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  • 99
    Expression Systems Inc sf9 cells
    Recombinant TRAIP supports CMG unloading at cisplatin-ICLs a, NPE immunodepleted of TRAIP was loaded alongside a dilution series of mock-depleted NPE and blotted for TRAIP. A relative loading amount of 100 corresponds to 2 µl of NPE. Non-specifically detected proteins are marked with asterisks. b, Bacterially-expressed rTRAIP WT , rTRAIP R18C , His 6 -SUMO-rTRAIP WT , and His 6 -SUMO-rTRAIP ΔPIP (comprising residues 1-455) were partially purified, resolved by SDS-PAGE, and visualized with Coomassie Brilliant Blue staining. Note that His 6 -SUMO-rTRAIP is obscured by co-migrating, contaminating proteins. Bacterially-expressed rTRAIP was used for all subsequent experiments, unless otherwise indicated. c, rTRAIP WT and rTRAIP R18C were expressed in <t>Sf9</t> insect cells and purified using an N-terminal 3×FLAG tag. The tag was then cleaved using 3C protease. The recombinant proteins, along with a buffer sample containing 3C protease only, were resolved by SDS-PAGE and visualized with Coomassie Brilliant Blue staining. d, Mock- and TRAIP-depleted extracts supplemented with rTRAIP WT or rTRAIP R18C used in Fig. 1b were analyzed by immunoblotting for TRAIP. The absence of the non-specific bands seen in a may be due to shorter incubation with the TRAIP antibody. The concentration of added recombinant TRAIP relative to endogenous TRAIP fluctuates among experiments (e.g. compare panel d and Extended Data Fig. 3b ). We ascribe this difference to variations in non-specific removal of endogenous TRAIP from extracts during the mock-depletion procedure, and possibly also in the delivery of recombinant TRAIP into extract. e, pICL Pt was replicated in mock- or TRAIP-depleted extracts supplemented with [α- 32 P]dATP and Sf9-expressed rTRAIP WT , rTRAIP R18C , or 3C protease alone and analyzed as in Fig. 1b . f, Extracts used in the replication reaction shown in e were analyzed as in d . g, pICL Pt was replicated in the indicated egg extracts with [α- 32 P]dATP and analyzed as in Fig. 1b . h, Extracts used in the replication reaction shown in g were analyzed as in d . Note that deleting the C-terminal PIP box disrupts the epitope for the TRAIP antibody used for immunoblotting. Therefore, to assess the activity of TRAIP ΔPIP in ICL repair relative to TRAIP WT , His 6 -SUMO-tagged proteins were added back to TRAIP-depleted extract and assayed in g . The relative amounts of His 6 -SUMO-TRAIP WT and His 6 -SUMO-TRAIP ΔPIP were compared by detecting the histidine tag. By blotting the same extracts for TRAIP, a comparison of the relative concentrations of His 6 -SUMO-TRAIP ΔPIP and endogenous TRAIP was made. i, Mock- and TRAIP-depleted extracts used in the replication reactions shown in Fig. 1c and d were analyzed as in d .
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    Zymo Research zr plasmid miniprep classic kit
    Recombinant TRAIP supports CMG unloading at cisplatin-ICLs a, NPE immunodepleted of TRAIP was loaded alongside a dilution series of mock-depleted NPE and blotted for TRAIP. A relative loading amount of 100 corresponds to 2 µl of NPE. Non-specifically detected proteins are marked with asterisks. b, Bacterially-expressed rTRAIP WT , rTRAIP R18C , His 6 -SUMO-rTRAIP WT , and His 6 -SUMO-rTRAIP ΔPIP (comprising residues 1-455) were partially purified, resolved by SDS-PAGE, and visualized with Coomassie Brilliant Blue staining. Note that His 6 -SUMO-rTRAIP is obscured by co-migrating, contaminating proteins. Bacterially-expressed rTRAIP was used for all subsequent experiments, unless otherwise indicated. c, rTRAIP WT and rTRAIP R18C were expressed in <t>Sf9</t> insect cells and purified using an N-terminal 3×FLAG tag. The tag was then cleaved using 3C protease. The recombinant proteins, along with a buffer sample containing 3C protease only, were resolved by SDS-PAGE and visualized with Coomassie Brilliant Blue staining. d, Mock- and TRAIP-depleted extracts supplemented with rTRAIP WT or rTRAIP R18C used in Fig. 1b were analyzed by immunoblotting for TRAIP. The absence of the non-specific bands seen in a may be due to shorter incubation with the TRAIP antibody. The concentration of added recombinant TRAIP relative to endogenous TRAIP fluctuates among experiments (e.g. compare panel d and Extended Data Fig. 3b ). We ascribe this difference to variations in non-specific removal of endogenous TRAIP from extracts during the mock-depletion procedure, and possibly also in the delivery of recombinant TRAIP into extract. e, pICL Pt was replicated in mock- or TRAIP-depleted extracts supplemented with [α- 32 P]dATP and Sf9-expressed rTRAIP WT , rTRAIP R18C , or 3C protease alone and analyzed as in Fig. 1b . f, Extracts used in the replication reaction shown in e were analyzed as in d . g, pICL Pt was replicated in the indicated egg extracts with [α- 32 P]dATP and analyzed as in Fig. 1b . h, Extracts used in the replication reaction shown in g were analyzed as in d . Note that deleting the C-terminal PIP box disrupts the epitope for the TRAIP antibody used for immunoblotting. Therefore, to assess the activity of TRAIP ΔPIP in ICL repair relative to TRAIP WT , His 6 -SUMO-tagged proteins were added back to TRAIP-depleted extract and assayed in g . The relative amounts of His 6 -SUMO-TRAIP WT and His 6 -SUMO-TRAIP ΔPIP were compared by detecting the histidine tag. By blotting the same extracts for TRAIP, a comparison of the relative concentrations of His 6 -SUMO-TRAIP ΔPIP and endogenous TRAIP was made. i, Mock- and TRAIP-depleted extracts used in the replication reactions shown in Fig. 1c and d were analyzed as in d .
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    Zymo Research zr plasmid miniprep kit
