dna ladder  (Thermo Fisher)


Bioz Verified Symbol Thermo Fisher is a verified supplier
Bioz Manufacturer Symbol Thermo Fisher manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 86

    Structured Review

    Thermo Fisher dna ladder
    Electrophoretic analysis of the nucleic acids associated to fractions F3 and F4 of S. coelicolor MVs. M: <t>DNA</t> Molecular Weight Marker IV (Roche).
    Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna ladder/product/Thermo Fisher
    Average 86 stars, based on 40 article reviews
    Price from $9.99 to $1999.99
    dna ladder - by Bioz Stars, 2022-11
    86/100 stars

    Images

    1) Product Images from "Unravelling the DNA sequences carried by Streptomyces coelicolor membrane vesicles"

    Article Title: Unravelling the DNA sequences carried by Streptomyces coelicolor membrane vesicles

    Journal: Scientific Reports

    doi: 10.1038/s41598-022-21002-z

    Electrophoretic analysis of the nucleic acids associated to fractions F3 and F4 of S. coelicolor MVs. M: DNA Molecular Weight Marker IV (Roche).
    Figure Legend Snippet: Electrophoretic analysis of the nucleic acids associated to fractions F3 and F4 of S. coelicolor MVs. M: DNA Molecular Weight Marker IV (Roche).

    Techniques Used: Molecular Weight, Marker

    2) Product Images from "Real-time monitoring of isothermal nucleic acid amplification on a smartphone by using a portable electrochemical device for home-testing of SARS-CoV-2"

    Article Title: Real-time monitoring of isothermal nucleic acid amplification on a smartphone by using a portable electrochemical device for home-testing of SARS-CoV-2

    Journal: Analytica Chimica Acta

    doi: 10.1016/j.aca.2022.340343

    (A) Normalized potential-time curves of electrochemical LAMP assays for E. coli O157:H7 samples in E-INAATs device. Inset is the agarose gel electrophoresis images of LAMP products of relevant samples. M represented DNA ladder (2000 bp). 1–5 represented the reaction systems containing 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , 2 × 10 2 , and 2 × 10 1 CFU E. coli O157:H7, respectively. NTC represented no template control. (B) Fluorescence curves of the LAMP reaction for the same samples. (C) Absorbance of the colorimetric LAMP reaction systems for the same samples. (D) Visible color change of the colorimetric LAMP reaction systems with reaction time for the same samples (unit: CFU).
    Figure Legend Snippet: (A) Normalized potential-time curves of electrochemical LAMP assays for E. coli O157:H7 samples in E-INAATs device. Inset is the agarose gel electrophoresis images of LAMP products of relevant samples. M represented DNA ladder (2000 bp). 1–5 represented the reaction systems containing 2 × 10 5 , 2 × 10 4 , 2 × 10 3 , 2 × 10 2 , and 2 × 10 1 CFU E. coli O157:H7, respectively. NTC represented no template control. (B) Fluorescence curves of the LAMP reaction for the same samples. (C) Absorbance of the colorimetric LAMP reaction systems for the same samples. (D) Visible color change of the colorimetric LAMP reaction systems with reaction time for the same samples (unit: CFU).

    Techniques Used: Agarose Gel Electrophoresis, Fluorescence

    (A) Normalized potential-time curves of electrochemical LAMP assays for the artificial samples containing various concentrations of SARS-CoV-2 pseudovirus in E-INAATs device. Inset is the agarose gel electrophoresis images of LAMP products of relevant artificial samples. M represented DNA ladder (2000 bp). 1–4 represented artificial nasopharyngeal swabs prepared with 10 8 , 10 7 , 10 6 , and 10 5 copies/mL SARS-CoV-2 pseudovirus suspensions, respectively. NTC represented no template control. (B) Fluorescence curves of the LAMP reaction for the same artificial samples. (C) Absorbance of the colorimetric LAMP reaction systems for the same artificial samples. (D) Visible color change of the colorimetric LAMP reaction systems with time for the same artificial samples (unit: copies/mL).
    Figure Legend Snippet: (A) Normalized potential-time curves of electrochemical LAMP assays for the artificial samples containing various concentrations of SARS-CoV-2 pseudovirus in E-INAATs device. Inset is the agarose gel electrophoresis images of LAMP products of relevant artificial samples. M represented DNA ladder (2000 bp). 1–4 represented artificial nasopharyngeal swabs prepared with 10 8 , 10 7 , 10 6 , and 10 5 copies/mL SARS-CoV-2 pseudovirus suspensions, respectively. NTC represented no template control. (B) Fluorescence curves of the LAMP reaction for the same artificial samples. (C) Absorbance of the colorimetric LAMP reaction systems for the same artificial samples. (D) Visible color change of the colorimetric LAMP reaction systems with time for the same artificial samples (unit: copies/mL).

    Techniques Used: Agarose Gel Electrophoresis, Fluorescence

    3) Product Images from "Genomic characterization of viruses associated with the parasitoid Anagyrus vladimiri (Hymenoptera: Encyrtidae)"

    Article Title: Genomic characterization of viruses associated with the parasitoid Anagyrus vladimiri (Hymenoptera: Encyrtidae)

    Journal: bioRxiv

    doi: 10.1101/2022.07.15.500286

    Electrophoresis pattern (using a 0.8% agarose gel) of VNAs extracted from A. vladimiri , which were treated by RNase and DNase separately. ‘AV’ denotes VNAs of A. vladimiri . ‘SSC’ denotes sodium citrate buffer, which was used in 0.01x and 2x ionic strengths. ‘10’/‘0.1’ denotes high/low concentration (μg/ml) of RNase respectively. Details by lane numbers: 1-3; no digestion treatment. 1; 1Kb ladder (1KB+, Invitrogen, MA, USA), 2; Phi6 – a ladder made of viral dsRNA (Invitrogen, MA, USA), 3; A. vladimiri VNA. 4-11; Digestion by RNase A in four buffer/enzyme concentrations. 4-7; Phi6 ladder as a control for the enzymatic activity of RNase. 8-11; AV digestion. 12-13; Digestion by DNase I, 12; 1Kb – a DNA ladder as a control for the enzymatic activity of DNase. 13; AV digestion.
    Figure Legend Snippet: Electrophoresis pattern (using a 0.8% agarose gel) of VNAs extracted from A. vladimiri , which were treated by RNase and DNase separately. ‘AV’ denotes VNAs of A. vladimiri . ‘SSC’ denotes sodium citrate buffer, which was used in 0.01x and 2x ionic strengths. ‘10’/‘0.1’ denotes high/low concentration (μg/ml) of RNase respectively. Details by lane numbers: 1-3; no digestion treatment. 1; 1Kb ladder (1KB+, Invitrogen, MA, USA), 2; Phi6 – a ladder made of viral dsRNA (Invitrogen, MA, USA), 3; A. vladimiri VNA. 4-11; Digestion by RNase A in four buffer/enzyme concentrations. 4-7; Phi6 ladder as a control for the enzymatic activity of RNase. 8-11; AV digestion. 12-13; Digestion by DNase I, 12; 1Kb – a DNA ladder as a control for the enzymatic activity of DNase. 13; AV digestion.

    Techniques Used: Electrophoresis, Agarose Gel Electrophoresis, Concentration Assay, Activity Assay

    4) Product Images from "Topical application of Porphyromonas gingivalis into the gingival pocket in mice leads to chronic-active infection, periodontitis and systemic inflammation"

    Article Title: Topical application of Porphyromonas gingivalis into the gingival pocket in mice leads to chronic-active infection, periodontitis and systemic inflammation

    Journal: International Journal of Molecular Medicine

    doi: 10.3892/ijmm.2022.5159

    Research design and electrophoretic images of amplified Pg DNA from the gingival pocket swabs of mice collected at 4 and 8 weeks after the final PBS or Pg inoculation for 5 weeks. (A) Schematic diagram of the research design. (B) Electrophoretic image of amplified Pg DNA from mice sacrificed 4 weeks after completing the last inoculation (inoculation duration, 5 weeks). (C) Electrophoretic image of amplified Pg DNA from mice sacrificed 8 weeks after completing the last inoculation (inoculation duration, 5 weeks). The lanes indicate the following: +, positive control (1,000 CFU of purified Pg DNA); -, negative control; 1–10, samples taken from the gingival pocket. Pg, Porphyromonas gingivalis.
    Figure Legend Snippet: Research design and electrophoretic images of amplified Pg DNA from the gingival pocket swabs of mice collected at 4 and 8 weeks after the final PBS or Pg inoculation for 5 weeks. (A) Schematic diagram of the research design. (B) Electrophoretic image of amplified Pg DNA from mice sacrificed 4 weeks after completing the last inoculation (inoculation duration, 5 weeks). (C) Electrophoretic image of amplified Pg DNA from mice sacrificed 8 weeks after completing the last inoculation (inoculation duration, 5 weeks). The lanes indicate the following: +, positive control (1,000 CFU of purified Pg DNA); -, negative control; 1–10, samples taken from the gingival pocket. Pg, Porphyromonas gingivalis.

