentage versus the results using non-B[a]P-treated controls, which was assigned a value of 100%, and as means + standard deviations. Significant difference versus non-B[a]P-treated control, *P < 0.05. B[a]P indicates benzo[a]pyrene; 16HBE, human bronchial epithelial cells; DAPI, 40,6-diamidino-2-phenylindole; SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis; DNMT, DNA methyltransferases; MBD2, methyl-CpG-binding protein 2.

Article Snippet: The following antibodies were used in this study: HDAC2 (C-8) antibody (sc-9959; Santa Cruz), HDAC3 (N-19) antibody (sc-8138; Santa Cruz), DNA (cytosine-5)-methyltransferase 1 (DNMT1) (H-12) antibody (sc-271729; Santa Cruz), DNA (cytosine-5-)methyltransferase 3 beta (DNMT3b) (52A1018) antibody (sc-52922; Santa Cruz), Methyl-CpG-binding domain protein 2 (MBD2) (H-70) antibody (sc-10752; Santa Cruz), BTD (K-17) antibody (sc-48432; Santa Cruz), HCS (N-19) antibody (sc-23732; Santa Cruz), anti-acetyl-histone H3 antibody (06-599; Upstate, Darmstadt, Germany), antihistone H3 antibody (ab137760; Abcam, Cambridge, United Kingdom), anti-acetyl-histone H4 antibody (06-598; Upstate), and antihistone H4 antibody (ab7311; Abcam).

Techniques: DNA Methylation Assay, Confocal Microscopy, Control, SDS Page, Polyacrylamide Gel Electrophoresis, Binding Assay

Fig. 7. O6-methylguanine (O6-MG)-DNA methyltransferase (MGMT) interacts with XRCC6 involved in the nonhomologous end joining. (A, B) Co-immunoprecipitation (Co-IP) of MGMT and XRCC6 in HCT116 (A) and SW480 (B) cells. (C, D) Reverse verification of the interaction between XRCC6 and MGMT in HCT116 (C) and SW480 (D) cells. (E) XRCC6 knockdown in HCT116 cells with or without MGMT overexpression. (F) Phospho-H2A.X (S139) (g-H2AX) staining for HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after cisplatin (DDP) treatment. (G) Percentage of g-H2AX positive cells in HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after DDP treatment. Data were statistically analyzed using Student's t-test. *P < 0.05. ns: no significance. IB: immunoblotting; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; sh: short hairpin; DAPI: 4,6-diamino-2-phenyl indole; OE: overexpression.

Journal: Journal of pharmaceutical analysis

Article Title: MGMT activated by Wnt pathway promotes cisplatin tolerance through inducing slow-cycling cells and nonhomologous end joining in colorectal cancer.

doi: 10.1016/j.jpha.2024.02.004

Figure Lengend Snippet: Fig. 7. O6-methylguanine (O6-MG)-DNA methyltransferase (MGMT) interacts with XRCC6 involved in the nonhomologous end joining. (A, B) Co-immunoprecipitation (Co-IP) of MGMT and XRCC6 in HCT116 (A) and SW480 (B) cells. (C, D) Reverse verification of the interaction between XRCC6 and MGMT in HCT116 (C) and SW480 (D) cells. (E) XRCC6 knockdown in HCT116 cells with or without MGMT overexpression. (F) Phospho-H2A.X (S139) (g-H2AX) staining for HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after cisplatin (DDP) treatment. (G) Percentage of g-H2AX positive cells in HCT116 cells with or without XRCC6 knockdown and MGMT overexpression after DDP treatment. Data were statistically analyzed using Student's t-test. *P < 0.05. ns: no significance. IB: immunoblotting; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; sh: short hairpin; DAPI: 4,6-diamino-2-phenyl indole; OE: overexpression.

Article Snippet: The tubes were heated and boiled at 100 C for 10 min. To detect CDK1 (ET1607-51; Huabio, Hangzhou, China), XRCC6 (66607-1-Ig; Proteintech), and HA tag (51064-2-AP; Proteintech) expression, Western blotting was performed.

Techniques: Immunoprecipitation, Co-Immunoprecipitation Assay, Knockdown, Over Expression, Staining, Western Blot