    Recombinant TRAIP supports CMG unloading at cisplatin-ICLs a, NPE immunodepleted of TRAIP was loaded alongside a dilution series of mock-depleted NPE and blotted for TRAIP. A relative loading amount of 100 corresponds to 2 µl of NPE. Non-specifically detected proteins are marked with asterisks. b, Bacterially-expressed rTRAIP WT , rTRAIP R18C , His 6 -SUMO-rTRAIP WT , and His 6 -SUMO-rTRAIP ΔPIP (comprising residues 1-455) were partially purified, resolved by SDS-PAGE, and visualized with Coomassie Brilliant Blue staining. Note that His 6 -SUMO-rTRAIP is obscured by co-migrating, contaminating proteins. Bacterially-expressed rTRAIP was used for all subsequent experiments, unless otherwise indicated. c, rTRAIP WT and rTRAIP R18C were expressed in <t>Sf9</t> insect cells and purified using an N-terminal 3×FLAG tag. The tag was then cleaved using 3C protease. The recombinant proteins, along with a buffer sample containing 3C protease only, were resolved by SDS-PAGE and visualized with Coomassie Brilliant Blue staining. d, Mock- and TRAIP-depleted extracts supplemented with rTRAIP WT or rTRAIP R18C used in Fig. 1b were analyzed by immunoblotting for TRAIP. The absence of the non-specific bands seen in a may be due to shorter incubation with the TRAIP antibody. The concentration of added recombinant TRAIP relative to endogenous TRAIP fluctuates among experiments (e.g. compare panel d and Extended Data Fig. 3b ). We ascribe this difference to variations in non-specific removal of endogenous TRAIP from extracts during the mock-depletion procedure, and possibly also in the delivery of recombinant TRAIP into extract. e, pICL Pt was replicated in mock- or TRAIP-depleted extracts supplemented with [α- 32 P]dATP and Sf9-expressed rTRAIP WT , rTRAIP R18C , or 3C protease alone and analyzed as in Fig. 1b . f, Extracts used in the replication reaction shown in e were analyzed as in d . g, pICL Pt was replicated in the indicated egg extracts with [α- 32 P]dATP and analyzed as in Fig. 1b . h, Extracts used in the replication reaction shown in g were analyzed as in d . Note that deleting the C-terminal PIP box disrupts the epitope for the TRAIP antibody used for immunoblotting. Therefore, to assess the activity of TRAIP ΔPIP in ICL repair relative to TRAIP WT , His 6 -SUMO-tagged proteins were added back to TRAIP-depleted extract and assayed in g . The relative amounts of His 6 -SUMO-TRAIP WT and His 6 -SUMO-TRAIP ΔPIP were compared by detecting the histidine tag. By blotting the same extracts for TRAIP, a comparison of the relative concentrations of His 6 -SUMO-TRAIP ΔPIP and endogenous TRAIP was made. i, Mock- and TRAIP-depleted extracts used in the replication reactions shown in Fig. 1c and d were analyzed as in d .
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    Zymo Research total rna
    Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded <t>RNA</t> (dsRNA) of <t>RNAi-5x</t> insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.
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    Zymo Research zr fungal bacterial dna miniprep kit
    Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded <t>RNA</t> (dsRNA) of <t>RNAi-5x</t> insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.
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    Thermo Fisher rna
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    Illumina Inc nextera xt kit
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    Qiagen qiaprep spin miniprep kit
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    Zymo Research zr bac dna miniprep kit
    Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded <t>RNA</t> (dsRNA) of <t>RNAi-5x</t> insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.
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    Zymo Research genomic dna
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    DeNovix ds 11 spectrophotometer
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    Illumina Inc nextera dna
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    Thermo Fisher one shot top10
    Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded <t>RNA</t> (dsRNA) of <t>RNAi-5x</t> insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.
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    Zymo Research zymoclean gel dna recovery kit
    Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded <t>RNA</t> (dsRNA) of <t>RNAi-5x</t> insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.
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    Thermo Fisher competent escherichia coli
    Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded <t>RNA</t> (dsRNA) of <t>RNAi-5x</t> insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.
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    Thermo Fisher t4 dna ligase
    Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded <t>RNA</t> (dsRNA) of <t>RNAi-5x</t> insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.
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    Thermo Fisher dntp set
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    Thermo Fisher ta cloning kit
    Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded <t>RNA</t> (dsRNA) of <t>RNAi-5x</t> insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.
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    Zymo Research ampicillin resistant clones
    Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded <t>RNA</t> (dsRNA) of <t>RNAi-5x</t> insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.
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    Santa Cruz Biotechnology captopril
    Effect of the ACE-inhibitor <t>Captopril,</t> the AngII-receptor blocker Losartan and AngII on adhesion of wild type (THP-1 WT), empty plasmid (Control) and ACE-overexpressing cells (ACE1). Calcein-labelled cells were incubated in the presence or absence of (A) 500 nM captopril or (B) 1 µM losartan for 30 min and tested for their adhesion abilities to endothelial HUVEC monolayers. (C) Endothelial-adhesion of ACE-negative wild type THP-1 cells in the presence of 1 µM AngII only or co-incubation with 1 µM losartan investigated for 30 min. Representative images for (A, B, C) are shown. Analyses for (A, B, C) were performed in 10 random microscopic fields each. * p
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    Image Search Results