    Techniques Used: Amplification, Mouse Assay, Positive Control, Purification, Negative Control

    5) Product Images from "Taf2 mediates DNA binding of Taf14"

    Article Title: Taf2 mediates DNA binding of Taf14

    Journal: Nature Communications

    doi: 10.1038/s41467-022-30937-w

    Binding of Taf14 FL to the nucleosome requires binding to Taf2 CT . a – c EMSAs of H3K9cr-NCP 147 in the presence of increasing amounts of the indicated GST-Taf14 or Taf14 proteins (and Taf2 CT in c). Architecture of each Taf14 construct is depicted above gels. Images are from single experiment. d EMSA of 37 bp dsDNA in the presence of increasing amounts of the indicated GST-Taf14 (and Taf2 CT in lane 9). Architecture of the Taf14 construct is depicted above the gel. GST-Taf14 FL and Taf2 CT were premixed at a 1:10 molar ratio prior to incubation with DNA. e A schematic of the mechanism for the engagement of Taf14 FL with NCP: following the interaction with Taf2 CT , the released Taf14 Linker binds DNA/NCP. f Reverse transcriptase qPCR analysis of various transcripts in the TAF14 full-length rescued strain, vector only strain, taf14 ET delete strain (Taf14 ΔET ), and taf14 mutant strains (Taf14 7k/Rmut and Taf14 W81A ). The mean ± SD are calculated from three biological replicates. ACT1 was used as a normalization control. Two-tailed multiple T tests were performed, * P
    Figure Legend Snippet: Binding of Taf14 FL to the nucleosome requires binding to Taf2 CT . a – c EMSAs of H3K9cr-NCP 147 in the presence of increasing amounts of the indicated GST-Taf14 or Taf14 proteins (and Taf2 CT in c). Architecture of each Taf14 construct is depicted above gels. Images are from single experiment. d EMSA of 37 bp dsDNA in the presence of increasing amounts of the indicated GST-Taf14 (and Taf2 CT in lane 9). Architecture of the Taf14 construct is depicted above the gel. GST-Taf14 FL and Taf2 CT were premixed at a 1:10 molar ratio prior to incubation with DNA. e A schematic of the mechanism for the engagement of Taf14 FL with NCP: following the interaction with Taf2 CT , the released Taf14 Linker binds DNA/NCP. f Reverse transcriptase qPCR analysis of various transcripts in the TAF14 full-length rescued strain, vector only strain, taf14 ET delete strain (Taf14 ΔET ), and taf14 mutant strains (Taf14 7k/Rmut and Taf14 W81A ). The mean ± SD are calculated from three biological replicates. ACT1 was used as a normalization control. Two-tailed multiple T tests were performed, * P

    Techniques Used: Binding Assay, Construct, Incubation, Real-time Polymerase Chain Reaction, Plasmid Preparation, Mutagenesis, Two Tailed Test

    DNA binding activity of Taf14 Linker . a Overlay of 1 H 15 ,N HSQC spectra of Taf14 FL in the presence of increasing amount of 147 bp 601 DNA. Spectra are color coded according to the protein:DNA molar ratio. b – e EMSAs of 147 bp 601 DNA in the presence of increasing amounts of the indicated GST-Taf14 proteins. DNA:protein ratio is shown below gel images. Images are from single experiment. Architecture of each Taf14 construct is depicted above the gels, and mutations are indicated with a blue asterisk. f , g Superimposed 1 H 15 ,N HSQC spectra of the indicated Taf14 proteins collected upon titration with 147 bp 601 DNA (f) or Taf2 Linker g . Spectra are colored according to the protein:ligand molar ratio. h MST binding curves for the Taf2 Linker interaction with Taf14 ET . The K d value represents average of two independent measurements, and error represents the standard deviation. n = 2 i , j Mass spectrometry analysis wheel diagram showing positions of DSSO-generated cross-links identified in the Taf14 FL ( i ) or Taf14 FL + 37 bp dsDNA j . Line thickness relates to the number of cross-link identifications. Taf14 domains within the circle are colored as in Fig. 1a . k Dimentionless Kratky plots of SAXS analysis for the indicated samples: Taf14 FL (blue), Taf14 FL + Taf2 CT (orange), or Taf14 FL + 37 bp dsDNA (green). l A model of the conformational rearrangement in Taf14 FL upon binding to DNA. m Overlay of 1 H 15 ,N HSQC spectra of Taf14 FL in the presence of increasing amounts of H3K9cr 1-19 peptide. Spectra are colored according to the protein:peptide molar ratio. Source data are provided in a Source Data file.
    Figure Legend Snippet: DNA binding activity of Taf14 Linker . a Overlay of 1 H 15 ,N HSQC spectra of Taf14 FL in the presence of increasing amount of 147 bp 601 DNA. Spectra are color coded according to the protein:DNA molar ratio. b – e EMSAs of 147 bp 601 DNA in the presence of increasing amounts of the indicated GST-Taf14 proteins. DNA:protein ratio is shown below gel images. Images are from single experiment. Architecture of each Taf14 construct is depicted above the gels, and mutations are indicated with a blue asterisk. f , g Superimposed 1 H 15 ,N HSQC spectra of the indicated Taf14 proteins collected upon titration with 147 bp 601 DNA (f) or Taf2 Linker g . Spectra are colored according to the protein:ligand molar ratio. h MST binding curves for the Taf2 Linker interaction with Taf14 ET . The K d value represents average of two independent measurements, and error represents the standard deviation. n = 2 i , j Mass spectrometry analysis wheel diagram showing positions of DSSO-generated cross-links identified in the Taf14 FL ( i ) or Taf14 FL + 37 bp dsDNA j . Line thickness relates to the number of cross-link identifications. Taf14 domains within the circle are colored as in Fig. 1a . k Dimentionless Kratky plots of SAXS analysis for the indicated samples: Taf14 FL (blue), Taf14 FL + Taf2 CT (orange), or Taf14 FL + 37 bp dsDNA (green). l A model of the conformational rearrangement in Taf14 FL upon binding to DNA. m Overlay of 1 H 15 ,N HSQC spectra of Taf14 FL in the presence of increasing amounts of H3K9cr 1-19 peptide. Spectra are colored according to the protein:peptide molar ratio. Source data are provided in a Source Data file.

    Techniques Used: Binding Assay, Activity Assay, Construct, Titration, Standard Deviation, Mass Spectrometry, Generated

    6) Product Images from "CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice"

    Article Title: CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice

    Journal: bioRxiv

    doi: 10.1101/2022.05.20.492479

    Bar plot showing colony forming units per µg DNA (CFU/µg DNA) in a logarithmic scale of transformed E. lenta DSM 15644 cells with plasmid pNZ123 and derivatives that provides chloramphenicol resistance. E. lenta DSM 15644 was transformed with pNZ123 (WT) and two derivatives containing each the same two protospacers but a different PAM (pNZ123::GGG-S2-GGG-S1, pNZ123::TTC-S2-TTC-S1, pNZ123::WT). Absence of plasmid transformation indicates interference activity of the type I-C CRISPR-Cas system. Transformation assays were performed 2, 2, 4, and 4 times, respectively.
    Figure Legend Snippet: Bar plot showing colony forming units per µg DNA (CFU/µg DNA) in a logarithmic scale of transformed E. lenta DSM 15644 cells with plasmid pNZ123 and derivatives that provides chloramphenicol resistance. E. lenta DSM 15644 was transformed with pNZ123 (WT) and two derivatives containing each the same two protospacers but a different PAM (pNZ123::GGG-S2-GGG-S1, pNZ123::TTC-S2-TTC-S1, pNZ123::WT). Absence of plasmid transformation indicates interference activity of the type I-C CRISPR-Cas system. Transformation assays were performed 2, 2, 4, and 4 times, respectively.

