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  • 98
    ATCC serratia sp
    Serratia Sp, supplied by ATCC, used in various techniques. Bioz Stars score: 98/100, based on 627 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 98 stars, based on 627 article reviews
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    99
    Millipore benzonase
    Benzonase, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 18969 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Merck & Co benzonase
    Benzonase, supplied by Merck & Co, used in various techniques. Bioz Stars score: 93/100, based on 2201 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Merck KGaA benzonase
    Schematic workflow of the fliX-MS pipeline. a A pulsed laser beam was generated using a femtosecond fiber laser with 515 nm wavelength, repetition rate of 0.5 MHz, and pulse duration of 500 fs. The wavelength was doubled to 258 nm by second harmonic generation (SHG) over a beta barium borate (BBO) crystal and the laser beam adjusted to fit the inner diameter of a regular 1.5 ml Eppendorf tube. b Protein–DNA complexes were irradiated or left untreated as control. Samples were denatured, DNA digested to mono/short oligonucleotides by a mix of Mnase, DNase I, and <t>Benzonase,</t> and proteins digested to peptides by trypsin and Lys-C. Peptides and peptide–nucleotide cross-links were separated from free DNA on C18 StageTips 25 , and cross-links subsequently enriched with TiO 2 beads. c Peptides were measured by LC–MS/MS and data analyzed with the RNP(xl) software package implemented in the proteome discoverer software 50 followed by manual annotation of candidate spectra.
    Benzonase, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 92/100, based on 2197 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    ATCC serratia marcescens
    Creation and dissolution of an active–passive interphase boundary in a bacterial swarm. a A series of snapshots of the expanding edge of a Serratia <t>marcescens</t> swarm taken over time. The colony was cultured on an agar substrate, and its expanding edge (marked by a precursor fluid film that appears as white curve) is moving from right to left. The swarm shows long-range collective flows, with strong velocity fields (PIV; overlaid color). A large domain of passive, immobile bacteria is created by exposing a region of the swarm to high intensity ultraviolet (UV) light (highlighted octagon). An interphase boundary forms between the passivated and active bacteria. When the light source is switched off ( t = 0 s), the active unexposed bacteria deform the interphase boundary and penetrate the passive region. Over time, active bacteria convect immobile bacteria away from the passive domain, causing the boundary to erode and propagate inward. The boundary is manually traced in white for visualization. The swarm dissolves the passive phase in 60 s, with interface speeds greater than that of expanding colony edge. b The swarm edge (close-up) features densely packed cells with local polarity and nematic order. c The swarm’s collective motion recovers after dissolution as shown by the probability distribution of bacterial speeds p ( v ), before and after exposure (data shown for representative experiment, collected from 5 s interval of PIV data). d A montage of the flow streamlines—from the highlighted box in a —reveals the motion of vortices (labeled by color) at the interface (blue line). Vortices starting in the bulk can collide and attach to the interface (labeled brown vortex for example); some vortices at the surface detach and move away (green, orange). Others fade away (purple) or split (dark blue splits from light blue vortex in right tile). Data shown here is from a single experiment; results were repeated for a minimum of N = 4 experiments
    Serratia Marcescens, supplied by ATCC, used in various techniques. Bioz Stars score: 97/100, based on 394 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    thermo fisher benzonase
    MCPH1 stabilizes RAD51 and DMC1 nucleoprotein filaments. ( A ) Schematic of our <t>Benzonase</t> protection assay. ( B ) The 5′- 32 P-labeled 80-mer ssDNA (1.5 μM nucleotides) was pre-incubated with RAD51 and then incubated with tag-free MCPH1 (lanes 5–7). RAD51 (lane 3) or MCPH1 alone (lane 4) were included as negative controls. RAD51 with AMP-PNP was included as a positive control. Then, Benzonase was added to challenge the filaments. The reactions were deproteinized and electrophoresed in 10% TBE polyacrylamide gels. The gels were dried and analyzed by phosphorimaging. The 32 P-label is denoted by the asterisk. ( C , D ) The assay was also conducted using DMC1 (C) or RecA (D) and analyzed in the same way. DMC1 with calcium (0.5 mM) or RecA with ATPγS were included as respective positive controls. Plots of percentage DNA protected are shown below the gels. Error bars represent the standard deviation (±SD) calculated from three independent experiments.
    Benzonase, supplied by thermo fisher, used in various techniques. Bioz Stars score: 92/100, based on 475 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    ATCC escherichia coli
    MCPH1 stabilizes RAD51 and DMC1 nucleoprotein filaments. ( A ) Schematic of our <t>Benzonase</t> protection assay. ( B ) The 5′- 32 P-labeled 80-mer ssDNA (1.5 μM nucleotides) was pre-incubated with RAD51 and then incubated with tag-free MCPH1 (lanes 5–7). RAD51 (lane 3) or MCPH1 alone (lane 4) were included as negative controls. RAD51 with AMP-PNP was included as a positive control. Then, Benzonase was added to challenge the filaments. The reactions were deproteinized and electrophoresed in 10% TBE polyacrylamide gels. The gels were dried and analyzed by phosphorimaging. The 32 P-label is denoted by the asterisk. ( C , D ) The assay was also conducted using DMC1 (C) or RecA (D) and analyzed in the same way. DMC1 with calcium (0.5 mM) or RecA with ATPγS were included as respective positive controls. Plots of percentage DNA protected are shown below the gels. Error bars represent the standard deviation (±SD) calculated from three independent experiments.
    Escherichia Coli, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 8321 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Merck KGaA benzonase nuclease
    KSHV LANA recruits Rad50 and Mre11 in the cytosol. ( A ) Co-immunoprecipitation of endogenous LANA, Rad50, Mre11 and Brd4 in BCBL-1 cells upon cytosolic-nuclear fractionation. Cells were lysed and cytoplasmic extracts (Cyto) and nuclear extracts (Nu) were prepared using the Thermo-Fischer Nu-Cyto fractionation kit following the manufacturer‘s instructions. Cytoplasmic and nuclear fractions were incubated overnight with sepharose beads coated with LANA-antibody or IgG-control. Left (INPUT, see Materials and methods ): Brd4, Lamin A/C and GAPDH immunoblots were analyzed to confirm the efficiency of the fractionation. Right (IP): immunoprecipitation with LANA-antibody or IgG-control coated-beads and immunoblot for endogenous Rad50, Mre11 and Brd4. ( B ) Co-immunoprecipitation of endogenous Rad50 and full-length LANA or ΔN mutants (Δ161 and Δ282) transfected into HEK293 cells. HEK293 cells were transfected with LANA constructs (or empty vector). 48 hours later cells were lysed and incubated with <t>benzonase.</t> After centrifugation, cells were incubated overnight with beads coated with LANA-antibody. Left (INPUT): immunoblot to check the expression of LANA constructs and the endogenous Rad50 in the cells. Right (IP from LANA-antibody-coated-beads): immunoblot for endogenous Rad50 co-immunoprecipitation. ( C ) Co-immunoprecipitation of endogenous LANA and Rad50, Mre11 and CARD9 in latently KSHV-infected THP-1 cells (TrK.219 cells, see Materials and methods ). Cells were lysed and incubated with benzonase. After centrifugation, whole cell lysates were incubated overnight with beads coated with anti-LANA or IgG-control antibody. Precipitated complexes were analysed by SDS-PAGE and immunoblotting with the indicated antibodies.
    Benzonase Nuclease, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 93/100, based on 372 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    ATCC pseudomonas aeruginosa