    Recombinant TRAIP supports CMG unloading at cisplatin-ICLs a, NPE immunodepleted of TRAIP was loaded alongside a dilution series of mock-depleted NPE and blotted for TRAIP. A relative loading amount of 100 corresponds to 2 µl of NPE. Non-specifically detected proteins are marked with asterisks. b, Bacterially-expressed rTRAIP WT , rTRAIP R18C , His 6 -SUMO-rTRAIP WT , and His 6 -SUMO-rTRAIP ΔPIP (comprising residues 1-455) were partially purified, resolved by SDS-PAGE, and visualized with Coomassie Brilliant Blue staining. Note that His 6 -SUMO-rTRAIP is obscured by co-migrating, contaminating proteins. Bacterially-expressed rTRAIP was used for all subsequent experiments, unless otherwise indicated. c, rTRAIP WT and rTRAIP R18C were expressed in Sf9 insect cells and purified using an N-terminal 3×FLAG tag. The tag was then cleaved using 3C protease. The recombinant proteins, along with a buffer sample containing 3C protease only, were resolved by SDS-PAGE and visualized with Coomassie Brilliant Blue staining. d, Mock- and TRAIP-depleted extracts supplemented with rTRAIP WT or rTRAIP R18C used in Fig. 1b were analyzed by immunoblotting for TRAIP. The absence of the non-specific bands seen in a may be due to shorter incubation with the TRAIP antibody. The concentration of added recombinant TRAIP relative to endogenous TRAIP fluctuates among experiments (e.g. compare panel d and Extended Data Fig. 3b ). We ascribe this difference to variations in non-specific removal of endogenous TRAIP from extracts during the mock-depletion procedure, and possibly also in the delivery of recombinant TRAIP into extract. e, pICL Pt was replicated in mock- or TRAIP-depleted extracts supplemented with [α- 32 P]dATP and Sf9-expressed rTRAIP WT , rTRAIP R18C , or 3C protease alone and analyzed as in Fig. 1b . f, Extracts used in the replication reaction shown in e were analyzed as in d . g, pICL Pt was replicated in the indicated egg extracts with [α- 32 P]dATP and analyzed as in Fig. 1b . h, Extracts used in the replication reaction shown in g were analyzed as in d . Note that deleting the C-terminal PIP box disrupts the epitope for the TRAIP antibody used for immunoblotting. Therefore, to assess the activity of TRAIP ΔPIP in ICL repair relative to TRAIP WT , His 6 -SUMO-tagged proteins were added back to TRAIP-depleted extract and assayed in g . The relative amounts of His 6 -SUMO-TRAIP WT and His 6 -SUMO-TRAIP ΔPIP were compared by detecting the histidine tag. By blotting the same extracts for TRAIP, a comparison of the relative concentrations of His 6 -SUMO-TRAIP ΔPIP and endogenous TRAIP was made. i, Mock- and TRAIP-depleted extracts used in the replication reactions shown in Fig. 1c and d were analyzed as in d .