    Techniques Used: Transformation Assay, Plasmid Preparation, Activity Assay, CRISPR

    Overview of spacer acquisitions in the in vivo settings. a) An agarose gel showing spacer acquisitions in selected samples representing EL+Phage mice from day 5, day 12, day 19, and day 26, as well as from controls at arrival (Day 1) and baseline mice. A 100-bp DNA ladder was used to estimate PCR product size. With the degenerate primers, the acquisition of one spacer “+1” was expected to yield a PCR product at ∼110 bp (Figure S1) and then ∼70 bp for additional spacers. The PCR-product at ∼40 bp likely represented primer dimers. b) The annotated phage genome of PMBT5 highlight the genes that are presented in c) with a line plot showing reads/spacers over time and d) as a bar plot showing the number of reads/spacers that matched at the phage genome. Only one phage gene coding for a hypothetical protein (YP_009807312.1) appeared as a source of spacer s . This is marked by a box with red dashed lines. HP = hypothetical protein.
    Figure Legend Snippet: Overview of spacer acquisitions in the in vivo settings. a) An agarose gel showing spacer acquisitions in selected samples representing EL+Phage mice from day 5, day 12, day 19, and day 26, as well as from controls at arrival (Day 1) and baseline mice. A 100-bp DNA ladder was used to estimate PCR product size. With the degenerate primers, the acquisition of one spacer “+1” was expected to yield a PCR product at ∼110 bp (Figure S1) and then ∼70 bp for additional spacers. The PCR-product at ∼40 bp likely represented primer dimers. b) The annotated phage genome of PMBT5 highlight the genes that are presented in c) with a line plot showing reads/spacers over time and d) as a bar plot showing the number of reads/spacers that matched at the phage genome. Only one phage gene coding for a hypothetical protein (YP_009807312.1) appeared as a source of spacer s . This is marked by a box with red dashed lines. HP = hypothetical protein.

    Techniques Used: In Vivo, Agarose Gel Electrophoresis, Mouse Assay, Polymerase Chain Reaction

    Overview of spacer acquisitions in the in vitro settings. a) Growth curve of E. lenta DSM 15644 during infection with phage PMBT5 at four different multiplicities of infections (MOI) and a control with no phages added. Bacterial growth was measured at several time points (absorbance at OD 600nm ) for 144 hours. b) Expanded CRISPR arrays in selected samples (Figure S8 for all samples) representing two replicates of all four MOI after 48 hours and 24 hours of incubation of E. lenta DSM 15644 exposed to phage PMBT5. DNA ladder is a 100-bp scale. With the degenerate primers, the expanded CRISPR array with one spacer “+1” was expected to yield a PCR product at ∼110 bp (Figure S1). No expanded CRISPR arrays were observed in samples with no added phages (after 48 hours incubation) or with MilliQ water added. The PCR-product at ∼40 bp likely represented primer dimers. c) The annotated genome of phage PMBT5 highlights the genes that are presented in d) with a bar plot showing the number of reads/spacers that matched to phage genes at MOI 10, 1, 0.01, and 0.01. Three genes appeared as hotspots of spacer acquisitions (coding for the portal protein (YP_009807283.1*) and two hypothetical proteins (YP_009807291.1** and YP_009807318.1***) and are marked by boxes with red dashed lines. A few genes were targeted at different positions (Pos) within the same gene. e) Graph illustrating a tendency of an inverse relation between MOI and cell density (OD 600nm ) of reads/spacer acquisitions in E. lenta DSM 15644 exposed to phage PMBT5.
    Figure Legend Snippet: Overview of spacer acquisitions in the in vitro settings. a) Growth curve of E. lenta DSM 15644 during infection with phage PMBT5 at four different multiplicities of infections (MOI) and a control with no phages added. Bacterial growth was measured at several time points (absorbance at OD 600nm ) for 144 hours. b) Expanded CRISPR arrays in selected samples (Figure S8 for all samples) representing two replicates of all four MOI after 48 hours and 24 hours of incubation of E. lenta DSM 15644 exposed to phage PMBT5. DNA ladder is a 100-bp scale. With the degenerate primers, the expanded CRISPR array with one spacer “+1” was expected to yield a PCR product at ∼110 bp (Figure S1). No expanded CRISPR arrays were observed in samples with no added phages (after 48 hours incubation) or with MilliQ water added. The PCR-product at ∼40 bp likely represented primer dimers. c) The annotated genome of phage PMBT5 highlights the genes that are presented in d) with a bar plot showing the number of reads/spacers that matched to phage genes at MOI 10, 1, 0.01, and 0.01. Three genes appeared as hotspots of spacer acquisitions (coding for the portal protein (YP_009807283.1*) and two hypothetical proteins (YP_009807291.1** and YP_009807318.1***) and are marked by boxes with red dashed lines. A few genes were targeted at different positions (Pos) within the same gene. e) Graph illustrating a tendency of an inverse relation between MOI and cell density (OD 600nm ) of reads/spacer acquisitions in E. lenta DSM 15644 exposed to phage PMBT5.

    Techniques Used: In Vitro, Infection, CRISPR, Incubation, Polymerase Chain Reaction

    7) Product Images from "Enzymatic hydrolysis of lignocellulosic biomass using a novel, thermotolerant recombinant xylosidase enzyme from Clostridium clariflavum: a potential addition for biofuel industry"

    Article Title: Enzymatic hydrolysis of lignocellulosic biomass using a novel, thermotolerant recombinant xylosidase enzyme from Clostridium clariflavum: a potential addition for biofuel industry

    Journal: RSC Advances

    doi: 10.1039/d2ra00304j

    Amplified C. clariflavum xylosidase gene is shown on agarose gel; DNA marker in lane 1, amplified xylosidase gene in lane 2, amplified xylosidase gene in lane 3, and single restricted recombinant pET-21a (+) along xylosidase gene in lane 4.
    Figure Legend Snippet: Amplified C. clariflavum xylosidase gene is shown on agarose gel; DNA marker in lane 1, amplified xylosidase gene in lane 2, amplified xylosidase gene in lane 3, and single restricted recombinant pET-21a (+) along xylosidase gene in lane 4.

    Techniques Used: Amplification, Agarose Gel Electrophoresis, Marker, Recombinant, Positron Emission Tomography

    8) Product Images from "CvkR, a novel MerR-type transcriptional regulator, is a repressor of class 2 type V-K CRISPR-associated transposase systems"

    Article Title: CvkR, a novel MerR-type transcriptional regulator, is a repressor of class 2 type V-K CRISPR-associated transposase systems

    Journal: bioRxiv

    doi: 10.1101/2022.05.13.491168

    Leaderless expression of cvkR genes. A. Deduced amino acid sequence alignment of 53 MerR-family CvkR homologs. The sequences of the MerR-family CvkR homologs for the multiple sequence alignment were recovered from public databases and are available as supplemental dataset S2. The sequences were aligned using MAFFT 60 and visualized with UGENE 61 . Only the N-terminal ∼200 amino acids are displayed for clarity reasons. B. Distances between the cas12k effector complex and cvkR genes are plotted according to the respective type of regulator, MerR-like (53 instances), CopG-like (11 cases), Omega-like (22 cases) and nonspecific HTH domain-containing proteins (8 cases). The box plots are colored according to the respective DNA-binding domain (HTH: blue; RHH: red). C. qRT–PCR analyses verify that cvkR is transcribed in Δ cvkR Com strains. The amounts of cvkR transcripts were normalized to those of rnpB as an internal standard. Three independent experiments were performed, which showed consistent results. D . Western blot analyses confirmed the leaderless expression of CvkR. Upper panel, Western blot against the C-terminal 3xFLAG tag; Lower panel, ponceau S staining shows that equal amounts of protein were loaded (100 μg). The calculated molecular masses for CvkR-S and CvkR-L were 20.03 kDa and 22.41 kDa, respectively. Two independent experiments were performed, which showed consistent results. The Δ cvkR Com-1, 2 and 3 strains are detailed in Fig. S1C .
    Figure Legend Snippet: Leaderless expression of cvkR genes. A. Deduced amino acid sequence alignment of 53 MerR-family CvkR homologs. The sequences of the MerR-family CvkR homologs for the multiple sequence alignment were recovered from public databases and are available as supplemental dataset S2. The sequences were aligned using MAFFT 60 and visualized with UGENE 61 . Only the N-terminal ∼200 amino acids are displayed for clarity reasons. B. Distances between the cas12k effector complex and cvkR genes are plotted according to the respective type of regulator, MerR-like (53 instances), CopG-like (11 cases), Omega-like (22 cases) and nonspecific HTH domain-containing proteins (8 cases). The box plots are colored according to the respective DNA-binding domain (HTH: blue; RHH: red). C. qRT–PCR analyses verify that cvkR is transcribed in Δ cvkR Com strains. The amounts of cvkR transcripts were normalized to those of rnpB as an internal standard. Three independent experiments were performed, which showed consistent results. D . Western blot analyses confirmed the leaderless expression of CvkR. Upper panel, Western blot against the C-terminal 3xFLAG tag; Lower panel, ponceau S staining shows that equal amounts of protein were loaded (100 μg). The calculated molecular masses for CvkR-S and CvkR-L were 20.03 kDa and 22.41 kDa, respectively. Two independent experiments were performed, which showed consistent results. The Δ cvkR Com-1, 2 and 3 strains are detailed in Fig. S1C .