    KSHV LANA recruits Rad50 and Mre11 in the cytosol. ( A ) Co-immunoprecipitation of endogenous LANA, Rad50, Mre11 and Brd4 in BCBL-1 cells upon cytosolic-nuclear fractionation. Cells were lysed and cytoplasmic extracts (Cyto) and nuclear extracts (Nu) were prepared using the Thermo-Fischer Nu-Cyto fractionation kit following the manufacturer‘s instructions. Cytoplasmic and nuclear fractions were incubated overnight with sepharose beads coated with LANA-antibody or IgG-control. Left (INPUT, see Materials and methods ): Brd4, Lamin A/C and GAPDH immunoblots were analyzed to confirm the efficiency of the fractionation. Right (IP): immunoprecipitation with LANA-antibody or IgG-control coated-beads and immunoblot for endogenous Rad50, Mre11 and Brd4. ( B ) Co-immunoprecipitation of endogenous Rad50 and full-length LANA or ΔN mutants (Δ161 and Δ282) transfected into HEK293 cells. HEK293 cells were transfected with LANA constructs (or empty vector). 48 hours later cells were lysed and incubated with <t>benzonase.</t> After centrifugation, cells were incubated overnight with beads coated with LANA-antibody. Left (INPUT): immunoblot to check the expression of LANA constructs and the endogenous Rad50 in the cells. Right (IP from LANA-antibody-coated-beads): immunoblot for endogenous Rad50 co-immunoprecipitation. ( C ) Co-immunoprecipitation of endogenous LANA and Rad50, Mre11 and CARD9 in latently KSHV-infected THP-1 cells (TrK.219 cells, see Materials and methods ). Cells were lysed and incubated with benzonase. After centrifugation, whole cell lysates were incubated overnight with beads coated with anti-LANA or IgG-control antibody. Precipitated complexes were analysed by SDS-PAGE and immunoblotting with the indicated antibodies.
    Pseudomonas Aeruginosa, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 5234 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    ATCC staphylococcus aureus
    KSHV LANA recruits Rad50 and Mre11 in the cytosol. ( A ) Co-immunoprecipitation of endogenous LANA, Rad50, Mre11 and Brd4 in BCBL-1 cells upon cytosolic-nuclear fractionation. Cells were lysed and cytoplasmic extracts (Cyto) and nuclear extracts (Nu) were prepared using the Thermo-Fischer Nu-Cyto fractionation kit following the manufacturer‘s instructions. Cytoplasmic and nuclear fractions were incubated overnight with sepharose beads coated with LANA-antibody or IgG-control. Left (INPUT, see Materials and methods ): Brd4, Lamin A/C and GAPDH immunoblots were analyzed to confirm the efficiency of the fractionation. Right (IP): immunoprecipitation with LANA-antibody or IgG-control coated-beads and immunoblot for endogenous Rad50, Mre11 and Brd4. ( B ) Co-immunoprecipitation of endogenous Rad50 and full-length LANA or ΔN mutants (Δ161 and Δ282) transfected into HEK293 cells. HEK293 cells were transfected with LANA constructs (or empty vector). 48 hours later cells were lysed and incubated with <t>benzonase.</t> After centrifugation, cells were incubated overnight with beads coated with LANA-antibody. Left (INPUT): immunoblot to check the expression of LANA constructs and the endogenous Rad50 in the cells. Right (IP from LANA-antibody-coated-beads): immunoblot for endogenous Rad50 co-immunoprecipitation. ( C ) Co-immunoprecipitation of endogenous LANA and Rad50, Mre11 and CARD9 in latently KSHV-infected THP-1 cells (TrK.219 cells, see Materials and methods ). Cells were lysed and incubated with benzonase. After centrifugation, whole cell lysates were incubated overnight with beads coated with anti-LANA or IgG-control antibody. Precipitated complexes were analysed by SDS-PAGE and immunoblotting with the indicated antibodies.
    Staphylococcus Aureus, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 6882 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Merck & Co benzonase nuclease
    <t>Benzonase</t> nuclease treatment does not change lamin mechanics. ( a ) Step unit, ( b ) force, ( c ) stiffness and ( d ) deformation of lamin filaments in the meshwork of X. laevis nuclear envelopes were measured after nuclease treatment at a pushing speed of 1 µm s −1 . The values of the parameters were comparable to those obtained without nuclease treatment, at 1 µm s −1 , suggesting that chromatin, ribonucleoproteins or RNA were not present in the experimental system and did not influence the mechanical properties of lamins in our experiments. – Benzonase-free NEs, n = 204 for each parameter; + Benzonase-treated NEs, n = 172 for each parameter.
    Benzonase Nuclease, supplied by Merck & Co, used in various techniques. Bioz Stars score: 92/100, based on 253 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    ATCC escherichia coli atcc 25922
    <t>Benzonase</t> nuclease treatment does not change lamin mechanics. ( a ) Step unit, ( b ) force, ( c ) stiffness and ( d ) deformation of lamin filaments in the meshwork of X. laevis nuclear envelopes were measured after nuclease treatment at a pushing speed of 1 µm s −1 . The values of the parameters were comparable to those obtained without nuclease treatment, at 1 µm s −1 , suggesting that chromatin, ribonucleoproteins or RNA were not present in the experimental system and did not influence the mechanical properties of lamins in our experiments. – Benzonase-free NEs, n = 204 for each parameter; + Benzonase-treated NEs, n = 172 for each parameter.
    Escherichia Coli Atcc 25922, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 7349 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Novozymes neutrase
    Effects of ovalbumin (O), lysozyme (L), ovomucoid (M), their hydrolysates with pepsin (P), <t>Neutrase</t> (N) and alcalase (A) (200 μg/mL), the inactivated enzymes at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, and the fractions with molecular mass lower than 10,000 and 3,000 Da on the secretion of TNF-α (a, d) and IL-8 (b, e), and intracellular ROS generation (c, f) by Th1-skewed peripheral blood leucocytes. Data are expressed as percentage of the values induced by IFN-γ and LPS ± standard error of the mean in 8 donors stimulated in triplicate and * indicates significant differences ( P
    Neutrase, supplied by Novozymes, used in various techniques. Bioz Stars score: 91/100, based on 79 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    ATCC klebsiella pneumoniae
    Effects of ovalbumin (O), lysozyme (L), ovomucoid (M), their hydrolysates with pepsin (P), <t>Neutrase</t> (N) and alcalase (A) (200 μg/mL), the inactivated enzymes at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, and the fractions with molecular mass lower than 10,000 and 3,000 Da on the secretion of TNF-α (a, d) and IL-8 (b, e), and intracellular ROS generation (c, f) by Th1-skewed peripheral blood leucocytes. Data are expressed as percentage of the values induced by IFN-γ and LPS ± standard error of the mean in 8 donors stimulated in triplicate and * indicates significant differences ( P
    Klebsiella Pneumoniae, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1780 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Millipore serratia marcescens
    Effects of ovalbumin (O), lysozyme (L), ovomucoid (M), their hydrolysates with pepsin (P), <t>Neutrase</t> (N) and alcalase (A) (200 μg/mL), the inactivated enzymes at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, and the fractions with molecular mass lower than 10,000 and 3,000 Da on the secretion of TNF-α (a, d) and IL-8 (b, e), and intracellular ROS generation (c, f) by Th1-skewed peripheral blood leucocytes. Data are expressed as percentage of the values induced by IFN-γ and LPS ± standard error of the mean in 8 donors stimulated in triplicate and * indicates significant differences ( P
    Serratia Marcescens, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 126 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher benzonase nuclease
    Effects of ovalbumin (O), lysozyme (L), ovomucoid (M), their hydrolysates with pepsin (P), <t>Neutrase</t> (N) and alcalase (A) (200 μg/mL), the inactivated enzymes at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, and the fractions with molecular mass lower than 10,000 and 3,000 Da on the secretion of TNF-α (a, d) and IL-8 (b, e), and intracellular ROS generation (c, f) by Th1-skewed peripheral blood leucocytes. Data are expressed as percentage of the values induced by IFN-γ and LPS ± standard error of the mean in 8 donors stimulated in triplicate and * indicates significant differences ( P
    Benzonase Nuclease, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 125 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Roche benzonase
    Effects of ovalbumin (O), lysozyme (L), ovomucoid (M), their hydrolysates with pepsin (P), <t>Neutrase</t> (N) and alcalase (A) (200 μg/mL), the inactivated enzymes at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, and the fractions with molecular mass lower than 10,000 and 3,000 Da on the secretion of TNF-α (a, d) and IL-8 (b, e), and intracellular ROS generation (c, f) by Th1-skewed peripheral blood leucocytes. Data are expressed as percentage of the values induced by IFN-γ and LPS ± standard error of the mean in 8 donors stimulated in triplicate and * indicates significant differences ( P