    Journal: Nature

    Article Title: TRAIP is a master regulator of DNA interstrand cross-link repair

    doi: 10.1038/s41586-019-1002-0

    Figure Lengend Snippet: Recombinant TRAIP supports CMG unloading at cisplatin-ICLs a, NPE immunodepleted of TRAIP was loaded alongside a dilution series of mock-depleted NPE and blotted for TRAIP. A relative loading amount of 100 corresponds to 2 µl of NPE. Non-specifically detected proteins are marked with asterisks. b, Bacterially-expressed rTRAIP WT , rTRAIP R18C , His 6 -SUMO-rTRAIP WT , and His 6 -SUMO-rTRAIP ΔPIP (comprising residues 1-455) were partially purified, resolved by SDS-PAGE, and visualized with Coomassie Brilliant Blue staining. Note that His 6 -SUMO-rTRAIP is obscured by co-migrating, contaminating proteins. Bacterially-expressed rTRAIP was used for all subsequent experiments, unless otherwise indicated. c, rTRAIP WT and rTRAIP R18C were expressed in Sf9 insect cells and purified using an N-terminal 3×FLAG tag. The tag was then cleaved using 3C protease. The recombinant proteins, along with a buffer sample containing 3C protease only, were resolved by SDS-PAGE and visualized with Coomassie Brilliant Blue staining. d, Mock- and TRAIP-depleted extracts supplemented with rTRAIP WT or rTRAIP R18C used in Fig. 1b were analyzed by immunoblotting for TRAIP. The absence of the non-specific bands seen in a may be due to shorter incubation with the TRAIP antibody. The concentration of added recombinant TRAIP relative to endogenous TRAIP fluctuates among experiments (e.g. compare panel d and Extended Data Fig. 3b ). We ascribe this difference to variations in non-specific removal of endogenous TRAIP from extracts during the mock-depletion procedure, and possibly also in the delivery of recombinant TRAIP into extract. e, pICL Pt was replicated in mock- or TRAIP-depleted extracts supplemented with [α- 32 P]dATP and Sf9-expressed rTRAIP WT , rTRAIP R18C , or 3C protease alone and analyzed as in Fig. 1b . f, Extracts used in the replication reaction shown in e were analyzed as in d . g, pICL Pt was replicated in the indicated egg extracts with [α- 32 P]dATP and analyzed as in Fig. 1b . h, Extracts used in the replication reaction shown in g were analyzed as in d . Note that deleting the C-terminal PIP box disrupts the epitope for the TRAIP antibody used for immunoblotting. Therefore, to assess the activity of TRAIP ΔPIP in ICL repair relative to TRAIP WT , His 6 -SUMO-tagged proteins were added back to TRAIP-depleted extract and assayed in g . The relative amounts of His 6 -SUMO-TRAIP WT and His 6 -SUMO-TRAIP ΔPIP were compared by detecting the histidine tag. By blotting the same extracts for TRAIP, a comparison of the relative concentrations of His 6 -SUMO-TRAIP ΔPIP and endogenous TRAIP was made. i, Mock- and TRAIP-depleted extracts used in the replication reactions shown in Fig. 1c and d were analyzed as in d .

    Article Snippet: CMG baculovirus was generated by transfecting pGC187 bacmid into Sf9 cells (Expression Systems) for 96 hr, and amplifying the virus in 2 rounds of 96 hr each.