    Techniques Used: Expressing, Sequencing, Binding Assay, Quantitative RT-PCR, Western Blot, Staining

    Assays to test cas12k promoter elements. A. Sequences of the tested promoter fragments. Putative -35 and -10 cas12k promoter elements are shown in blue and green, respectively. B. EMSA of the P cas12k full-length and truncated fragments after DNA incubation for 40 min with different concentrations of CvkR. C. CvkR was expressed from vector pET28a and was detected by Western blot analysis via the N-terminal 6xHis tag (upper panel), and the stained membrane is shown in the lower panel. The corresponding size for 6xHis-CvkR is 19.9 kDa. The prestained PageRuler (Thermo Scientific) was used as a size marker. D. The full-length version of P cas12k and the P43 fragment encompassing 43 nt upstream of the cas12k TSS were tested in the TXTL system 24 for their capacity to drive deGFP expression and mediate repression upon parallel expression of CvkR. CvkR was expressed together with the corresponding p70a plasmids (5 nM) with the two promoter variants upstream of deGFP. E. TXTL assay for the promoter sequences P39 (positions -56 to -18 relative to the TSS of cas12k ), P26 (positions -42 to -18) and P20 (positions -42 to -18). F. TXTL assay to compare the promoter activities of cas12k , cvkR and tracrRNA (P cas12k , P cvkR , Ptracr). CvkR was used to repress transcription. Error bars show standard deviations calculated from 2 technical replicates in panels D to F.
    Figure Legend Snippet: Assays to test cas12k promoter elements. A. Sequences of the tested promoter fragments. Putative -35 and -10 cas12k promoter elements are shown in blue and green, respectively. B. EMSA of the P cas12k full-length and truncated fragments after DNA incubation for 40 min with different concentrations of CvkR. C. CvkR was expressed from vector pET28a and was detected by Western blot analysis via the N-terminal 6xHis tag (upper panel), and the stained membrane is shown in the lower panel. The corresponding size for 6xHis-CvkR is 19.9 kDa. The prestained PageRuler (Thermo Scientific) was used as a size marker. D. The full-length version of P cas12k and the P43 fragment encompassing 43 nt upstream of the cas12k TSS were tested in the TXTL system 24 for their capacity to drive deGFP expression and mediate repression upon parallel expression of CvkR. CvkR was expressed together with the corresponding p70a plasmids (5 nM) with the two promoter variants upstream of deGFP. E. TXTL assay for the promoter sequences P39 (positions -56 to -18 relative to the TSS of cas12k ), P26 (positions -42 to -18) and P20 (positions -42 to -18). F. TXTL assay to compare the promoter activities of cas12k , cvkR and tracrRNA (P cas12k , P cvkR , Ptracr). CvkR was used to repress transcription. Error bars show standard deviations calculated from 2 technical replicates in panels D to F.

    Techniques Used: Incubation, Plasmid Preparation, Western Blot, Staining, Marker, Expressing

    Overall structure of CvkR. A . Ribbon representation of the CvkR-ATP complex in ASU. The DNA-binding, dimerization, and effector-binding domains are shown in blue, magenta, and yellow, respectively. The typical helix-turn-helix (HTH) and two “wing” loops W1 and W2 in the DNA-binding domain are indicated. The ATP ligand is represented in green sticks and colored by the atom type. The secondary structure elements of CvkR are labeled. B . Ribbon representation of the homodimer structure of CvkR through a crystallographic symmetry operator. The novel dimerization is formed by three antiparallel β-strands (β2-β1-β3) and one short α-helix (α6) from the two protomers in the dimer. The distances between two α2-helices and between two W1 regions are measured and labeled, respectively. C . Structural comparison of MerR-type proteins. The DNA-binding domain of one subunit of CueR (PDB code 1Q07), MerR (PDB code 4UA1) and HiNmlR (PDB code 5D90) is separately superimposed on that of CvkR. The structural data can be accessed under the PDB accession number 7XN2.
    Figure Legend Snippet: Overall structure of CvkR. A . Ribbon representation of the CvkR-ATP complex in ASU. The DNA-binding, dimerization, and effector-binding domains are shown in blue, magenta, and yellow, respectively. The typical helix-turn-helix (HTH) and two “wing” loops W1 and W2 in the DNA-binding domain are indicated. The ATP ligand is represented in green sticks and colored by the atom type. The secondary structure elements of CvkR are labeled. B . Ribbon representation of the homodimer structure of CvkR through a crystallographic symmetry operator. The novel dimerization is formed by three antiparallel β-strands (β2-β1-β3) and one short α-helix (α6) from the two protomers in the dimer. The distances between two α2-helices and between two W1 regions are measured and labeled, respectively. C . Structural comparison of MerR-type proteins. The DNA-binding domain of one subunit of CueR (PDB code 1Q07), MerR (PDB code 4UA1) and HiNmlR (PDB code 5D90) is separately superimposed on that of CvkR. The structural data can be accessed under the PDB accession number 7XN2.

    Techniques Used: Binding Assay, Labeling

    CvkR interaction with cas12k promoter fragments and predicted binding motifs. A. Left panel, EMSA showing the direct binding of different amounts of CvkR to the cas12k promoter DNA. Right panel, DNase I footprinting assay. The cas12k promoter DNA was digested in the presence of different concentrations of CvkR. The fragmentation pattern indicated a core region of 43 nt that was protected from DNase I degradation in the presence of CvkR (inner dot-and-dashed lines) embedded in a longer segment protected at higher CvkR concentrations (outer dot-and-dashed lines). B. The intergenic spacers between cvkR and cas12k from 6 different CASTs were aligned and analyzed for potential promoter elements. The -35 (blue) and -10 (green) regions for both promoters as well as the transcription start site of cas12k (black) are marked, which were previously identified 21 or predicted by PromoterHunter 23 (nucleotides in italics). The CvkR protected region in the DNase I footprinting assay is marked, which contains a conserved inverted repeat surrounding the -35 region of the cas12k promoter (boxed and highlighted in yellow). The sequences are also visualized as sequence logo.
    Figure Legend Snippet: CvkR interaction with cas12k promoter fragments and predicted binding motifs. A. Left panel, EMSA showing the direct binding of different amounts of CvkR to the cas12k promoter DNA. Right panel, DNase I footprinting assay. The cas12k promoter DNA was digested in the presence of different concentrations of CvkR. The fragmentation pattern indicated a core region of 43 nt that was protected from DNase I degradation in the presence of CvkR (inner dot-and-dashed lines) embedded in a longer segment protected at higher CvkR concentrations (outer dot-and-dashed lines). B. The intergenic spacers between cvkR and cas12k from 6 different CASTs were aligned and analyzed for potential promoter elements. The -35 (blue) and -10 (green) regions for both promoters as well as the transcription start site of cas12k (black) are marked, which were previously identified 21 or predicted by PromoterHunter 23 (nucleotides in italics). The CvkR protected region in the DNase I footprinting assay is marked, which contains a conserved inverted repeat surrounding the -35 region of the cas12k promoter (boxed and highlighted in yellow). The sequences are also visualized as sequence logo.