    Benzonase, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 1278 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Santa Cruz Biotechnology benzonase
    Structural characteristics of protein-solubilising oligonucleotides and renaturation of ALS brain-derived protein aggregates. a Cartoons of ds/ss/ds oligonucleotides having either pyrimidines (T or C) or purines (A) in the ss-region. b Proportion of protein aggregation following renaturing with the ds/ss/ds oligonucleotides shown in (a). c Renaturing capacity of structurally different oligonucleotides. The diagrams on the right show a theoretical structure of each oligonucleotide. All oligonucleotides, except the 3x-loop and 3x-bulges, contain a stretch of 30 Ts in the single-stranded region and the same sequences (15 nucleotides each) in the double stranded regions. The 3x-loops and bulges oligonucleotides have 3 stretches of 9 Ts and the same sequence in the ds-regions. d Proportion of protein aggregation in Jurkat cell lysate supplemented with various amounts and configurations of the M1×4 or M2×4 DNA oligonucleotides. e Insoluble proteins from two ALS brain tissues were chemically denatured in guanidine hydrochloride and treated with either buffer (Vehicle), total RNA from Jurkat cells or the complementary strands of the M1×4 DNA oligonucleotides (M1 F/R) (Pellet 1, top panel). After removal of GuHCl, the soluble fraction from these samples was treated with RNase and any aggregated proteins (Pellet 2), analysed by western blot (middle panel). Remaining supernatants were then treated with <t>Benzonase</t> to degrade any remaining nucleic acids and aggregated proteins collected by centrifugation and analysed by western blot (bottom panel). Proteins aggregated by enzymatic RNA degradation in Jurkat cell lysates, which do not contain NF-H, were used as a control. Data in b and c are expressed as a fraction of vehicle (Ve-), while data in d are expressed as the amount of aggregation observed without any oligonucleotides present (A/T1). All bars represent the mean ± s.d of two to four independent experiments. **= p
    Benzonase, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 92/100, based on 105 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    ATCC bacillus cereus
    Structural characteristics of protein-solubilising oligonucleotides and renaturation of ALS brain-derived protein aggregates. a Cartoons of ds/ss/ds oligonucleotides having either pyrimidines (T or C) or purines (A) in the ss-region. b Proportion of protein aggregation following renaturing with the ds/ss/ds oligonucleotides shown in (a). c Renaturing capacity of structurally different oligonucleotides. The diagrams on the right show a theoretical structure of each oligonucleotide. All oligonucleotides, except the 3x-loop and 3x-bulges, contain a stretch of 30 Ts in the single-stranded region and the same sequences (15 nucleotides each) in the double stranded regions. The 3x-loops and bulges oligonucleotides have 3 stretches of 9 Ts and the same sequence in the ds-regions. d Proportion of protein aggregation in Jurkat cell lysate supplemented with various amounts and configurations of the M1×4 or M2×4 DNA oligonucleotides. e Insoluble proteins from two ALS brain tissues were chemically denatured in guanidine hydrochloride and treated with either buffer (Vehicle), total RNA from Jurkat cells or the complementary strands of the M1×4 DNA oligonucleotides (M1 F/R) (Pellet 1, top panel). After removal of GuHCl, the soluble fraction from these samples was treated with RNase and any aggregated proteins (Pellet 2), analysed by western blot (middle panel). Remaining supernatants were then treated with <t>Benzonase</t> to degrade any remaining nucleic acids and aggregated proteins collected by centrifugation and analysed by western blot (bottom panel). Proteins aggregated by enzymatic RNA degradation in Jurkat cell lysates, which do not contain NF-H, were used as a control. Data in b and c are expressed as a fraction of vehicle (Ve-), while data in d are expressed as the amount of aggregation observed without any oligonucleotides present (A/T1). All bars represent the mean ± s.d of two to four independent experiments. **= p
    Bacillus Cereus, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 1179 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore benzonase treatment
    Linker histone H1.2 inhibits ATM recruitment and activation by interacting with MRN. a Wild type and H1.2 KO (1#) HeLa cells were transfected with GFP-NBS1 and subjected to laser micro-irradiation-coupled live-cell imaging. Images were taken every 10 s for 10 min and the relative intensity of the irradiation path signal was shown. The data represent the mean ± SD. Scale bars, 10 μm. b HeLa cells extracts were analyzed by Co-IP assay with or without <t>benzonase</t> treatment with the indicated antibodies. c GST alone or GST-MRE11, RAD50 and NBS1 were incubated with HIS-H1.2 for GST pull-down assay. * indicates specific protein bands. d GST alone or GST-H1.2 fragments were incubated with HIS-MRE11 for GST pull-down assay. * indicates specific protein bands. e Wild type or NBS1 KO HeLa cells were transfected with the indicated siRNAs and treated with 40 μM etoposide for 2 h and analyzed by immunoblotting. f HeLa cells were transfected with the indicated siRNAs and treated with 40 μM etoposide for 2 h and analyzed by immunoblotting. g , h HeLa cells were transfected with the indicated plasmids, and the whole cell lysates were immunoprecipitated with ATM antibody and analyzed by immunoblotting. i HeLa cells were transfected with the indicated plasmids and treated with 40 μM etoposide for 2 h. Whole cell extracts were prepared and analyzed by Co-IP assay and immunoblotting with the indicated antibodies
    Benzonase Treatment, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 157 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    ATCC s marcescens atcc 13880
    Linker histone H1.2 inhibits ATM recruitment and activation by interacting with MRN. a Wild type and H1.2 KO (1#) HeLa cells were transfected with GFP-NBS1 and subjected to laser micro-irradiation-coupled live-cell imaging. Images were taken every 10 s for 10 min and the relative intensity of the irradiation path signal was shown. The data represent the mean ± SD. Scale bars, 10 μm. b HeLa cells extracts were analyzed by Co-IP assay with or without <t>benzonase</t> treatment with the indicated antibodies. c GST alone or GST-MRE11, RAD50 and NBS1 were incubated with HIS-H1.2 for GST pull-down assay. * indicates specific protein bands. d GST alone or GST-H1.2 fragments were incubated with HIS-MRE11 for GST pull-down assay. * indicates specific protein bands. e Wild type or NBS1 KO HeLa cells were transfected with the indicated siRNAs and treated with 40 μM etoposide for 2 h and analyzed by immunoblotting. f HeLa cells were transfected with the indicated siRNAs and treated with 40 μM etoposide for 2 h and analyzed by immunoblotting. g , h HeLa cells were transfected with the indicated plasmids, and the whole cell lysates were immunoprecipitated with ATM antibody and analyzed by immunoblotting. i HeLa cells were transfected with the indicated plasmids and treated with 40 μM etoposide for 2 h. Whole cell extracts were prepared and analyzed by Co-IP assay and immunoblotting with the indicated antibodies
    S Marcescens Atcc 13880, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Becton Dickinson t241
    Construction of expression plasmids containing synthetic 2,3-BD operon. The budR , budA and budB from S. marcescens H30 encode the transcriptional activator, α-acetolactate decarboxylase and α-acetolactate synthase, respectively. The bdh1 , bdh2 , bdh3 and gdh genes from Serratia sp. <t>T241</t> encode the putative 2,3-butanediol dehydrogenase or glycerol dehydrogenase.
    T241, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 90/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    ATCC enterococcus faecalis
    Construction of expression plasmids containing synthetic 2,3-BD operon. The budR , budA and budB from S. marcescens H30 encode the transcriptional activator, α-acetolactate decarboxylase and α-acetolactate synthase, respectively. The bdh1 , bdh2 , bdh3 and gdh genes from Serratia sp. <t>T241</t> encode the putative 2,3-butanediol dehydrogenase or glycerol dehydrogenase.
    Enterococcus Faecalis, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 2526 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/enterococcus faecalis/product/ATCC
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    enterococcus faecalis - by Bioz Stars, 2020-11
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    Image Search Results