    Techniques: Recombinant, Purification, SDS Page, Staining, Incubation, Concentration Assay, Activity Assay

    TRAIP ubiquitylates numerous CMG subunits with heterotypically-linked chains upon fork convergence at an ICL a, pICL- lacO Pt was incubated with LacR prior to replication in mock- or TRAIP-depleted extracts. After 1 hr of replication (to allow for termination of replication forks that do not converge on the ICL or lacO array as depicted in Fig. 2c ), 0.3 mM NMS-873 was added and the extracts were incubated for 5 min to inhibit p97. 10 mM IPTG and Sf9-expressed rTRAIP WT were then added as indicated and the extract was incubated for 2 hr to disrupt LacR DNA binding and allow fork convergence and TRAIP-dependent ubiquitylation. The plasmid was recovered and blotted for the indicated proteins. b, The extracts described in a were blotted for TRAIP. c, pICL- lacO Pt was incubated with LacR prior to replication in undepleted egg extracts. After 30 min of replication (to allow for termination of replication forks that do not converge on the ICL or lacO array as depicted in Fig. 2c ), 0.3 mM NMS-873 was added and the extracts were incubated for 5 min to inhibit p97. 10 mM IPTG was then added as indicated to disrupt LacR DNA binding and the extract was incubated for 1 hr to allow fork convergence. The plasmid was recovered and blotted for the indicated proteins. d, Recombinant CMG was purified, resolved by SDS-PAGE, and visualized with SYPRO ruby staining. e, rTRAIP ubiquitin ligase activity. rTRAIP WT or rTRAIP R18C was combined with ubiquitin, E1, three E2s (UbcH5a/b/c), and ATP as indicated. Polyubiquitin chain synthesis (top gel) and TRAIP autoubiquitylation (bottom gel) were detected by immunoblotting the reactions with ubiquitin and TRAIP antibody, respectively. Notably, rTRAIP R18C was much more compromised in forming free polyubiquitin chains in this assay than it was in ubiquitylating rCMG (see Fig. 2d ). The data suggest that the interaction between TRAIP and CMG can suppress, to a great extent, the profound ubiquitylation defect of the R18C mutation. f, pCTRL- lacO and pICL- lacO Pt were replicated in undepleted extract as in c and recovered. Samples were treated with the indicated DUBs and blotted for the indicated proteins. g, pCTRL- lacO and pICL- lacO Pt pre-bound with LacR were replicated in undepleted extract as in c . At the time of IPTG addition to release the LacR array and allow fork convergence, 100 µM recombinant ubiquitin (wild-type or various lysine-to-arginine mutants) was added to the extract (which contains ~8 µM endogenous ubiquitin) and incubated for 1 hr. The plasmid was recovered and blotted for the indicated proteins. h, Extracts used in g were blotted for ubiquitin. Some ubiquitin mutants contain a di-ubiquitin species (marked with asterisk). Whether this arises upon addition to extract is unclear.

    Journal: Nature

    Article Title: TRAIP is a master regulator of DNA interstrand cross-link repair

    doi: 10.1038/s41586-019-1002-0

    Figure Lengend Snippet: TRAIP ubiquitylates numerous CMG subunits with heterotypically-linked chains upon fork convergence at an ICL a, pICL- lacO Pt was incubated with LacR prior to replication in mock- or TRAIP-depleted extracts. After 1 hr of replication (to allow for termination of replication forks that do not converge on the ICL or lacO array as depicted in Fig. 2c ), 0.3 mM NMS-873 was added and the extracts were incubated for 5 min to inhibit p97. 10 mM IPTG and Sf9-expressed rTRAIP WT were then added as indicated and the extract was incubated for 2 hr to disrupt LacR DNA binding and allow fork convergence and TRAIP-dependent ubiquitylation. The plasmid was recovered and blotted for the indicated proteins. b, The extracts described in a were blotted for TRAIP. c, pICL- lacO Pt was incubated with LacR prior to replication in undepleted egg extracts. After 30 min of replication (to allow for termination of replication forks that do not converge on the ICL or lacO array as depicted in Fig. 2c ), 0.3 mM NMS-873 was added and the extracts were incubated for 5 min to inhibit p97. 10 mM IPTG was then added as indicated to disrupt LacR DNA binding and the extract was incubated for 1 hr to allow fork convergence. The plasmid was recovered and blotted for the indicated proteins. d, Recombinant CMG was purified, resolved by SDS-PAGE, and visualized with SYPRO ruby staining. e, rTRAIP ubiquitin ligase activity. rTRAIP WT or rTRAIP R18C was combined with ubiquitin, E1, three E2s (UbcH5a/b/c), and ATP as indicated. Polyubiquitin chain synthesis (top gel) and TRAIP autoubiquitylation (bottom gel) were detected by immunoblotting the reactions with ubiquitin and TRAIP antibody, respectively. Notably, rTRAIP R18C was much more compromised in forming free polyubiquitin chains in this assay than it was in ubiquitylating rCMG (see Fig. 2d ). The data suggest that the interaction between TRAIP and CMG can suppress, to a great extent, the profound ubiquitylation defect of the R18C mutation. f, pCTRL- lacO and pICL- lacO Pt were replicated in undepleted extract as in c and recovered. Samples were treated with the indicated DUBs and blotted for the indicated proteins. g, pCTRL- lacO and pICL- lacO Pt pre-bound with LacR were replicated in undepleted extract as in c . At the time of IPTG addition to release the LacR array and allow fork convergence, 100 µM recombinant ubiquitin (wild-type or various lysine-to-arginine mutants) was added to the extract (which contains ~8 µM endogenous ubiquitin) and incubated for 1 hr. The plasmid was recovered and blotted for the indicated proteins. h, Extracts used in g were blotted for ubiquitin. Some ubiquitin mutants contain a di-ubiquitin species (marked with asterisk). Whether this arises upon addition to extract is unclear.