    Techniques Used: Binding Assay, Footprinting, Sequencing

    Phylogenetic tree of all CvkR homologs. The identified CvkR proteins were aligned using M-coffee 48 , 49 and analyzed by BEAST 50 . As a prior tree module, we used a Yule process for 1,000,000 states, log processed every 1,000 steps. The resulting tree is depicted with branches labeled with their respective posterior probability until a threshold of 0.5. For better recognition, the proteins were also labeled with their host organism as well as their repressor type and DNA interaction domain. The Anabaena 7120 CvkR (Alr3614) (NCBI: BAB75313.1) (green dashed box) is marked as well as its most similar homologs ( > 70% shared identity, highlighted by a blue-dashed box). Asterisks label four instances of CvkRs fused to an hsdR restriction enzyme domain. The multiple sequence alignment is available as supplemental dataset S1 .
    Figure Legend Snippet: Phylogenetic tree of all CvkR homologs. The identified CvkR proteins were aligned using M-coffee 48 , 49 and analyzed by BEAST 50 . As a prior tree module, we used a Yule process for 1,000,000 states, log processed every 1,000 steps. The resulting tree is depicted with branches labeled with their respective posterior probability until a threshold of 0.5. For better recognition, the proteins were also labeled with their host organism as well as their repressor type and DNA interaction domain. The Anabaena 7120 CvkR (Alr3614) (NCBI: BAB75313.1) (green dashed box) is marked as well as its most similar homologs ( > 70% shared identity, highlighted by a blue-dashed box). Asterisks label four instances of CvkRs fused to an hsdR restriction enzyme domain. The multiple sequence alignment is available as supplemental dataset S1 .

    Techniques Used: Labeling, Sequencing

    9) Product Images from "Simple, sensitive, and cost-effective detection of wAlbB Wolbachia in Aedes mosquitoes, using loop mediated isothermal amplification combined with the electrochemical biosensing method"

    Article Title: Simple, sensitive, and cost-effective detection of wAlbB Wolbachia in Aedes mosquitoes, using loop mediated isothermal amplification combined with the electrochemical biosensing method

    Journal: PLoS Neglected Tropical Diseases

    doi: 10.1371/journal.pntd.0009600

    Sensitivity of LAMP (A and B) and PCR (C) detections with sample dilution experiment (Left) and mosquito pool sample experiment (Right). LAMP assay with ethidium bromide-stained gel (A) and HNB indicator (B) of a fold-dilution of an individual crude boiling Aedes aegypti ( w AlbB-TH) sample (182 ng/μl, 260/280 = 1.90, 260/230 = 0.99) diluted 10 −1 –10 −6 times (6.4 units of Bst 2.0 DNA polymerase, 65°C for 90 min and 80°C for 10 min, volume 10 μl). Polymerase chain reaction with wsp primers (691R and 183F) of the same dilution (C). (O) is a non-diluted original sample, (P) is Wolbachia trans-infected Ae . aegypti ( w AlbB-TH), (N1) is wild-type Ae . aegypti (Aae-JJ), (N2) is 100 wild-type Ae . aegypti (Aae-JJ), (NTC) is no template control, (M) is Invitrogen 100 bp DNA Ladder. For mosquito pooled experiment, the ratio of 1/25 indicates the DNA extraction was performed with one Wolbachia trans-infected Ae . aegypti and 24 wild-type Ae . aegypti . Other pooled samples included 1/50, 1/75, and 1/100, which were equivalent to one w AlbB-TH mosquito in 49, 74, and 99 Aae-JJ, respectively.
    Figure Legend Snippet: Sensitivity of LAMP (A and B) and PCR (C) detections with sample dilution experiment (Left) and mosquito pool sample experiment (Right). LAMP assay with ethidium bromide-stained gel (A) and HNB indicator (B) of a fold-dilution of an individual crude boiling Aedes aegypti ( w AlbB-TH) sample (182 ng/μl, 260/280 = 1.90, 260/230 = 0.99) diluted 10 −1 –10 −6 times (6.4 units of Bst 2.0 DNA polymerase, 65°C for 90 min and 80°C for 10 min, volume 10 μl). Polymerase chain reaction with wsp primers (691R and 183F) of the same dilution (C). (O) is a non-diluted original sample, (P) is Wolbachia trans-infected Ae . aegypti ( w AlbB-TH), (N1) is wild-type Ae . aegypti (Aae-JJ), (N2) is 100 wild-type Ae . aegypti (Aae-JJ), (NTC) is no template control, (M) is Invitrogen 100 bp DNA Ladder. For mosquito pooled experiment, the ratio of 1/25 indicates the DNA extraction was performed with one Wolbachia trans-infected Ae . aegypti and 24 wild-type Ae . aegypti . Other pooled samples included 1/50, 1/75, and 1/100, which were equivalent to one w AlbB-TH mosquito in 49, 74, and 99 Aae-JJ, respectively.

    Techniques Used: Polymerase Chain Reaction, Lamp Assay, Staining, Infection, DNA Extraction

    Detection of Wolbachia w AlbB gene in different mosquito species using LAMP assay with HNB indicator (A) and ethidium bromide-stained gel (B): (1) no template control, (2) wild-type Aedes aegypti (AegW, Aae-JJ), (3) Wobachia trans-infected Thai Ae . aegypti (AegB, w AlbB-TH), (4) Aedes albopictus (Alb, Aal-CH), and (5) Culex quinquefasciatus (Cq-BK). M is 1 kb plus DNA Ladder from Invitrogen. The condition for LAMP reaction was 6.4 units of Bst 2.0 DNA polymerase, 65°C for 60 min and 80°C for 10 min.
    Figure Legend Snippet: Detection of Wolbachia w AlbB gene in different mosquito species using LAMP assay with HNB indicator (A) and ethidium bromide-stained gel (B): (1) no template control, (2) wild-type Aedes aegypti (AegW, Aae-JJ), (3) Wobachia trans-infected Thai Ae . aegypti (AegB, w AlbB-TH), (4) Aedes albopictus (Alb, Aal-CH), and (5) Culex quinquefasciatus (Cq-BK). M is 1 kb plus DNA Ladder from Invitrogen. The condition for LAMP reaction was 6.4 units of Bst 2.0 DNA polymerase, 65°C for 60 min and 80°C for 10 min.

    Techniques Used: Lamp Assay, Staining, Infection

    10) Product Images from "The Sigma Factor AlgU Regulates Exopolysaccharide Production and Nitrogen-Fixing Biofilm Formation by Directly Activating the Transcription of pslA in Pseudomonas stutzeri A1501"

    Article Title: The Sigma Factor AlgU Regulates Exopolysaccharide Production and Nitrogen-Fixing Biofilm Formation by Directly Activating the Transcription of pslA in Pseudomonas stutzeri A1501