    Schematic workflow of the fliX-MS pipeline. a A pulsed laser beam was generated using a femtosecond fiber laser with 515 nm wavelength, repetition rate of 0.5 MHz, and pulse duration of 500 fs. The wavelength was doubled to 258 nm by second harmonic generation (SHG) over a beta barium borate (BBO) crystal and the laser beam adjusted to fit the inner diameter of a regular 1.5 ml Eppendorf tube. b Protein–DNA complexes were irradiated or left untreated as control. Samples were denatured, DNA digested to mono/short oligonucleotides by a mix of Mnase, DNase I, and Benzonase, and proteins digested to peptides by trypsin and Lys-C. Peptides and peptide–nucleotide cross-links were separated from free DNA on C18 StageTips 25 , and cross-links subsequently enriched with TiO 2 beads. c Peptides were measured by LC–MS/MS and data analyzed with the RNP(xl) software package implemented in the proteome discoverer software 50 followed by manual annotation of candidate spectra.

    Journal: Nature Communications

    Article Title: Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry

    doi: 10.1038/s41467-020-16837-x

    Figure Lengend Snippet: Schematic workflow of the fliX-MS pipeline. a A pulsed laser beam was generated using a femtosecond fiber laser with 515 nm wavelength, repetition rate of 0.5 MHz, and pulse duration of 500 fs. The wavelength was doubled to 258 nm by second harmonic generation (SHG) over a beta barium borate (BBO) crystal and the laser beam adjusted to fit the inner diameter of a regular 1.5 ml Eppendorf tube. b Protein–DNA complexes were irradiated or left untreated as control. Samples were denatured, DNA digested to mono/short oligonucleotides by a mix of Mnase, DNase I, and Benzonase, and proteins digested to peptides by trypsin and Lys-C. Peptides and peptide–nucleotide cross-links were separated from free DNA on C18 StageTips 25 , and cross-links subsequently enriched with TiO 2 beads. c Peptides were measured by LC–MS/MS and data analyzed with the RNP(xl) software package implemented in the proteome discoverer software 50 followed by manual annotation of candidate spectra.

    Article Snippet: One microliter of MNase (New England Biolabs, M0247S), one microliter of DNase I (New England Biolabs, M0303S), and three microliters of Benzonase (Merck Millipore, 70746) were added to every 150 pmol of DNA.

    Techniques: Generated, Irradiation, Liquid Chromatography with Mass Spectroscopy, Software

    Creation and dissolution of an active–passive interphase boundary in a bacterial swarm. a A series of snapshots of the expanding edge of a Serratia marcescens swarm taken over time. The colony was cultured on an agar substrate, and its expanding edge (marked by a precursor fluid film that appears as white curve) is moving from right to left. The swarm shows long-range collective flows, with strong velocity fields (PIV; overlaid color). A large domain of passive, immobile bacteria is created by exposing a region of the swarm to high intensity ultraviolet (UV) light (highlighted octagon). An interphase boundary forms between the passivated and active bacteria. When the light source is switched off ( t = 0 s), the active unexposed bacteria deform the interphase boundary and penetrate the passive region. Over time, active bacteria convect immobile bacteria away from the passive domain, causing the boundary to erode and propagate inward. The boundary is manually traced in white for visualization. The swarm dissolves the passive phase in 60 s, with interface speeds greater than that of expanding colony edge. b The swarm edge (close-up) features densely packed cells with local polarity and nematic order. c The swarm’s collective motion recovers after dissolution as shown by the probability distribution of bacterial speeds p ( v ), before and after exposure (data shown for representative experiment, collected from 5 s interval of PIV data). d A montage of the flow streamlines—from the highlighted box in a —reveals the motion of vortices (labeled by color) at the interface (blue line). Vortices starting in the bulk can collide and attach to the interface (labeled brown vortex for example); some vortices at the surface detach and move away (green, orange). Others fade away (purple) or split (dark blue splits from light blue vortex in right tile). Data shown here is from a single experiment; results were repeated for a minimum of N = 4 experiments

    Journal: Nature Communications

    Article Title: The propagation of active-passive interfaces in bacterial swarms

    doi: 10.1038/s41467-018-07781-y

    Figure Lengend Snippet: Creation and dissolution of an active–passive interphase boundary in a bacterial swarm. a A series of snapshots of the expanding edge of a Serratia marcescens swarm taken over time. The colony was cultured on an agar substrate, and its expanding edge (marked by a precursor fluid film that appears as white curve) is moving from right to left. The swarm shows long-range collective flows, with strong velocity fields (PIV; overlaid color). A large domain of passive, immobile bacteria is created by exposing a region of the swarm to high intensity ultraviolet (UV) light (highlighted octagon). An interphase boundary forms between the passivated and active bacteria. When the light source is switched off ( t = 0 s), the active unexposed bacteria deform the interphase boundary and penetrate the passive region. Over time, active bacteria convect immobile bacteria away from the passive domain, causing the boundary to erode and propagate inward. The boundary is manually traced in white for visualization. The swarm dissolves the passive phase in 60 s, with interface speeds greater than that of expanding colony edge. b The swarm edge (close-up) features densely packed cells with local polarity and nematic order. c The swarm’s collective motion recovers after dissolution as shown by the probability distribution of bacterial speeds p ( v ), before and after exposure (data shown for representative experiment, collected from 5 s interval of PIV data). d A montage of the flow streamlines—from the highlighted box in a —reveals the motion of vortices (labeled by color) at the interface (blue line). Vortices starting in the bulk can collide and attach to the interface (labeled brown vortex for example); some vortices at the surface detach and move away (green, orange). Others fade away (purple) or split (dark blue splits from light blue vortex in right tile). Data shown here is from a single experiment; results were repeated for a minimum of N = 4 experiments

    Article Snippet: Once the agar cools and solidifies, Serratia marcescens (strain ATCC 274, Manassas, VA) from frozen glycerol stocks are inoculated on the agar plates and incubated at 34 °C.