    Article Snippet: CMG baculovirus was generated by transfecting pGC187 bacmid into Sf9 cells (Expression Systems) for 96 hr, and amplifying the virus in 2 rounds of 96 hr each.

    Techniques: Incubation, Binding Assay, Plasmid Preparation, Recombinant, Purification, SDS Page, Staining, Activity Assay, Mutagenesis

    Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded RNA (dsRNA) of RNAi-5x insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.

    Journal: Scientific Reports

    Article Title: Analysis of small RNA populations generated in peanut leaves after exogenous application of dsRNA and dsDNA targeting aflatoxin synthesis genes

    doi: 10.1038/s41598-020-70618-6

    Figure Lengend Snippet: Schematic representation of the treatments using particle bombardment with the dsRNA insert. ( A ) Double-stranded RNA (dsRNA) of RNAi-5x insert. ( B ) Plasmid DNA (p5xCAPD) containing inverted repeats to generate dsDNA. ( C ) In-vitro -grown peanut plants, carved weighing dish, and Helios gene gun used for delivery of RNAi-5x insert.

    Article Snippet: Total RNA was extracted from these leaves (control, RNAi-5x, and dsDNA) using the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA, USA), according to manufacturer’s instructions.

    Techniques: Plasmid Preparation, In Vitro

    Effect of the ACE-inhibitor Captopril, the AngII-receptor blocker Losartan and AngII on adhesion of wild type (THP-1 WT), empty plasmid (Control) and ACE-overexpressing cells (ACE1). Calcein-labelled cells were incubated in the presence or absence of (A) 500 nM captopril or (B) 1 µM losartan for 30 min and tested for their adhesion abilities to endothelial HUVEC monolayers. (C) Endothelial-adhesion of ACE-negative wild type THP-1 cells in the presence of 1 µM AngII only or co-incubation with 1 µM losartan investigated for 30 min. Representative images for (A, B, C) are shown. Analyses for (A, B, C) were performed in 10 random microscopic fields each. * p

    Journal: PLoS ONE

    Article Title: Uremic Conditions Drive Human Monocytes to Pro-Atherogenic Differentiation via an Angiotensin-Dependent Mechanism

    doi: 10.1371/journal.pone.0102137

    Figure Lengend Snippet: Effect of the ACE-inhibitor Captopril, the AngII-receptor blocker Losartan and AngII on adhesion of wild type (THP-1 WT), empty plasmid (Control) and ACE-overexpressing cells (ACE1). Calcein-labelled cells were incubated in the presence or absence of (A) 500 nM captopril or (B) 1 µM losartan for 30 min and tested for their adhesion abilities to endothelial HUVEC monolayers. (C) Endothelial-adhesion of ACE-negative wild type THP-1 cells in the presence of 1 µM AngII only or co-incubation with 1 µM losartan investigated for 30 min. Representative images for (A, B, C) are shown. Analyses for (A, B, C) were performed in 10 random microscopic fields each. * p

    Article Snippet: ACE/AngII-receptor inhibition studies were performed with captopril (ACE inhibitor, Santa Cruz Biotechnology) or losartan (Angiotensin II type 1 receptor (AT1R) antagonist, Santa Cruz Biotechnology) or angiotensin II (Sigma).

    Techniques: Plasmid Preparation, Incubation