    Journal: Genes

    doi: 10.3390/genes13050867

    Regulation of the algU gene in A1501. ( A ) The relative expression levels of algU and pslA in P. stutzeri wild-type A1501 under two different growth conditions (growth with 6 mM NH 4 + : A1501 incubated in minimal K medium containing 50 mM lactate and 6 mM NH 4 + for 4 h under an aerobic atmosphere (O 2 , 21%); nitrogen-fixing growth: A1501 was incubated in minimal K medium containing 50 mM lactate and 0 mM NH 4 + under a microaerobic atmosphere (O 2 , 0.5%) for 4 h). ( B ) Relative expression levels of algU in P. stutzeri wild-type A1501, rpoN mutant Δ rpoN , nifA mutant Δ nifA and ntrC mutant Δ ntrC . ( C ) Promoter analysis of the algU gene. The predicted AlgU-binding site RpoN-binding site and RsmA-binding site were located within the upstream region of the start codon of algU . The corresponding −10 and −35 regions of the AlgU-binding site were underlined and the RpoN-binding sites were boxed. +1 indicated the transcriptional start site determined by the 5′ RACE assay. The predicted RsmA-binding site was shown in bold font. ( D ) Gel mobility shift analysis of RpoN and the algU promoter. A DNA fragment from Halomonas venusta was used as negative control and the nifA promoter from A1501 was used as a positive control. ( E ) Gel mobility shift analysis of the RsmA protein with AlgU 5′UTR RNA oligonucleotides. 80 nM AlgU RNA was used to bind the RsmA protein. The positions of free and bound RNA were indicated. The RNA oligonucleotides AlgU and RsmY were synthesized in Genepharma Company. The RsmA binding site AGGA was in bold, and the initiation codon (AUG) for algU was indicated in red. Error bars represent the standard deviation (SD) of the three biological replicates. Asterisks indicate statistical significance by one-way ANOVA: ** p
    Figure Legend Snippet: Regulation of the algU gene in A1501. ( A ) The relative expression levels of algU and pslA in P. stutzeri wild-type A1501 under two different growth conditions (growth with 6 mM NH 4 + : A1501 incubated in minimal K medium containing 50 mM lactate and 6 mM NH 4 + for 4 h under an aerobic atmosphere (O 2 , 21%); nitrogen-fixing growth: A1501 was incubated in minimal K medium containing 50 mM lactate and 0 mM NH 4 + under a microaerobic atmosphere (O 2 , 0.5%) for 4 h). ( B ) Relative expression levels of algU in P. stutzeri wild-type A1501, rpoN mutant Δ rpoN , nifA mutant Δ nifA and ntrC mutant Δ ntrC . ( C ) Promoter analysis of the algU gene. The predicted AlgU-binding site RpoN-binding site and RsmA-binding site were located within the upstream region of the start codon of algU . The corresponding −10 and −35 regions of the AlgU-binding site were underlined and the RpoN-binding sites were boxed. +1 indicated the transcriptional start site determined by the 5′ RACE assay. The predicted RsmA-binding site was shown in bold font. ( D ) Gel mobility shift analysis of RpoN and the algU promoter. A DNA fragment from Halomonas venusta was used as negative control and the nifA promoter from A1501 was used as a positive control. ( E ) Gel mobility shift analysis of the RsmA protein with AlgU 5′UTR RNA oligonucleotides. 80 nM AlgU RNA was used to bind the RsmA protein. The positions of free and bound RNA were indicated. The RNA oligonucleotides AlgU and RsmY were synthesized in Genepharma Company. The RsmA binding site AGGA was in bold, and the initiation codon (AUG) for algU was indicated in red. Error bars represent the standard deviation (SD) of the three biological replicates. Asterisks indicate statistical significance by one-way ANOVA: ** p

    Techniques Used: Expressing, Incubation, Mutagenesis, Binding Assay, Mobility Shift, Negative Control, Positive Control, Synthesized, Standard Deviation

    AlgU directly activates the transcriptional expression of pslA . ( A ) Promoter sequence analysis of pslA . +1 indicates the transcriptional start site of pslA . The predicted RpoN-binding site was underlined with a double line, 12–25 bases upstream of the +1 site. The predicted AlgU-binding site was underlined with a single line, 14–40 bases upstream of the +1 site. In addition, the predicted RsmA-binding site is shown in bold font. ( B ) Sequence alignment of the pslA AlgU-binding site with the AlgU-binding consensus sequence. ( C ) DNase I footprinting analysis of the pslA promoter probe using the purified AlgU protein added at 0 (upper panel) and 15 μg (lower panel). The AlgU-protected region is marked by a dotted box and the DNA sequence is shown at the bottom. The AlgU-binding site is indicated by a red box. ( D ) The β-Galactosidase activities of lacZ fusions to the pslA promoter region (1–500 bases upstream of the +1 site) with the wild-type AlgU-binding site or mutated AlgU-binding sites. The mutated positions are shown in red. Data are in Miller units and are the means of at least three biological replicates ± standard deviations. Asterisks indicate statistical significance when compared to the WT AlgU-binding site by one-way ANOVA test: ** p
    Figure Legend Snippet: AlgU directly activates the transcriptional expression of pslA . ( A ) Promoter sequence analysis of pslA . +1 indicates the transcriptional start site of pslA . The predicted RpoN-binding site was underlined with a double line, 12–25 bases upstream of the +1 site. The predicted AlgU-binding site was underlined with a single line, 14–40 bases upstream of the +1 site. In addition, the predicted RsmA-binding site is shown in bold font. ( B ) Sequence alignment of the pslA AlgU-binding site with the AlgU-binding consensus sequence. ( C ) DNase I footprinting analysis of the pslA promoter probe using the purified AlgU protein added at 0 (upper panel) and 15 μg (lower panel). The AlgU-protected region is marked by a dotted box and the DNA sequence is shown at the bottom. The AlgU-binding site is indicated by a red box. ( D ) The β-Galactosidase activities of lacZ fusions to the pslA promoter region (1–500 bases upstream of the +1 site) with the wild-type AlgU-binding site or mutated AlgU-binding sites. The mutated positions are shown in red. Data are in Miller units and are the means of at least three biological replicates ± standard deviations. Asterisks indicate statistical significance when compared to the WT AlgU-binding site by one-way ANOVA test: ** p

    Techniques Used: Expressing, Sequencing, Binding Assay, Footprinting, Purification

    11) Product Images from "Potent activation of NAD+-dependent deacetylase Sirt7 by nucleosome binding"

    Article Title: Potent activation of NAD+-dependent deacetylase Sirt7 by nucleosome binding

    Journal: bioRxiv

    doi: 10.1101/2022.05.11.491540

    Sirt7 interaction and activation by short double-stranded oligo-DNA, tRNA, and nucleosomes. a. Michaelis-Menten profiles of Sirt7 H3K18Deca deacylation in the presence of various activator DNAs and corresponding kinetic parameters ( Table1 ). b. Fluorescence polarization (FP) analysis of Sirt7 interaction with 20bp double-stranded FAM-labeled DNA. c. Kinetic titration of long 146bp DNA and short 20bp DNA into Sirt7 in the presence of saturating substrates. d. Titration of 20bp double-stranded DNA, tRNA, and nucleosomes into Sirt7 in the presence of saturating substrates.
    Figure Legend Snippet: Sirt7 interaction and activation by short double-stranded oligo-DNA, tRNA, and nucleosomes. a. Michaelis-Menten profiles of Sirt7 H3K18Deca deacylation in the presence of various activator DNAs and corresponding kinetic parameters ( Table1 ). b. Fluorescence polarization (FP) analysis of Sirt7 interaction with 20bp double-stranded FAM-labeled DNA. c. Kinetic titration of long 146bp DNA and short 20bp DNA into Sirt7 in the presence of saturating substrates. d. Titration of 20bp double-stranded DNA, tRNA, and nucleosomes into Sirt7 in the presence of saturating substrates.

    Techniques Used: Activation Assay, Fluorescence, Labeling, Titration

    Effect of modulators on Sirt7 kinetics with various H3K18 acylated substrates. Michaelis-Menten profiles and bar plots of corresponding catalytic efficiencies in the absence of modulators (a), and in the presence of DNA (b), tRNA (c), or nucleosomes (d). The values of catalytic efficiencies ( Table 3 ) of apoSirt7, apoSirt6, Sirt7-DNA, Sirt7-tRNA, and Sirt7-nucleosome complexes towards H3K18Ac (e) and H3K18Deca (f) substrates presented as bar plot on the vertical logarithmic
    Figure Legend Snippet: Effect of modulators on Sirt7 kinetics with various H3K18 acylated substrates. Michaelis-Menten profiles and bar plots of corresponding catalytic efficiencies in the absence of modulators (a), and in the presence of DNA (b), tRNA (c), or nucleosomes (d). The values of catalytic efficiencies ( Table 3 ) of apoSirt7, apoSirt6, Sirt7-DNA, Sirt7-tRNA, and Sirt7-nucleosome complexes towards H3K18Ac (e) and H3K18Deca (f) substrates presented as bar plot on the vertical logarithmic

    Techniques Used:

    Development and application of NanoLuc nucleosome binding assay. a. The principle of the novel in vitro NanoLuc complementation binding assay designed to study Sirt7-nucleosome interaction. b, c. Effect of ADP-ribose on Sirt7 binding affinity to unmodified and H3K18-acetylated nucleosomes, respectively. d. NanoLuc luminescence decay associated with competitive displacement of Sirt7- CLB from SMB-Nucs by 20bp DNA and tRNA. e. Fluorescence anisotropy reduction associated with competitive displacement of 20bp FAM-DNA from Sirt7 by nucleosomes and tRNA. f. Inhibition of Sirt7 deacetylation activity by DNA. Reduction of Sirt7 deacetylation activity associated with competitive displacement of nucleosomes by 20bp DNA in the presence of H3K18Ac peptide.
    Figure Legend Snippet: Development and application of NanoLuc nucleosome binding assay. a. The principle of the novel in vitro NanoLuc complementation binding assay designed to study Sirt7-nucleosome interaction. b, c. Effect of ADP-ribose on Sirt7 binding affinity to unmodified and H3K18-acetylated nucleosomes, respectively. d. NanoLuc luminescence decay associated with competitive displacement of Sirt7- CLB from SMB-Nucs by 20bp DNA and tRNA. e. Fluorescence anisotropy reduction associated with competitive displacement of 20bp FAM-DNA from Sirt7 by nucleosomes and tRNA. f. Inhibition of Sirt7 deacetylation activity by DNA. Reduction of Sirt7 deacetylation activity associated with competitive displacement of nucleosomes by 20bp DNA in the presence of H3K18Ac peptide.