    Techniques: Cell Culture, Flow Cytometry, Labeling

    MCPH1 stabilizes RAD51 and DMC1 nucleoprotein filaments. ( A ) Schematic of our Benzonase protection assay. ( B ) The 5′- 32 P-labeled 80-mer ssDNA (1.5 μM nucleotides) was pre-incubated with RAD51 and then incubated with tag-free MCPH1 (lanes 5–7). RAD51 (lane 3) or MCPH1 alone (lane 4) were included as negative controls. RAD51 with AMP-PNP was included as a positive control. Then, Benzonase was added to challenge the filaments. The reactions were deproteinized and electrophoresed in 10% TBE polyacrylamide gels. The gels were dried and analyzed by phosphorimaging. The 32 P-label is denoted by the asterisk. ( C , D ) The assay was also conducted using DMC1 (C) or RecA (D) and analyzed in the same way. DMC1 with calcium (0.5 mM) or RecA with ATPγS were included as respective positive controls. Plots of percentage DNA protected are shown below the gels. Error bars represent the standard deviation (±SD) calculated from three independent experiments.

    Journal: Nucleic Acids Research

    Article Title: Microcephaly family protein MCPH1 stabilizes RAD51 filaments

    doi: 10.1093/nar/gkaa636

    Figure Lengend Snippet: MCPH1 stabilizes RAD51 and DMC1 nucleoprotein filaments. ( A ) Schematic of our Benzonase protection assay. ( B ) The 5′- 32 P-labeled 80-mer ssDNA (1.5 μM nucleotides) was pre-incubated with RAD51 and then incubated with tag-free MCPH1 (lanes 5–7). RAD51 (lane 3) or MCPH1 alone (lane 4) were included as negative controls. RAD51 with AMP-PNP was included as a positive control. Then, Benzonase was added to challenge the filaments. The reactions were deproteinized and electrophoresed in 10% TBE polyacrylamide gels. The gels were dried and analyzed by phosphorimaging. The 32 P-label is denoted by the asterisk. ( C , D ) The assay was also conducted using DMC1 (C) or RecA (D) and analyzed in the same way. DMC1 with calcium (0.5 mM) or RecA with ATPγS were included as respective positive controls. Plots of percentage DNA protected are shown below the gels. Error bars represent the standard deviation (±SD) calculated from three independent experiments.

    Article Snippet: Then, indicated amounts of tag-free MCPH1 were included in the reaction mixtures for a further 5 min. To challenge filament stability, Benzonase (Endonuclease, 20 units; New England Biolabs) was added into the reaction mixtures (10 μl final volume).

    Techniques: Labeling, Incubation, Positive Control, Standard Deviation

    KSHV LANA recruits Rad50 and Mre11 in the cytosol. ( A ) Co-immunoprecipitation of endogenous LANA, Rad50, Mre11 and Brd4 in BCBL-1 cells upon cytosolic-nuclear fractionation. Cells were lysed and cytoplasmic extracts (Cyto) and nuclear extracts (Nu) were prepared using the Thermo-Fischer Nu-Cyto fractionation kit following the manufacturer‘s instructions. Cytoplasmic and nuclear fractions were incubated overnight with sepharose beads coated with LANA-antibody or IgG-control. Left (INPUT, see Materials and methods ): Brd4, Lamin A/C and GAPDH immunoblots were analyzed to confirm the efficiency of the fractionation. Right (IP): immunoprecipitation with LANA-antibody or IgG-control coated-beads and immunoblot for endogenous Rad50, Mre11 and Brd4. ( B ) Co-immunoprecipitation of endogenous Rad50 and full-length LANA or ΔN mutants (Δ161 and Δ282) transfected into HEK293 cells. HEK293 cells were transfected with LANA constructs (or empty vector). 48 hours later cells were lysed and incubated with benzonase. After centrifugation, cells were incubated overnight with beads coated with LANA-antibody. Left (INPUT): immunoblot to check the expression of LANA constructs and the endogenous Rad50 in the cells. Right (IP from LANA-antibody-coated-beads): immunoblot for endogenous Rad50 co-immunoprecipitation. ( C ) Co-immunoprecipitation of endogenous LANA and Rad50, Mre11 and CARD9 in latently KSHV-infected THP-1 cells (TrK.219 cells, see Materials and methods ). Cells were lysed and incubated with benzonase. After centrifugation, whole cell lysates were incubated overnight with beads coated with anti-LANA or IgG-control antibody. Precipitated complexes were analysed by SDS-PAGE and immunoblotting with the indicated antibodies.

    Journal: PLoS Pathogens

    Article Title: Kaposi Sarcoma Herpesvirus (KSHV) Latency-Associated Nuclear Antigen (LANA) recruits components of the MRN (Mre11-Rad50-NBS1) repair complex to modulate an innate immune signaling pathway and viral latency

    doi: 10.1371/journal.ppat.1006335

    Figure Lengend Snippet: KSHV LANA recruits Rad50 and Mre11 in the cytosol. ( A ) Co-immunoprecipitation of endogenous LANA, Rad50, Mre11 and Brd4 in BCBL-1 cells upon cytosolic-nuclear fractionation. Cells were lysed and cytoplasmic extracts (Cyto) and nuclear extracts (Nu) were prepared using the Thermo-Fischer Nu-Cyto fractionation kit following the manufacturer‘s instructions. Cytoplasmic and nuclear fractions were incubated overnight with sepharose beads coated with LANA-antibody or IgG-control. Left (INPUT, see Materials and methods ): Brd4, Lamin A/C and GAPDH immunoblots were analyzed to confirm the efficiency of the fractionation. Right (IP): immunoprecipitation with LANA-antibody or IgG-control coated-beads and immunoblot for endogenous Rad50, Mre11 and Brd4. ( B ) Co-immunoprecipitation of endogenous Rad50 and full-length LANA or ΔN mutants (Δ161 and Δ282) transfected into HEK293 cells. HEK293 cells were transfected with LANA constructs (or empty vector). 48 hours later cells were lysed and incubated with benzonase. After centrifugation, cells were incubated overnight with beads coated with LANA-antibody. Left (INPUT): immunoblot to check the expression of LANA constructs and the endogenous Rad50 in the cells. Right (IP from LANA-antibody-coated-beads): immunoblot for endogenous Rad50 co-immunoprecipitation. ( C ) Co-immunoprecipitation of endogenous LANA and Rad50, Mre11 and CARD9 in latently KSHV-infected THP-1 cells (TrK.219 cells, see Materials and methods ). Cells were lysed and incubated with benzonase. After centrifugation, whole cell lysates were incubated overnight with beads coated with anti-LANA or IgG-control antibody. Precipitated complexes were analysed by SDS-PAGE and immunoblotting with the indicated antibodies.

    Article Snippet: Benzonase nuclease (Merck Millipore, 71205–3) was added to whole cell lysates (50U each 2x106 cells) for 30 minutes at RT to digest nucleic acids.

    Techniques: Immunoprecipitation, Fractionation, Incubation, Western Blot, Transfection, Construct, Plasmid Preparation, Centrifugation, Expressing, Infection, SDS Page

    KSHV LANA recruits MRN (Mre11-Rad50-NBS1) complex. ( A ) Co-immunoprecipitation of endogenous LANA and MRN proteins in BC3 cells. Cells were lysed using TBS-T buffer and the cell lysate was incubated with benzonase. After centrifugation, supernatant was incubated overnight with anti-LANA or IgG-control beads. The precipitated complexes were analyzed for the presence of endogenous Rad50, Mre11 and NBS1 by SDS-PAGE and immunoblotting. For the input, see Materials and methods . ( B ) Co-immunoprecipitation of endogenous LANA and Rad50 in BC3 cells. Co-immunoprecipitation of endogenous Rad50 was performed and analysed as in (A), but with anti-Rad50-antibody-coated-beads (left) or anti-LANA coated beads (right). The arrowhead indicates the smaller LANA forms co-immunoprecipitating with Rad50 (see text). ( C ) Schematic representation of LANA domain structure. NLS: Nuclear Localization Signal; TR: KSHV Terminal Repeats. ( D ) Pull-down assay with GST-fused LANA-C (aa 931–1162) and LANA-N (aa 1–312) proteins and HEK293T cell lysates. HEK293T were lysed with TBS-T buffer and incubated 4 hours with GST-fused proteins or GST alone, as negative control. Top : immunoblot for endogenous Rad50, Mre11 and NBS1 bound to GST-fused LANA fragments. Bottom : Ponceau staining to detect GST-fused proteins. (M) for marker.

    Journal: PLoS Pathogens

    Article Title: Kaposi Sarcoma Herpesvirus (KSHV) Latency-Associated Nuclear Antigen (LANA) recruits components of the MRN (Mre11-Rad50-NBS1) repair complex to modulate an innate immune signaling pathway and viral latency

    doi: 10.1371/journal.ppat.1006335

    Figure Lengend Snippet: KSHV LANA recruits MRN (Mre11-Rad50-NBS1) complex. ( A ) Co-immunoprecipitation of endogenous LANA and MRN proteins in BC3 cells. Cells were lysed using TBS-T buffer and the cell lysate was incubated with benzonase. After centrifugation, supernatant was incubated overnight with anti-LANA or IgG-control beads. The precipitated complexes were analyzed for the presence of endogenous Rad50, Mre11 and NBS1 by SDS-PAGE and immunoblotting. For the input, see Materials and methods . ( B ) Co-immunoprecipitation of endogenous LANA and Rad50 in BC3 cells. Co-immunoprecipitation of endogenous Rad50 was performed and analysed as in (A), but with anti-Rad50-antibody-coated-beads (left) or anti-LANA coated beads (right). The arrowhead indicates the smaller LANA forms co-immunoprecipitating with Rad50 (see text). ( C ) Schematic representation of LANA domain structure. NLS: Nuclear Localization Signal; TR: KSHV Terminal Repeats. ( D ) Pull-down assay with GST-fused LANA-C (aa 931–1162) and LANA-N (aa 1–312) proteins and HEK293T cell lysates. HEK293T were lysed with TBS-T buffer and incubated 4 hours with GST-fused proteins or GST alone, as negative control. Top : immunoblot for endogenous Rad50, Mre11 and NBS1 bound to GST-fused LANA fragments. Bottom : Ponceau staining to detect GST-fused proteins. (M) for marker.

    Article Snippet: Benzonase nuclease (Merck Millipore, 71205–3) was added to whole cell lysates (50U each 2x106 cells) for 30 minutes at RT to digest nucleic acids.

    Techniques: Immunoprecipitation, Incubation, Centrifugation, SDS Page, Pull Down Assay, Negative Control, Staining, Marker

    Benzonase nuclease treatment does not change lamin mechanics. ( a ) Step unit, ( b ) force, ( c ) stiffness and ( d ) deformation of lamin filaments in the meshwork of X. laevis nuclear envelopes were measured after nuclease treatment at a pushing speed of 1 µm s −1 . The values of the parameters were comparable to those obtained without nuclease treatment, at 1 µm s −1 , suggesting that chromatin, ribonucleoproteins or RNA were not present in the experimental system and did not influence the mechanical properties of lamins in our experiments. – Benzonase-free NEs, n = 204 for each parameter; + Benzonase-treated NEs, n = 172 for each parameter.

    Journal: bioRxiv

    Article Title: Nonlinear mechanics of lamin filaments and the meshwork topology build an emergent nuclear lamina

    doi: 10.1101/846550

    Figure Lengend Snippet: Benzonase nuclease treatment does not change lamin mechanics. ( a ) Step unit, ( b ) force, ( c ) stiffness and ( d ) deformation of lamin filaments in the meshwork of X. laevis nuclear envelopes were measured after nuclease treatment at a pushing speed of 1 µm s −1 . The values of the parameters were comparable to those obtained without nuclease treatment, at 1 µm s −1 , suggesting that chromatin, ribonucleoproteins or RNA were not present in the experimental system and did not influence the mechanical properties of lamins in our experiments. – Benzonase-free NEs, n = 204 for each parameter; + Benzonase-treated NEs, n = 172 for each parameter.

    Article Snippet: The nuclei were then treated with Benzonase® nuclease (Merck) in PBS (supplemented with 2 mM Mg2+ ) to digest the chromatin, washed with a high-salt buffer (PBS with 300 mM NaCl, pH 7.4), and then re-equilibrated in PBS.

    Techniques:

    Effects of ovalbumin (O), lysozyme (L), ovomucoid (M), their hydrolysates with pepsin (P), Neutrase (N) and alcalase (A) (200 μg/mL), the inactivated enzymes at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, and the fractions with molecular mass lower than 10,000 and 3,000 Da on the secretion of TNF-α (a, d) and IL-8 (b, e), and intracellular ROS generation (c, f) by Th1-skewed peripheral blood leucocytes. Data are expressed as percentage of the values induced by IFN-γ and LPS ± standard error of the mean in 8 donors stimulated in triplicate and * indicates significant differences ( P

    Journal: PLoS ONE

    Article Title: Regulation of Exacerbated Immune Responses in Human Peripheral Blood Cells by Hydrolysed Egg White Proteins

    doi: 10.1371/journal.pone.0151813

    Figure Lengend Snippet: Effects of ovalbumin (O), lysozyme (L), ovomucoid (M), their hydrolysates with pepsin (P), Neutrase (N) and alcalase (A) (200 μg/mL), the inactivated enzymes at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, and the fractions with molecular mass lower than 10,000 and 3,000 Da on the secretion of TNF-α (a, d) and IL-8 (b, e), and intracellular ROS generation (c, f) by Th1-skewed peripheral blood leucocytes. Data are expressed as percentage of the values induced by IFN-γ and LPS ± standard error of the mean in 8 donors stimulated in triplicate and * indicates significant differences ( P

    Article Snippet: Neutrase (EC 3.4.24.28, ≥ 0.8 U/g) and alcalase (EC 3.4.21.62, 2.4 U/g) were both from Novozymes A/S (Bagsvaerd, Denmark).

    Techniques: Concentration Assay

    Effects of different concentrations (20, 100 and 200 μg/mL) of ovalbumin (O), lysozyme (L), ovomucoid (M), and their hydrolysates with pepsin (P), Neutrase (N) and alcalase (A), as well as the inactivated enzymes (IE) at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, on the secretion of IgE by Th2-skewed human peripheral blood mononuclear cells. Data are expressed as percentage of the values induced by anti-CD40 and IL-4 ± standard error of the mean in 6 donors stimulated in triplicate and * indicates significant differences ( P

    Journal: PLoS ONE

    Article Title: Regulation of Exacerbated Immune Responses in Human Peripheral Blood Cells by Hydrolysed Egg White Proteins

    doi: 10.1371/journal.pone.0151813

    Figure Lengend Snippet: Effects of different concentrations (20, 100 and 200 μg/mL) of ovalbumin (O), lysozyme (L), ovomucoid (M), and their hydrolysates with pepsin (P), Neutrase (N) and alcalase (A), as well as the inactivated enzymes (IE) at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, on the secretion of IgE by Th2-skewed human peripheral blood mononuclear cells. Data are expressed as percentage of the values induced by anti-CD40 and IL-4 ± standard error of the mean in 6 donors stimulated in triplicate and * indicates significant differences ( P

    Article Snippet: Neutrase (EC 3.4.24.28, ≥ 0.8 U/g) and alcalase (EC 3.4.21.62, 2.4 U/g) were both from Novozymes A/S (Bagsvaerd, Denmark).