    Techniques Used: Binding Assay, In Vitro, Fluorescence, Inhibition, Activity Assay

    Design and validation of novel HPLC-based sirtuin deacetylation assay a. Sirtuin deacetylation assay optimization concept that improves its sensitivity and high-throughput capability. HPLC separation profiles of Sirt7-deacetylated 1.4- dinitrobenzene (DNB) and tryptophan (W) labeled peptides. b. Validation of DNB- labeled Sirt7 substrate demonstrates that its kinetic behavior is unaffected by the peptide labeling strategy. c. Effect of DNA, tRNA, and nucleosomes on Sirt7 NAD + - catalytic efficiencies in the presence of saturating H3K18Ac or long-chained H3K18Deca substrates. The Sirt7 kinetic parameters are summarized in the table, and corresponding Michaelis-Menten profiles are shown in Supplementary figure S4.
    Figure Legend Snippet: Design and validation of novel HPLC-based sirtuin deacetylation assay a. Sirtuin deacetylation assay optimization concept that improves its sensitivity and high-throughput capability. HPLC separation profiles of Sirt7-deacetylated 1.4- dinitrobenzene (DNB) and tryptophan (W) labeled peptides. b. Validation of DNB- labeled Sirt7 substrate demonstrates that its kinetic behavior is unaffected by the peptide labeling strategy. c. Effect of DNA, tRNA, and nucleosomes on Sirt7 NAD + - catalytic efficiencies in the presence of saturating H3K18Ac or long-chained H3K18Deca substrates. The Sirt7 kinetic parameters are summarized in the table, and corresponding Michaelis-Menten profiles are shown in Supplementary figure S4.

    Techniques Used: High Performance Liquid Chromatography, High Throughput Screening Assay, Labeling

    Analysis of Sirt7 interaction with DNA, tRNA, and nucleosomes. N tive EMSA gel analysis of Sirt7 interaction with Widom 601 DNA (a), tRNA (b), and nucleosome core particles (c). Sirt7 was titrated into 146bp DNA (a), tRNA (b), or nucleosomes (c), andformed species were identified by native EMSA. Detected complexes are marked arrows. The proposed interactional model and total enzymatic H3K18Deca deacyltion activity for each EMSA-analyzed Sirt7/macromolecule ratio is presented. d. Design of the LANA-FAM/Sirt7 competition experiment; e. FP analysis of LANA-FAM interaction nucleosomes. f. FP analysis of LANA-FAM displacement by Sirt7.
    Figure Legend Snippet: Analysis of Sirt7 interaction with DNA, tRNA, and nucleosomes. N tive EMSA gel analysis of Sirt7 interaction with Widom 601 DNA (a), tRNA (b), and nucleosome core particles (c). Sirt7 was titrated into 146bp DNA (a), tRNA (b), or nucleosomes (c), andformed species were identified by native EMSA. Detected complexes are marked arrows. The proposed interactional model and total enzymatic H3K18Deca deacyltion activity for each EMSA-analyzed Sirt7/macromolecule ratio is presented. d. Design of the LANA-FAM/Sirt7 competition experiment; e. FP analysis of LANA-FAM interaction nucleosomes. f. FP analysis of LANA-FAM displacement by Sirt7.

    Techniques Used: Activity Assay

    12) Product Images from "Neuroprotective effects of combined trimetazidine and progesterone on cerebral reperfusion injury"

    Article Title: Neuroprotective effects of combined trimetazidine and progesterone on cerebral reperfusion injury

    Journal: Current Research in Pharmacology and Drug Discovery

    doi: 10.1016/j.crphar.2022.100108

    DNA damage and fragmentation Gel electrophoresis of ipsilateral hemisphere of brain; Lane 1, 1-kb DNA standard; Lane 2, Sham control; Lane 3, IR control, indicates apoptotic cellular injury in the form laddering pattern; Lane 4, Progesterone treated, no fragmented DNA; Lane 5, Trimetazidine, absence of laddering of DNA stands; Lane 6, combination treated rat brain without any apparent DNA breaks.
    Figure Legend Snippet: DNA damage and fragmentation Gel electrophoresis of ipsilateral hemisphere of brain; Lane 1, 1-kb DNA standard; Lane 2, Sham control; Lane 3, IR control, indicates apoptotic cellular injury in the form laddering pattern; Lane 4, Progesterone treated, no fragmented DNA; Lane 5, Trimetazidine, absence of laddering of DNA stands; Lane 6, combination treated rat brain without any apparent DNA breaks.

    Techniques Used: Nucleic Acid Electrophoresis

    13) Product Images from "Intranasal administration of a VLP‐based vaccine induces neutralizing antibodies against SARS‐CoV‐2 and variants of concern, et al. Intranasal administration of a VLP‐based vaccine induces neutralizing antibodies against SARS‐CoV‐2 and variants of concern"

    Article Title: Intranasal administration of a VLP‐based vaccine induces neutralizing antibodies against SARS‐CoV‐2 and variants of concern, et al. Intranasal administration of a VLP‐based vaccine induces neutralizing antibodies against SARS‐CoV‐2 and variants of concern

    Journal: Allergy

    doi: 10.1111/all.15311

    CuMV TT constitute an efficient platform for vaccine development. (A) Schematic representation of the chemical coupling of RBD to CuMV TT via SMPH bifunctional cross‐linker. (B) Agarose gel analysis of CuMV TT ‐RBD and CuMV TT depicting nucleic acids packaged in CuMV TT . M. DNA Ladder, 1. CuMV TT ‐RBD, 2. CuMV TT containing bands are labelled with red circle. (C) 12% SDS‐PAGE for CuMV TT ‐RBD production. M. Protein marker, 1. RBD, 2. CuMV TT , 3. CuMV TT ‐RBD post wash. Red star indicate the coupled CuMV TT ‐RBD product and blue star indicate the RBD. Bands were visualized with InstantBlue TM Coomassie stain. (D) Western blot specific for RBD. M. Protein marker, 1. RBD, 2. CuMV TT , 3. CuMV TT ‐RBD post‐wash. Red star indicate the coupled CuMV TT ‐RBD product and blue star indicate the RBD. (E) Electron microscopy of CuMV TT ‐RBD, scale bar 200 nm. (F) ACE2 binding of CuMV TT ‐RBD, CuMV TT and RBD. Binding revealed with an anti‐CuMV mAb
    Figure Legend Snippet: CuMV TT constitute an efficient platform for vaccine development. (A) Schematic representation of the chemical coupling of RBD to CuMV TT via SMPH bifunctional cross‐linker. (B) Agarose gel analysis of CuMV TT ‐RBD and CuMV TT depicting nucleic acids packaged in CuMV TT . M. DNA Ladder, 1. CuMV TT ‐RBD, 2. CuMV TT containing bands are labelled with red circle. (C) 12% SDS‐PAGE for CuMV TT ‐RBD production. M. Protein marker, 1. RBD, 2. CuMV TT , 3. CuMV TT ‐RBD post wash. Red star indicate the coupled CuMV TT ‐RBD product and blue star indicate the RBD. Bands were visualized with InstantBlue TM Coomassie stain. (D) Western blot specific for RBD. M. Protein marker, 1. RBD, 2. CuMV TT , 3. CuMV TT ‐RBD post‐wash. Red star indicate the coupled CuMV TT ‐RBD product and blue star indicate the RBD. (E) Electron microscopy of CuMV TT ‐RBD, scale bar 200 nm. (F) ACE2 binding of CuMV TT ‐RBD, CuMV TT and RBD. Binding revealed with an anti‐CuMV mAb

    Techniques Used: Agarose Gel Electrophoresis, SDS Page, Marker, Staining, Western Blot, Electron Microscopy, Binding Assay

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 96
    Thermo Fisher generuler 1 kb plus dna ladder
    Generuler 1 Kb Plus Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/generuler 1 kb plus dna ladder/product/Thermo Fisher
    Average 96 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    generuler 1 kb plus dna ladder - by Bioz Stars, 2022-11
    96/100 stars
      Buy from Supplier

    88
    Thermo Fisher generuler ultra low range dna ladder
    Oleic acid inhibits the regulatory activity of Musashi-1 in bacteria. a) Three-dimensional structural schematic of the allosteric regulation. RRM1 of MSI-1 is shown alone, in complex with the RNA motif, and in complex with oleic acid. b) Gel electrophoretic assay to test the allosteric inhibition of MSI-1* with oleic acid. A purified MSI-1* protein (45 μM), the RNA motif as a label-free sRNA molecule (11 μM), and oleic acid (1 mM) were mixed in a combinatorial way in vitro . On the left, nucleic acid-stained gel. On the right, protein-stained gel (Coomassie). The different formed species are indicated. M denotes molecular marker <t>(GeneRuler</t> <t>ultra-low</t> <t>range</t> <t>DNA</t> <t>ladder,</t> 10-300 bp, Thermo). BSA was used as a control. c) On the top, images of E. coli colonies harboring pRM1+ and pREP6. Bacteria were seeded in LB-agar plates with suitable inducers (1 mM lactose or 1 mM lactose + 20 mM oleic acid). Fluorescence and bright field images are shown. On the bottom, schematics of the working mode of the synthetic gene circuit according to the different induction conditions. d) Quantification of the green fluorescence of the colonies from panel c (denoted by ΣsfGFP as it is from populations; n = 5). e) Images of E. coli colonies harboring pRM1+ and pREP7. f) Quantification of the green fluorescence of the colonies from panel e. AU, arbitrary units.
    Generuler Ultra Low Range Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/generuler ultra low range dna ladder/product/Thermo Fisher
    Average 88 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    generuler ultra low range dna ladder - by Bioz Stars, 2022-11
    88/100 stars
      Buy from Supplier

    88
    Thermo Fisher generuler 100 bp plus dna ladder
    Oleic acid inhibits the regulatory activity of Musashi-1 in bacteria. a) Three-dimensional structural schematic of the allosteric regulation. RRM1 of MSI-1 is shown alone, in complex with the RNA motif, and in complex with oleic acid. b) Gel electrophoretic assay to test the allosteric inhibition of MSI-1* with oleic acid. A purified MSI-1* protein (45 μM), the RNA motif as a label-free sRNA molecule (11 μM), and oleic acid (1 mM) were mixed in a combinatorial way in vitro . On the left, nucleic acid-stained gel. On the right, protein-stained gel (Coomassie). The different formed species are indicated. M denotes molecular marker <t>(GeneRuler</t> <t>ultra-low</t> <t>range</t> <t>DNA</t> <t>ladder,</t> 10-300 bp, Thermo). BSA was used as a control. c) On the top, images of E. coli colonies harboring pRM1+ and pREP6. Bacteria were seeded in LB-agar plates with suitable inducers (1 mM lactose or 1 mM lactose + 20 mM oleic acid). Fluorescence and bright field images are shown. On the bottom, schematics of the working mode of the synthetic gene circuit according to the different induction conditions. d) Quantification of the green fluorescence of the colonies from panel c (denoted by ΣsfGFP as it is from populations; n = 5). e) Images of E. coli colonies harboring pRM1+ and pREP7. f) Quantification of the green fluorescence of the colonies from panel e. AU, arbitrary units.
    Generuler 100 Bp Plus Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/generuler 100 bp plus dna ladder/product/Thermo Fisher
    Average 88 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    generuler 100 bp plus dna ladder - by Bioz Stars, 2022-11
    88/100 stars
      Buy from Supplier

    88
    Thermo Fisher 100 bp dna ladder
    Oleic acid inhibits the regulatory activity of Musashi-1 in bacteria. a) Three-dimensional structural schematic of the allosteric regulation. RRM1 of MSI-1 is shown alone, in complex with the RNA motif, and in complex with oleic acid. b) Gel electrophoretic assay to test the allosteric inhibition of MSI-1* with oleic acid. A purified MSI-1* protein (45 μM), the RNA motif as a label-free sRNA molecule (11 μM), and oleic acid (1 mM) were mixed in a combinatorial way in vitro . On the left, nucleic acid-stained gel. On the right, protein-stained gel (Coomassie). The different formed species are indicated. M denotes molecular marker <t>(GeneRuler</t> <t>ultra-low</t> <t>range</t> <t>DNA</t> <t>ladder,</t> 10-300 bp, Thermo). BSA was used as a control. c) On the top, images of E. coli colonies harboring pRM1+ and pREP6. Bacteria were seeded in LB-agar plates with suitable inducers (1 mM lactose or 1 mM lactose + 20 mM oleic acid). Fluorescence and bright field images are shown. On the bottom, schematics of the working mode of the synthetic gene circuit according to the different induction conditions. d) Quantification of the green fluorescence of the colonies from panel c (denoted by ΣsfGFP as it is from populations; n = 5). e) Images of E. coli colonies harboring pRM1+ and pREP7. f) Quantification of the green fluorescence of the colonies from panel e. AU, arbitrary units.
    100 Bp Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/100 bp dna ladder/product/Thermo Fisher
    Average 88 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    100 bp dna ladder - by Bioz Stars, 2022-11
    88/100 stars
      Buy from Supplier

    Image Search Results


    Oleic acid inhibits the regulatory activity of Musashi-1 in bacteria. a) Three-dimensional structural schematic of the allosteric regulation. RRM1 of MSI-1 is shown alone, in complex with the RNA motif, and in complex with oleic acid. b) Gel electrophoretic assay to test the allosteric inhibition of MSI-1* with oleic acid. A purified MSI-1* protein (45 μM), the RNA motif as a label-free sRNA molecule (11 μM), and oleic acid (1 mM) were mixed in a combinatorial way in vitro . On the left, nucleic acid-stained gel. On the right, protein-stained gel (Coomassie). The different formed species are indicated. M denotes molecular marker (GeneRuler ultra-low range DNA ladder, 10-300 bp, Thermo). BSA was used as a control. c) On the top, images of E. coli colonies harboring pRM1+ and pREP6. Bacteria were seeded in LB-agar plates with suitable inducers (1 mM lactose or 1 mM lactose + 20 mM oleic acid). Fluorescence and bright field images are shown. On the bottom, schematics of the working mode of the synthetic gene circuit according to the different induction conditions. d) Quantification of the green fluorescence of the colonies from panel c (denoted by ΣsfGFP as it is from populations; n = 5). e) Images of E. coli colonies harboring pRM1+ and pREP7. f) Quantification of the green fluorescence of the colonies from panel e. AU, arbitrary units.

    Journal: bioRxiv

    Article Title: Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria

    doi: 10.1101/2022.11.22.516435

    Figure Lengend Snippet: Oleic acid inhibits the regulatory activity of Musashi-1 in bacteria. a) Three-dimensional structural schematic of the allosteric regulation. RRM1 of MSI-1 is shown alone, in complex with the RNA motif, and in complex with oleic acid. b) Gel electrophoretic assay to test the allosteric inhibition of MSI-1* with oleic acid. A purified MSI-1* protein (45 μM), the RNA motif as a label-free sRNA molecule (11 μM), and oleic acid (1 mM) were mixed in a combinatorial way in vitro . On the left, nucleic acid-stained gel. On the right, protein-stained gel (Coomassie). The different formed species are indicated. M denotes molecular marker (GeneRuler ultra-low range DNA ladder, 10-300 bp, Thermo). BSA was used as a control. c) On the top, images of E. coli colonies harboring pRM1+ and pREP6. Bacteria were seeded in LB-agar plates with suitable inducers (1 mM lactose or 1 mM lactose + 20 mM oleic acid). Fluorescence and bright field images are shown. On the bottom, schematics of the working mode of the synthetic gene circuit according to the different induction conditions. d) Quantification of the green fluorescence of the colonies from panel c (denoted by ΣsfGFP as it is from populations; n = 5). e) Images of E. coli colonies harboring pRM1+ and pREP7. f) Quantification of the green fluorescence of the colonies from panel e. AU, arbitrary units.

    Article Snippet: Gels ran for 45 min at room temperature applying 110 V. The GeneRuler ultra-low range DNA ladder (10-300 bp, Thermo) was used.

    Techniques: Activity Assay, Inhibition, Purification, In Vitro, Staining, Marker, Fluorescence