    Techniques: Concentration Assay

    Effects of different concentrations (20, 100 and 200 μg/mL) of ovalbumin (O), lysozyme (L), ovomucoid (M), and their hydrolysates with pepsin (P), Neutrase (N) and alcalase (A), as well as the inactivated enzymes (IE) at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, on the secretion of IL-13 (a), IL-5 (b), IFN-γ (c) and IL-10 (d) by Th2-skewed human peripheral blood mononuclear cells. Data are expressed as percentage of the values induced by anti-CD40 and IL-4 ± standard error of the mean in 6 donors stimulated in triplicate and * indicates significant differences ( P

    Journal: PLoS ONE

    Article Title: Regulation of Exacerbated Immune Responses in Human Peripheral Blood Cells by Hydrolysed Egg White Proteins

    doi: 10.1371/journal.pone.0151813

    Figure Lengend Snippet: Effects of different concentrations (20, 100 and 200 μg/mL) of ovalbumin (O), lysozyme (L), ovomucoid (M), and their hydrolysates with pepsin (P), Neutrase (N) and alcalase (A), as well as the inactivated enzymes (IE) at a concentration equivalent to that present in 200 μg/mL of the hydrolysates, on the secretion of IL-13 (a), IL-5 (b), IFN-γ (c) and IL-10 (d) by Th2-skewed human peripheral blood mononuclear cells. Data are expressed as percentage of the values induced by anti-CD40 and IL-4 ± standard error of the mean in 6 donors stimulated in triplicate and * indicates significant differences ( P

    Article Snippet: Neutrase (EC 3.4.24.28, ≥ 0.8 U/g) and alcalase (EC 3.4.21.62, 2.4 U/g) were both from Novozymes A/S (Bagsvaerd, Denmark).

    Techniques: Concentration Assay

    Structural characteristics of protein-solubilising oligonucleotides and renaturation of ALS brain-derived protein aggregates. a Cartoons of ds/ss/ds oligonucleotides having either pyrimidines (T or C) or purines (A) in the ss-region. b Proportion of protein aggregation following renaturing with the ds/ss/ds oligonucleotides shown in (a). c Renaturing capacity of structurally different oligonucleotides. The diagrams on the right show a theoretical structure of each oligonucleotide. All oligonucleotides, except the 3x-loop and 3x-bulges, contain a stretch of 30 Ts in the single-stranded region and the same sequences (15 nucleotides each) in the double stranded regions. The 3x-loops and bulges oligonucleotides have 3 stretches of 9 Ts and the same sequence in the ds-regions. d Proportion of protein aggregation in Jurkat cell lysate supplemented with various amounts and configurations of the M1×4 or M2×4 DNA oligonucleotides. e Insoluble proteins from two ALS brain tissues were chemically denatured in guanidine hydrochloride and treated with either buffer (Vehicle), total RNA from Jurkat cells or the complementary strands of the M1×4 DNA oligonucleotides (M1 F/R) (Pellet 1, top panel). After removal of GuHCl, the soluble fraction from these samples was treated with RNase and any aggregated proteins (Pellet 2), analysed by western blot (middle panel). Remaining supernatants were then treated with Benzonase to degrade any remaining nucleic acids and aggregated proteins collected by centrifugation and analysed by western blot (bottom panel). Proteins aggregated by enzymatic RNA degradation in Jurkat cell lysates, which do not contain NF-H, were used as a control. Data in b and c are expressed as a fraction of vehicle (Ve-), while data in d are expressed as the amount of aggregation observed without any oligonucleotides present (A/T1). All bars represent the mean ± s.d of two to four independent experiments. **= p

    Journal: bioRxiv

    Article Title: Enzymatic degradation of RNA causes widespread protein aggregation in cell and tissue lysates

    doi: 10.1101/841577

    Figure Lengend Snippet: Structural characteristics of protein-solubilising oligonucleotides and renaturation of ALS brain-derived protein aggregates. a Cartoons of ds/ss/ds oligonucleotides having either pyrimidines (T or C) or purines (A) in the ss-region. b Proportion of protein aggregation following renaturing with the ds/ss/ds oligonucleotides shown in (a). c Renaturing capacity of structurally different oligonucleotides. The diagrams on the right show a theoretical structure of each oligonucleotide. All oligonucleotides, except the 3x-loop and 3x-bulges, contain a stretch of 30 Ts in the single-stranded region and the same sequences (15 nucleotides each) in the double stranded regions. The 3x-loops and bulges oligonucleotides have 3 stretches of 9 Ts and the same sequence in the ds-regions. d Proportion of protein aggregation in Jurkat cell lysate supplemented with various amounts and configurations of the M1×4 or M2×4 DNA oligonucleotides. e Insoluble proteins from two ALS brain tissues were chemically denatured in guanidine hydrochloride and treated with either buffer (Vehicle), total RNA from Jurkat cells or the complementary strands of the M1×4 DNA oligonucleotides (M1 F/R) (Pellet 1, top panel). After removal of GuHCl, the soluble fraction from these samples was treated with RNase and any aggregated proteins (Pellet 2), analysed by western blot (middle panel). Remaining supernatants were then treated with Benzonase to degrade any remaining nucleic acids and aggregated proteins collected by centrifugation and analysed by western blot (bottom panel). Proteins aggregated by enzymatic RNA degradation in Jurkat cell lysates, which do not contain NF-H, were used as a control. Data in b and c are expressed as a fraction of vehicle (Ve-), while data in d are expressed as the amount of aggregation observed without any oligonucleotides present (A/T1). All bars represent the mean ± s.d of two to four independent experiments. **= p

    Article Snippet: Aggregated proteins (Pellet 2) were collected by centrifugation as above and the supernatant supplemented with MgCl2 , 1 mM final concentration, and Benzonase (sc-391121B, Santa Cruz) and incubated at 37°C for 1 hour, shaking as above.

    Techniques: Derivative Assay, Sequencing, Western Blot, Centrifugation

    Linker histone H1.2 inhibits ATM recruitment and activation by interacting with MRN. a Wild type and H1.2 KO (1#) HeLa cells were transfected with GFP-NBS1 and subjected to laser micro-irradiation-coupled live-cell imaging. Images were taken every 10 s for 10 min and the relative intensity of the irradiation path signal was shown. The data represent the mean ± SD. Scale bars, 10 μm. b HeLa cells extracts were analyzed by Co-IP assay with or without benzonase treatment with the indicated antibodies. c GST alone or GST-MRE11, RAD50 and NBS1 were incubated with HIS-H1.2 for GST pull-down assay. * indicates specific protein bands. d GST alone or GST-H1.2 fragments were incubated with HIS-MRE11 for GST pull-down assay. * indicates specific protein bands. e Wild type or NBS1 KO HeLa cells were transfected with the indicated siRNAs and treated with 40 μM etoposide for 2 h and analyzed by immunoblotting. f HeLa cells were transfected with the indicated siRNAs and treated with 40 μM etoposide for 2 h and analyzed by immunoblotting. g , h HeLa cells were transfected with the indicated plasmids, and the whole cell lysates were immunoprecipitated with ATM antibody and analyzed by immunoblotting. i HeLa cells were transfected with the indicated plasmids and treated with 40 μM etoposide for 2 h. Whole cell extracts were prepared and analyzed by Co-IP assay and immunoblotting with the indicated antibodies

    Journal: Cell Research

    Article Title: Destabilization of linker histone H1.2 is essential for ATM activation and DNA damage repair

    doi: 10.1038/s41422-018-0048-0

    Figure Lengend Snippet: Linker histone H1.2 inhibits ATM recruitment and activation by interacting with MRN. a Wild type and H1.2 KO (1#) HeLa cells were transfected with GFP-NBS1 and subjected to laser micro-irradiation-coupled live-cell imaging. Images were taken every 10 s for 10 min and the relative intensity of the irradiation path signal was shown. The data represent the mean ± SD. Scale bars, 10 μm. b HeLa cells extracts were analyzed by Co-IP assay with or without benzonase treatment with the indicated antibodies. c GST alone or GST-MRE11, RAD50 and NBS1 were incubated with HIS-H1.2 for GST pull-down assay. * indicates specific protein bands. d GST alone or GST-H1.2 fragments were incubated with HIS-MRE11 for GST pull-down assay. * indicates specific protein bands. e Wild type or NBS1 KO HeLa cells were transfected with the indicated siRNAs and treated with 40 μM etoposide for 2 h and analyzed by immunoblotting. f HeLa cells were transfected with the indicated siRNAs and treated with 40 μM etoposide for 2 h and analyzed by immunoblotting. g , h HeLa cells were transfected with the indicated plasmids, and the whole cell lysates were immunoprecipitated with ATM antibody and analyzed by immunoblotting. i HeLa cells were transfected with the indicated plasmids and treated with 40 μM etoposide for 2 h. Whole cell extracts were prepared and analyzed by Co-IP assay and immunoblotting with the indicated antibodies

    Article Snippet: For benzonase treatment, the supernatant was treated with benzonase (Millipore, USA) at 10 U/mL at 4 °C while rotating for 2 h before incubating with the antibodies.

    Techniques: Activation Assay, Transfection, Irradiation, Live Cell Imaging, Co-Immunoprecipitation Assay, Incubation, Pull Down Assay, Immunoprecipitation

    Construction of expression plasmids containing synthetic 2,3-BD operon. The budR , budA and budB from S. marcescens H30 encode the transcriptional activator, α-acetolactate decarboxylase and α-acetolactate synthase, respectively. The bdh1 , bdh2 , bdh3 and gdh genes from Serratia sp. T241 encode the putative 2,3-butanediol dehydrogenase or glycerol dehydrogenase.

    Journal: Scientific Reports

    Article Title: Mechanism of 2,3-butanediol stereoisomers formation in a newly isolated Serratia sp. T241

    doi: 10.1038/srep19257

    Figure Lengend Snippet: Construction of expression plasmids containing synthetic 2,3-BD operon. The budR , budA and budB from S. marcescens H30 encode the transcriptional activator, α-acetolactate decarboxylase and α-acetolactate synthase, respectively. The bdh1 , bdh2 , bdh3 and gdh genes from Serratia sp. T241 encode the putative 2,3-butanediol dehydrogenase or glycerol dehydrogenase.

    Article Snippet: For Serratia sp. T241, four enzymes including meso -BDH, (2S ,3S )-BDH, (2R ,3R )-BDH and GDH were identified and contributed to three configuration of 2,3-BD formation, which showed that the model of 2,3-BD stereoisomers formation in Serratia sp. T241 was more complicated than that of K . pneumoniae .

    Techniques: Expressing

    Catalysis reactions of BDH1 ( A–D ), BDH2 ( E-H ), BDH3 ( I–L ) and GDH ( M–P ) enzymes from Serratia sp. T241 using DA, AC and 2,3-BD as substrates. DA (empty square), (3 S )-AC (empty circle), (3 R )-AC (filled circle), (2 S ,3 S )-2,3-BD (upright triangle), (2 R ,3 R )-2,3-BD (inverted triangle), meso -2,3-BD (filled square). Error bars represents standard deviation from the mean (n = 3).

    Journal: Scientific Reports

    Article Title: Mechanism of 2,3-butanediol stereoisomers formation in a newly isolated Serratia sp. T241

    doi: 10.1038/srep19257

    Figure Lengend Snippet: Catalysis reactions of BDH1 ( A–D ), BDH2 ( E-H ), BDH3 ( I–L ) and GDH ( M–P ) enzymes from Serratia sp. T241 using DA, AC and 2,3-BD as substrates. DA (empty square), (3 S )-AC (empty circle), (3 R )-AC (filled circle), (2 S ,3 S )-2,3-BD (upright triangle), (2 R ,3 R )-2,3-BD (inverted triangle), meso -2,3-BD (filled square). Error bars represents standard deviation from the mean (n = 3).

    Article Snippet: For Serratia sp. T241, four enzymes including meso -BDH, (2S ,3S )-BDH, (2R ,3R )-BDH and GDH were identified and contributed to three configuration of 2,3-BD formation, which showed that the model of 2,3-BD stereoisomers formation in Serratia sp. T241 was more complicated than that of K . pneumoniae .

    Techniques: Standard Deviation

    Batch fermentations using Serratia sp. T241 ( A–C ) and its mutants including Δbdh1 ( D–F ), Δbdh2 ( G–I ), Δbdh3 ( J–L ) and Δgdh ( M–O ). DCW (empty square), meso -2,3-BD (filled square), (3 S )-AC (empty circle), (3 R )-AC (filled circle), (2 S ,3 S )-2,3-BD (empty triangle) and (2 R ,3 R )-2,3-BD (filled triangle). Error bars represents standard deviation from the mean (n = 3).

    Journal: Scientific Reports

    Article Title: Mechanism of 2,3-butanediol stereoisomers formation in a newly isolated Serratia sp. T241

    doi: 10.1038/srep19257

    Figure Lengend Snippet: Batch fermentations using Serratia sp. T241 ( A–C ) and its mutants including Δbdh1 ( D–F ), Δbdh2 ( G–I ), Δbdh3 ( J–L ) and Δgdh ( M–O ). DCW (empty square), meso -2,3-BD (filled square), (3 S )-AC (empty circle), (3 R )-AC (filled circle), (2 S ,3 S )-2,3-BD (empty triangle) and (2 R ,3 R )-2,3-BD (filled triangle). Error bars represents standard deviation from the mean (n = 3).

    Article Snippet: For Serratia sp. T241, four enzymes including meso -BDH, (2S ,3S )-BDH, (2R ,3R )-BDH and GDH were identified and contributed to three configuration of 2,3-BD formation, which showed that the model of 2,3-BD stereoisomers formation in Serratia sp. T241 was more complicated than that of K . pneumoniae .

    Techniques: Standard Deviation

    2,3-Butanediol biosynthesis pathway and mechanism of 2,3-butanediol stereoisomer formation in Serratia sp. T241. ALS (acetolactate synthase), ALDC (acetolactate decarboxylase), BDH1 ( meso -2,3-butanediol dehydrogenase), BDH2, ((2 S ,3 S )-2,3-butanediol dehydrogenase), BDH3 ((2 R ,3 R )-2,3-butanediol dehydrogenase), GDH (glycerol dehydrogenase).

    Journal: Scientific Reports

    Article Title: Mechanism of 2,3-butanediol stereoisomers formation in a newly isolated Serratia sp. T241

    doi: 10.1038/srep19257

    Figure Lengend Snippet: 2,3-Butanediol biosynthesis pathway and mechanism of 2,3-butanediol stereoisomer formation in Serratia sp. T241. ALS (acetolactate synthase), ALDC (acetolactate decarboxylase), BDH1 ( meso -2,3-butanediol dehydrogenase), BDH2, ((2 S ,3 S )-2,3-butanediol dehydrogenase), BDH3 ((2 R ,3 R )-2,3-butanediol dehydrogenase), GDH (glycerol dehydrogenase).

    Article Snippet: For Serratia sp. T241, four enzymes including meso -BDH, (2S ,3S )-BDH, (2R ,3R )-BDH and GDH were identified and contributed to three configuration of 2,3-BD formation, which showed that the model of 2,3-BD stereoisomers formation in Serratia sp. T241 was more complicated than that of K . pneumoniae .

    Techniques: