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  • 99
    New England Biolabs micrococcal nuclease
    Micrococcal Nuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2706 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher subcellular protein fractionation kit
    Identification of ER membrane <t>protein</t> interactomes by proximity proteomics. (A) Schematic of known (SEC61 translocon, OST complex), and candidate (SEC62, LRRC59) ER-ribosome receptors. SEC61β (purple), a subunit of the SEC61 translocon, RPN1 (green), a subunit of the OST complex, SEC62 (orange), and LRRC59 (blue) are expressed as BioID chimeras, labeling interacting and near-neighbor proteins (indicated by starred ribosomes and proteins W, X, Y, and Z). (B) Left panel: Streptavidin blots examining the <t>subcellular</t> distribution of biotin-labeled proteins within HEK293 cells expressing either the LRRC59-, SEC62-, SEC61β-, or RPN1-BirA reporter constructs. Biotin labeling (doxycycline (dox)-inducible expression of reporters) was performed over a time course spanning 0-6 hours and cytosol (C) and membrane (M) extracts prepared by detergent <t>fractionation.</t> Right panel: Densitometric quantifications of biotin labeling intensities for cytosolic and membrane fractions. (C) Canine pancreas rough microsomes with (+BirA) or without (-BirA) the addition of BirA* in trans . Biotin labeling of proteins was conducted over 0-18 hours (top, left). Biotin labeling intensities were quantified using densitometric analyses (top, right). As a loading control, total protein lysate was analyzed by India ink staining (bottom, left) and quantified by densitometric analysis (bottom, right).
    Subcellular Protein Fractionation Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3662 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher bsa
    Representative images of large accumulations of membrane folds in BHK-21 cells after 3 h of incubation with <t>BSA-GNRs.</t> (a) GNRs can be seen on the membranes in the enlarged areas of the photo. (b)–(d) Lysosomes formed due to the compression of membrane accumulations and digestion of membranes, containing BSA-GNRs. TEM of ultrathin sections.
    Bsa, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 28305 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher ne per nuclear
    Minnelide treatment delays leukemogenesis and inhibits HSP90 function in an in vivo model of CLL A. Average radiance of the mice at the indicated times from an in vivo Mec-1luciferase expressing xenograft model of CLL in Rag2−/−IL2Rγ−/− mice ( n = 8 <t>per</t> group) B. Bioluminescent images of control and minnelide-treated mice acquired at the same exposure conditions at week 3 following injection of Mec-1 luciferase cells. C. Kaplan Meier survival plots for control and minnelide-treated mice following indicated days of treatment. D. Spleen weight of deceased control mice and minnelide-treated mice on day 50 (* p = 0.04). E. <t>Immunoblot</t> analysis of BTK-PLCγ2-AKT signaling pathway and the indicated HSPs from control (from spleen collected at the time of death) and minnelide-treated mice (euthanized on day 50).
    Ne Per Nuclear, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 21501 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Diagenode bioruptor
    Minnelide treatment delays leukemogenesis and inhibits HSP90 function in an in vivo model of CLL A. Average radiance of the mice at the indicated times from an in vivo Mec-1luciferase expressing xenograft model of CLL in Rag2−/−IL2Rγ−/− mice ( n = 8 <t>per</t> group) B. Bioluminescent images of control and minnelide-treated mice acquired at the same exposure conditions at week 3 following injection of Mec-1 luciferase cells. C. Kaplan Meier survival plots for control and minnelide-treated mice following indicated days of treatment. D. Spleen weight of deceased control mice and minnelide-treated mice on day 50 (* p = 0.04). E. <t>Immunoblot</t> analysis of BTK-PLCγ2-AKT signaling pathway and the indicated HSPs from control (from spleen collected at the time of death) and minnelide-treated mice (euthanized on day 50).
    Bioruptor, supplied by Diagenode, used in various techniques. Bioz Stars score: 95/100, based on 16837 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher propidium iodide
    Cell cycle analysis for A549 cells treated with trichostatin A (TSA). Cells were treated with 0~1,000 nM TSA for 18 hr, and collected, fixed and stained with <t>propidium</t> iodide, and then analyzed using flow cytometry.
    Propidium Iodide, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 23893 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher dynabeads protein g
    PFE1605w binds to the RBC cytoskeleton. A. LC‐ESI‐MS/MS results of two independent Co‐IP experiments using parasites expressing PFE1605w‐HA. B. LC‐ESI‐MS/MS results of two independent reverse Co‐IP experiments with α‐band 4.2 antibodies coupled to <t>protein</t> G <t>Dynabeads.</t> All experiments were performed twice. C. Elution fractions of the reverse Co‐IP experiment were also analysed by Western blot with α‐PFE1605w antibodies. D. Fluorescence polarization titrations of 5‐FAM‐labelled PFE1605w‐C with unlabelled band 3 cytosolic domain or BSA as a negative control. Data points, normalized to the fraction of PFE1605w‐C bound at each titrant concentration, are shown as coloured circles. The error bars were derived from three replicates. The fit to a single‐site association model is shown as solid line. The interaction of PFE1605w‐C with BSA could not be fitted.
    Dynabeads Protein G, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 16937 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rna
    Electrophoretogram of sequencing libraries. The graph shows the length distribution curves of sequencing libraries obtained with Illumina TruSeqTM <t>RNA</t> sample preparation kit (Low-Throughput protocol) according to manufacturer’s protocol. The length of <t>DNA</t> fragments was between 200 and 700 pb. Curves were generated on a 2100 bioanalyzer using DNA 1000 chip (Agilent Technologies). For each sample three biological replicates were performed
    Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 177224 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher hoechst 33342
    Analysis of PLGA and PLGA- b -HA particles tethered to cells. (a) Schematic showing the procedure to tether particles onto stem cells for 15 min at room temperature, followed by centrifugation to remove unbound particles. The particles were labeled by loading bovine serum albumin conjugated with Rhodamine B (red). (b) Representative confocal images of the cells tethered with the particles. Cell nuclei and cell membrane were stained with <t>Hoechst</t> 33342 (blue) and DiO dye (green), respectively. Scale bar = 10 μm.
    Hoechst 33342, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 54383 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore micrococcal nuclease
    Analysis of PLGA and PLGA- b -HA particles tethered to cells. (a) Schematic showing the procedure to tether particles onto stem cells for 15 min at room temperature, followed by centrifugation to remove unbound particles. The particles were labeled by loading bovine serum albumin conjugated with Rhodamine B (red). (b) Representative confocal images of the cells tethered with the particles. Cell nuclei and cell membrane were stained with <t>Hoechst</t> 33342 (blue) and DiO dye (green), respectively. Scale bar = 10 μm.
    Micrococcal Nuclease, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1897 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher protein g dynabeads
    SUMOylation blocks Rts1 binding to Sgo1 and release of this interaction is important for stable biorientation. (A) The Sgo1-3A mutant which fails to associate with PP2A-Rts1 or CPC shows enhanced SUMOylation. In vivo SUMOylation assay was performed on wild type (AMy7655) and sgo1-3A (AMy25988) strains carrying SGO1-6HA . (B) SUMOylated Sgo1 has reduced binding affinity for Rts1. Recombinant V5-tagged Sgo1 was mixed with components of the SUMOylation pathway in the presence or absence of ATP. Anti-V5 antibody coupled <t>Protein</t> G <t>dynabeads</t> were added to the mixture, washed thoroughly and incubated with extract from sgo1 Δ or sgo1 Δ RTS1-9MYC (AMy8832). Levels of Sgo1 and Rts1 bound to beads were probed by anti-V5 and anti-Myc western blotting, respectively. (C) Rts1 preferentially binds to unsumoylated Sgo1. Rts1-9MYC was immunoprecipitated from sgo1 Δ RTS1-9MYC (AMy8832) using anti-MYC antibody coupled to Protein G dynabeads. Beads were incubated with in vitro SUMOylation reaction mixture containing Sgo1. Levels of Sgo1 and Rts1 bound to beads were probed by anti-V5 and anti-Myc western blotting, respectively. (D-F) Biorientation is unstable when Rts1 is tethered to wild type Sgo1 or Sgo1-4R. Strains used contained CEN4-mNeonGreen MET-CDC20 and SPC42-tdTOMATO and were SGO1-GBP (AMy28389), SGO1-GBP RTS1-non-fluorescent GFP (AMy28092), sgo1-4R-GBP (AMy28417) and sgo1-4R-GBP RTS1-non-fluorescent GFP (AMy28416). The assay was performed as described in Figure 5C . (D) Tethering Rts1 to wild type Sgo1 or Sgo1-4R does not affect the initial establishment of biorientation. (E) Increased reassociation of CEN4-mNeonGreen dots was observed when Rts1 was tethered to wild type Sgo1 or Sgo1-4R. (F) Mis-segregation is only modestly increased when Rts1 is tethered to wild type Sgo1 or Sgo1-4R. (G) Schematic model of how Sgo1 SUMOylation may alter the kinase-phosphatase balance to initiate error correction silencing and promote anaphase onset. For details, see text
    Protein G Dynabeads, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 11512 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Diagenode lysis buffer
    SUMOylation blocks Rts1 binding to Sgo1 and release of this interaction is important for stable biorientation. (A) The Sgo1-3A mutant which fails to associate with PP2A-Rts1 or CPC shows enhanced SUMOylation. In vivo SUMOylation assay was performed on wild type (AMy7655) and sgo1-3A (AMy25988) strains carrying SGO1-6HA . (B) SUMOylated Sgo1 has reduced binding affinity for Rts1. Recombinant V5-tagged Sgo1 was mixed with components of the SUMOylation pathway in the presence or absence of ATP. Anti-V5 antibody coupled <t>Protein</t> G <t>dynabeads</t> were added to the mixture, washed thoroughly and incubated with extract from sgo1 Δ or sgo1 Δ RTS1-9MYC (AMy8832). Levels of Sgo1 and Rts1 bound to beads were probed by anti-V5 and anti-Myc western blotting, respectively. (C) Rts1 preferentially binds to unsumoylated Sgo1. Rts1-9MYC was immunoprecipitated from sgo1 Δ RTS1-9MYC (AMy8832) using anti-MYC antibody coupled to Protein G dynabeads. Beads were incubated with in vitro SUMOylation reaction mixture containing Sgo1. Levels of Sgo1 and Rts1 bound to beads were probed by anti-V5 and anti-Myc western blotting, respectively. (D-F) Biorientation is unstable when Rts1 is tethered to wild type Sgo1 or Sgo1-4R. Strains used contained CEN4-mNeonGreen MET-CDC20 and SPC42-tdTOMATO and were SGO1-GBP (AMy28389), SGO1-GBP RTS1-non-fluorescent GFP (AMy28092), sgo1-4R-GBP (AMy28417) and sgo1-4R-GBP RTS1-non-fluorescent GFP (AMy28416). The assay was performed as described in Figure 5C . (D) Tethering Rts1 to wild type Sgo1 or Sgo1-4R does not affect the initial establishment of biorientation. (E) Increased reassociation of CEN4-mNeonGreen dots was observed when Rts1 was tethered to wild type Sgo1 or Sgo1-4R. (F) Mis-segregation is only modestly increased when Rts1 is tethered to wild type Sgo1 or Sgo1-4R. (G) Schematic model of how Sgo1 SUMOylation may alter the kinase-phosphatase balance to initiate error correction silencing and promote anaphase onset. For details, see text
    Lysis Buffer, supplied by Diagenode, used in various techniques. Bioz Stars score: 92/100, based on 2457 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore protease inhibitor cocktail
    SUMOylation blocks Rts1 binding to Sgo1 and release of this interaction is important for stable biorientation. (A) The Sgo1-3A mutant which fails to associate with PP2A-Rts1 or CPC shows enhanced SUMOylation. In vivo SUMOylation assay was performed on wild type (AMy7655) and sgo1-3A (AMy25988) strains carrying SGO1-6HA . (B) SUMOylated Sgo1 has reduced binding affinity for Rts1. Recombinant V5-tagged Sgo1 was mixed with components of the SUMOylation pathway in the presence or absence of ATP. Anti-V5 antibody coupled <t>Protein</t> G <t>dynabeads</t> were added to the mixture, washed thoroughly and incubated with extract from sgo1 Δ or sgo1 Δ RTS1-9MYC (AMy8832). Levels of Sgo1 and Rts1 bound to beads were probed by anti-V5 and anti-Myc western blotting, respectively. (C) Rts1 preferentially binds to unsumoylated Sgo1. Rts1-9MYC was immunoprecipitated from sgo1 Δ RTS1-9MYC (AMy8832) using anti-MYC antibody coupled to Protein G dynabeads. Beads were incubated with in vitro SUMOylation reaction mixture containing Sgo1. Levels of Sgo1 and Rts1 bound to beads were probed by anti-V5 and anti-Myc western blotting, respectively. (D-F) Biorientation is unstable when Rts1 is tethered to wild type Sgo1 or Sgo1-4R. Strains used contained CEN4-mNeonGreen MET-CDC20 and SPC42-tdTOMATO and were SGO1-GBP (AMy28389), SGO1-GBP RTS1-non-fluorescent GFP (AMy28092), sgo1-4R-GBP (AMy28417) and sgo1-4R-GBP RTS1-non-fluorescent GFP (AMy28416). The assay was performed as described in Figure 5C . (D) Tethering Rts1 to wild type Sgo1 or Sgo1-4R does not affect the initial establishment of biorientation. (E) Increased reassociation of CEN4-mNeonGreen dots was observed when Rts1 was tethered to wild type Sgo1 or Sgo1-4R. (F) Mis-segregation is only modestly increased when Rts1 is tethered to wild type Sgo1 or Sgo1-4R. (G) Schematic model of how Sgo1 SUMOylation may alter the kinase-phosphatase balance to initiate error correction silencing and promote anaphase onset. For details, see text
    Protease Inhibitor Cocktail, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 134786 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore benzonase
    TCTP interacts with components of DNA damage sensing and repair. ( A ) <t>Benzonase-treated</t> chromatin-enriched fractions that were isolated from confluent U2OS cells 30 min after no (−) or acute [50 cGy, (+)] irradiation (IR) were immunoprecipitated
    Benzonase, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 18516 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore triton x 100
    TCTP interacts with components of DNA damage sensing and repair. ( A ) <t>Benzonase-treated</t> chromatin-enriched fractions that were isolated from confluent U2OS cells 30 min after no (−) or acute [50 cGy, (+)] irradiation (IR) were immunoprecipitated
    Triton X 100, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 65173 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher micrococcal nuclease
    TCTP interacts with components of DNA damage sensing and repair. ( A ) <t>Benzonase-treated</t> chromatin-enriched fractions that were isolated from confluent U2OS cells 30 min after no (−) or acute [50 cGy, (+)] irradiation (IR) were immunoprecipitated
    Micrococcal Nuclease, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 999 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore formaldehyde
    TCTP interacts with components of DNA damage sensing and repair. ( A ) <t>Benzonase-treated</t> chromatin-enriched fractions that were isolated from confluent U2OS cells 30 min after no (−) or acute [50 cGy, (+)] irradiation (IR) were immunoprecipitated
    Formaldehyde, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 15340 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Identification of ER membrane protein interactomes by proximity proteomics. (A) Schematic of known (SEC61 translocon, OST complex), and candidate (SEC62, LRRC59) ER-ribosome receptors. SEC61β (purple), a subunit of the SEC61 translocon, RPN1 (green), a subunit of the OST complex, SEC62 (orange), and LRRC59 (blue) are expressed as BioID chimeras, labeling interacting and near-neighbor proteins (indicated by starred ribosomes and proteins W, X, Y, and Z). (B) Left panel: Streptavidin blots examining the subcellular distribution of biotin-labeled proteins within HEK293 cells expressing either the LRRC59-, SEC62-, SEC61β-, or RPN1-BirA reporter constructs. Biotin labeling (doxycycline (dox)-inducible expression of reporters) was performed over a time course spanning 0-6 hours and cytosol (C) and membrane (M) extracts prepared by detergent fractionation. Right panel: Densitometric quantifications of biotin labeling intensities for cytosolic and membrane fractions. (C) Canine pancreas rough microsomes with (+BirA) or without (-BirA) the addition of BirA* in trans . Biotin labeling of proteins was conducted over 0-18 hours (top, left). Biotin labeling intensities were quantified using densitometric analyses (top, right). As a loading control, total protein lysate was analyzed by India ink staining (bottom, left) and quantified by densitometric analysis (bottom, right).

    Journal: bioRxiv

    Article Title: Quantitative proteomics links the LRRC59 interactome to mRNA translation on the ER membrane

    doi: 10.1101/2020.03.04.975474

    Figure Lengend Snippet: Identification of ER membrane protein interactomes by proximity proteomics. (A) Schematic of known (SEC61 translocon, OST complex), and candidate (SEC62, LRRC59) ER-ribosome receptors. SEC61β (purple), a subunit of the SEC61 translocon, RPN1 (green), a subunit of the OST complex, SEC62 (orange), and LRRC59 (blue) are expressed as BioID chimeras, labeling interacting and near-neighbor proteins (indicated by starred ribosomes and proteins W, X, Y, and Z). (B) Left panel: Streptavidin blots examining the subcellular distribution of biotin-labeled proteins within HEK293 cells expressing either the LRRC59-, SEC62-, SEC61β-, or RPN1-BirA reporter constructs. Biotin labeling (doxycycline (dox)-inducible expression of reporters) was performed over a time course spanning 0-6 hours and cytosol (C) and membrane (M) extracts prepared by detergent fractionation. Right panel: Densitometric quantifications of biotin labeling intensities for cytosolic and membrane fractions. (C) Canine pancreas rough microsomes with (+BirA) or without (-BirA) the addition of BirA* in trans . Biotin labeling of proteins was conducted over 0-18 hours (top, left). Biotin labeling intensities were quantified using densitometric analyses (top, right). As a loading control, total protein lysate was analyzed by India ink staining (bottom, left) and quantified by densitometric analysis (bottom, right).

    Article Snippet: Subcellular fractions were cleared by centrifugation (15,300 x g for 10 minutes).

    Techniques: Labeling, Expressing, Construct, Fractionation, Staining

    Representative images of large accumulations of membrane folds in BHK-21 cells after 3 h of incubation with BSA-GNRs. (a) GNRs can be seen on the membranes in the enlarged areas of the photo. (b)–(d) Lysosomes formed due to the compression of membrane accumulations and digestion of membranes, containing BSA-GNRs. TEM of ultrathin sections.

    Journal: BioMed Research International

    Article Title: Comparison of Behaviour in Different Liquids and in Cells of Gold Nanorods and Spherical Nanoparticles Modified by Linear Polyethyleneimine and Bovine Serum Albumin

    doi: 10.1155/2014/908175

    Figure Lengend Snippet: Representative images of large accumulations of membrane folds in BHK-21 cells after 3 h of incubation with BSA-GNRs. (a) GNRs can be seen on the membranes in the enlarged areas of the photo. (b)–(d) Lysosomes formed due to the compression of membrane accumulations and digestion of membranes, containing BSA-GNRs. TEM of ultrathin sections.

    Article Snippet: To study the behaviour of GNPs in different solutions used in cell cultivation, the pellets of citrate-, BSA-, and PEI-sGNPs and CTAB-, BSA-, and PEI-GNRs were diluted (1 : 9 to a concentration of 0.04 mg/L) with (1) Dulbecco's Modified Eagle Medium (DMEM, Gibco BRL, Germany) supplemented with 10% FBS (Gibco BRL, Germany), (2) conditioned DMEM (collected from Madin-Darby canine kidney epithelial cells (MDCK) after 48 h of cultivation at 37°C with 5% CО2 ), (3) 10% aqueous solution of FBS, and (4) PBS.

    Techniques: Incubation, Transmission Electron Microscopy

    Differences in the accumulation of (a) PEI-GNRs and (b) BSA-GNRs in BHK-21 cells after 24 h of incubation. Insets show enlarged fragments of lysosomes containing GNRs. TEM of ultrathin sections.

    Journal: BioMed Research International

    Article Title: Comparison of Behaviour in Different Liquids and in Cells of Gold Nanorods and Spherical Nanoparticles Modified by Linear Polyethyleneimine and Bovine Serum Albumin

    doi: 10.1155/2014/908175

    Figure Lengend Snippet: Differences in the accumulation of (a) PEI-GNRs and (b) BSA-GNRs in BHK-21 cells after 24 h of incubation. Insets show enlarged fragments of lysosomes containing GNRs. TEM of ultrathin sections.

    Article Snippet: To study the behaviour of GNPs in different solutions used in cell cultivation, the pellets of citrate-, BSA-, and PEI-sGNPs and CTAB-, BSA-, and PEI-GNRs were diluted (1 : 9 to a concentration of 0.04 mg/L) with (1) Dulbecco's Modified Eagle Medium (DMEM, Gibco BRL, Germany) supplemented with 10% FBS (Gibco BRL, Germany), (2) conditioned DMEM (collected from Madin-Darby canine kidney epithelial cells (MDCK) after 48 h of cultivation at 37°C with 5% CО2 ), (3) 10% aqueous solution of FBS, and (4) PBS.

    Techniques: Incubation, Transmission Electron Microscopy

    Representative images of BSA-GNRs associated with cell detritus (enlarged in the box) near the surface of a B16 cell after 3 h of incubation. TEM of ultrathin sections.

    Journal: BioMed Research International

    Article Title: Comparison of Behaviour in Different Liquids and in Cells of Gold Nanorods and Spherical Nanoparticles Modified by Linear Polyethyleneimine and Bovine Serum Albumin

    doi: 10.1155/2014/908175

    Figure Lengend Snippet: Representative images of BSA-GNRs associated with cell detritus (enlarged in the box) near the surface of a B16 cell after 3 h of incubation. TEM of ultrathin sections.

    Article Snippet: To study the behaviour of GNPs in different solutions used in cell cultivation, the pellets of citrate-, BSA-, and PEI-sGNPs and CTAB-, BSA-, and PEI-GNRs were diluted (1 : 9 to a concentration of 0.04 mg/L) with (1) Dulbecco's Modified Eagle Medium (DMEM, Gibco BRL, Germany) supplemented with 10% FBS (Gibco BRL, Germany), (2) conditioned DMEM (collected from Madin-Darby canine kidney epithelial cells (MDCK) after 48 h of cultivation at 37°C with 5% CО2 ), (3) 10% aqueous solution of FBS, and (4) PBS.

    Techniques: Incubation, Transmission Electron Microscopy

    Minnelide treatment delays leukemogenesis and inhibits HSP90 function in an in vivo model of CLL A. Average radiance of the mice at the indicated times from an in vivo Mec-1luciferase expressing xenograft model of CLL in Rag2−/−IL2Rγ−/− mice ( n = 8 per group) B. Bioluminescent images of control and minnelide-treated mice acquired at the same exposure conditions at week 3 following injection of Mec-1 luciferase cells. C. Kaplan Meier survival plots for control and minnelide-treated mice following indicated days of treatment. D. Spleen weight of deceased control mice and minnelide-treated mice on day 50 (* p = 0.04). E. Immunoblot analysis of BTK-PLCγ2-AKT signaling pathway and the indicated HSPs from control (from spleen collected at the time of death) and minnelide-treated mice (euthanized on day 50).

    Journal: Oncotarget

    Article Title: Targeting HSF1 disrupts HSP90 chaperone function in chronic lymphocytic leukemia

    doi:

    Figure Lengend Snippet: Minnelide treatment delays leukemogenesis and inhibits HSP90 function in an in vivo model of CLL A. Average radiance of the mice at the indicated times from an in vivo Mec-1luciferase expressing xenograft model of CLL in Rag2−/−IL2Rγ−/− mice ( n = 8 per group) B. Bioluminescent images of control and minnelide-treated mice acquired at the same exposure conditions at week 3 following injection of Mec-1 luciferase cells. C. Kaplan Meier survival plots for control and minnelide-treated mice following indicated days of treatment. D. Spleen weight of deceased control mice and minnelide-treated mice on day 50 (* p = 0.04). E. Immunoblot analysis of BTK-PLCγ2-AKT signaling pathway and the indicated HSPs from control (from spleen collected at the time of death) and minnelide-treated mice (euthanized on day 50).

    Article Snippet: Nuclear-cytosolic fractionation, immunoprecipitation and immunoblot analyses CLL cell pellets were subjected to nuclear-cytosolic fractionation using NE-PER nuclear and cytoplasmic extraction kit (Pierce biotechnology, Rockford, IL).

    Techniques: In Vivo, Mouse Assay, Expressing, Injection, Luciferase

    Cell cycle analysis for A549 cells treated with trichostatin A (TSA). Cells were treated with 0~1,000 nM TSA for 18 hr, and collected, fixed and stained with propidium iodide, and then analyzed using flow cytometry.

    Journal:

    Article Title: A Histone Deacetylase Inhibitor, Trichostatin A, Enhances Radiosensitivity by Abrogating G2/M Arrest in Human Carcinoma Cells

    doi: 10.4143/crt.2005.37.2.122

    Figure Lengend Snippet: Cell cycle analysis for A549 cells treated with trichostatin A (TSA). Cells were treated with 0~1,000 nM TSA for 18 hr, and collected, fixed and stained with propidium iodide, and then analyzed using flow cytometry.

    Article Snippet: The fixed cells were then washed twice with PBS, suspended in 1 ml 0.25% Triton X-100 (Merck) in PBS on ice for 5 min, centrifuged, washed, and resuspended in PBS containing 5 µg/ml propidium iodide (Molecular Probes, Eugene, OR) and 0.1% RNase A (Sigma).

    Techniques: Cell Cycle Assay, Staining, Flow Cytometry, Cytometry

    Morphological analysis of filtrates of seed cultures. Filtrates were obtained through the sequential filtering of TSBS cultures which had been grown for 24, 48, or 72 h, through cell strainers with a pore size of 100 (Top) , 40 and 5 μm (Lower) . Prior to imaging, samples were stained with Syto-9 (green) and propidium iodide (red) for the visualization of viable and dead mycelium, respectively. The scale bar represents 100 μm. The white arrowheads represent spores.

    Journal: Frontiers in Microbiology

    Article Title: Dynamics of Pellet Fragmentation and Aggregation in Liquid-Grown Cultures of Streptomyces lividans

    doi: 10.3389/fmicb.2018.00943

    Figure Lengend Snippet: Morphological analysis of filtrates of seed cultures. Filtrates were obtained through the sequential filtering of TSBS cultures which had been grown for 24, 48, or 72 h, through cell strainers with a pore size of 100 (Top) , 40 and 5 μm (Lower) . Prior to imaging, samples were stained with Syto-9 (green) and propidium iodide (red) for the visualization of viable and dead mycelium, respectively. The scale bar represents 100 μm. The white arrowheads represent spores.

    Article Snippet: For the visualization of viable and dead mycelium, samples were stained with Syto-9 and propidium iodide (PI) (Invitrogen).

    Techniques: Imaging, Staining

    PFE1605w binds to the RBC cytoskeleton. A. LC‐ESI‐MS/MS results of two independent Co‐IP experiments using parasites expressing PFE1605w‐HA. B. LC‐ESI‐MS/MS results of two independent reverse Co‐IP experiments with α‐band 4.2 antibodies coupled to protein G Dynabeads. All experiments were performed twice. C. Elution fractions of the reverse Co‐IP experiment were also analysed by Western blot with α‐PFE1605w antibodies. D. Fluorescence polarization titrations of 5‐FAM‐labelled PFE1605w‐C with unlabelled band 3 cytosolic domain or BSA as a negative control. Data points, normalized to the fraction of PFE1605w‐C bound at each titrant concentration, are shown as coloured circles. The error bars were derived from three replicates. The fit to a single‐site association model is shown as solid line. The interaction of PFE1605w‐C with BSA could not be fitted.

    Journal: Cellular Microbiology

    Article Title: Plasmodium falciparum Plasmodium helical interspersed subtelomeric proteins contribute to cytoadherence and anchor P. falciparum erythrocyte membrane protein 1 to the host cell cytoskeleton) Plasmodium falciparum Plasmodium helical interspersed subtelomeric proteins contribute to cytoadherence and anchor P. falciparum erythrocyte membrane protein 1 to the host cell cytoskeleton

    doi: 10.1111/cmi.12583

    Figure Lengend Snippet: PFE1605w binds to the RBC cytoskeleton. A. LC‐ESI‐MS/MS results of two independent Co‐IP experiments using parasites expressing PFE1605w‐HA. B. LC‐ESI‐MS/MS results of two independent reverse Co‐IP experiments with α‐band 4.2 antibodies coupled to protein G Dynabeads. All experiments were performed twice. C. Elution fractions of the reverse Co‐IP experiment were also analysed by Western blot with α‐PFE1605w antibodies. D. Fluorescence polarization titrations of 5‐FAM‐labelled PFE1605w‐C with unlabelled band 3 cytosolic domain or BSA as a negative control. Data points, normalized to the fraction of PFE1605w‐C bound at each titrant concentration, are shown as coloured circles. The error bars were derived from three replicates. The fit to a single‐site association model is shown as solid line. The interaction of PFE1605w‐C with BSA could not be fitted.

    Article Snippet: For the reverse Co‐IP with α‐band 4.2 antibodies, Dynabeads Protein G were used together with the cross‐linking reagent BS3 to avoid coelution of antibodies, according to the manufacturer's protocol (Life Technologies).

    Techniques: Mass Spectrometry, Co-Immunoprecipitation Assay, Expressing, Western Blot, Fluorescence, Negative Control, Concentration Assay, Derivative Assay

    Electrophoretogram of sequencing libraries. The graph shows the length distribution curves of sequencing libraries obtained with Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer’s protocol. The length of DNA fragments was between 200 and 700 pb. Curves were generated on a 2100 bioanalyzer using DNA 1000 chip (Agilent Technologies). For each sample three biological replicates were performed

    Journal: SpringerPlus

    Article Title: High quality RNA extraction from Maqui berry for its application in next-generation sequencing

    doi: 10.1186/s40064-016-2906-x

    Figure Lengend Snippet: Electrophoretogram of sequencing libraries. The graph shows the length distribution curves of sequencing libraries obtained with Illumina TruSeqTM RNA sample preparation kit (Low-Throughput protocol) according to manufacturer’s protocol. The length of DNA fragments was between 200 and 700 pb. Curves were generated on a 2100 bioanalyzer using DNA 1000 chip (Agilent Technologies). For each sample three biological replicates were performed

    Article Snippet: In order to eliminate any genomic DNA contamination that could interfere with gene expression studies, the total RNA obtained by our method was subjected to an exhaustive DNase I digestion (Ambion), according to the manufacturer's instructions.

    Techniques: Sequencing, Sample Prep, Generated, Chromatin Immunoprecipitation

    Analysis of PLGA and PLGA- b -HA particles tethered to cells. (a) Schematic showing the procedure to tether particles onto stem cells for 15 min at room temperature, followed by centrifugation to remove unbound particles. The particles were labeled by loading bovine serum albumin conjugated with Rhodamine B (red). (b) Representative confocal images of the cells tethered with the particles. Cell nuclei and cell membrane were stained with Hoechst 33342 (blue) and DiO dye (green), respectively. Scale bar = 10 μm.

    Journal: Biomaterials

    Article Title: Surface Tethering of Stem Cells with H2O2-Responsive Anti-Oxidizing Colloidal Particles for Protection Against Oxidation-Induced Death

    doi: 10.1016/j.biomaterials.2019.01.039

    Figure Lengend Snippet: Analysis of PLGA and PLGA- b -HA particles tethered to cells. (a) Schematic showing the procedure to tether particles onto stem cells for 15 min at room temperature, followed by centrifugation to remove unbound particles. The particles were labeled by loading bovine serum albumin conjugated with Rhodamine B (red). (b) Representative confocal images of the cells tethered with the particles. Cell nuclei and cell membrane were stained with Hoechst 33342 (blue) and DiO dye (green), respectively. Scale bar = 10 μm.

    Article Snippet: To examine the possibility of cellular uptake, the cell pellet was resuspended in cell media and seeded on coverslips over a period of 72 h. The nuclei and plasma membrane of the cells were stained with Hoechst 33342 (5 μg/mL, Thermo Fisher Scientific, U.S.A.) and DiO (25 ng/ml, Invitrogen, U.S.A.).

    Techniques: Centrifugation, Labeling, Staining

    SUMOylation blocks Rts1 binding to Sgo1 and release of this interaction is important for stable biorientation. (A) The Sgo1-3A mutant which fails to associate with PP2A-Rts1 or CPC shows enhanced SUMOylation. In vivo SUMOylation assay was performed on wild type (AMy7655) and sgo1-3A (AMy25988) strains carrying SGO1-6HA . (B) SUMOylated Sgo1 has reduced binding affinity for Rts1. Recombinant V5-tagged Sgo1 was mixed with components of the SUMOylation pathway in the presence or absence of ATP. Anti-V5 antibody coupled Protein G dynabeads were added to the mixture, washed thoroughly and incubated with extract from sgo1 Δ or sgo1 Δ RTS1-9MYC (AMy8832). Levels of Sgo1 and Rts1 bound to beads were probed by anti-V5 and anti-Myc western blotting, respectively. (C) Rts1 preferentially binds to unsumoylated Sgo1. Rts1-9MYC was immunoprecipitated from sgo1 Δ RTS1-9MYC (AMy8832) using anti-MYC antibody coupled to Protein G dynabeads. Beads were incubated with in vitro SUMOylation reaction mixture containing Sgo1. Levels of Sgo1 and Rts1 bound to beads were probed by anti-V5 and anti-Myc western blotting, respectively. (D-F) Biorientation is unstable when Rts1 is tethered to wild type Sgo1 or Sgo1-4R. Strains used contained CEN4-mNeonGreen MET-CDC20 and SPC42-tdTOMATO and were SGO1-GBP (AMy28389), SGO1-GBP RTS1-non-fluorescent GFP (AMy28092), sgo1-4R-GBP (AMy28417) and sgo1-4R-GBP RTS1-non-fluorescent GFP (AMy28416). The assay was performed as described in Figure 5C . (D) Tethering Rts1 to wild type Sgo1 or Sgo1-4R does not affect the initial establishment of biorientation. (E) Increased reassociation of CEN4-mNeonGreen dots was observed when Rts1 was tethered to wild type Sgo1 or Sgo1-4R. (F) Mis-segregation is only modestly increased when Rts1 is tethered to wild type Sgo1 or Sgo1-4R. (G) Schematic model of how Sgo1 SUMOylation may alter the kinase-phosphatase balance to initiate error correction silencing and promote anaphase onset. For details, see text

    Journal: bioRxiv

    Article Title: SUMOylation targets shugoshin to stabilize sister kinetochore biorientation

    doi: 10.1101/840157

    Figure Lengend Snippet: SUMOylation blocks Rts1 binding to Sgo1 and release of this interaction is important for stable biorientation. (A) The Sgo1-3A mutant which fails to associate with PP2A-Rts1 or CPC shows enhanced SUMOylation. In vivo SUMOylation assay was performed on wild type (AMy7655) and sgo1-3A (AMy25988) strains carrying SGO1-6HA . (B) SUMOylated Sgo1 has reduced binding affinity for Rts1. Recombinant V5-tagged Sgo1 was mixed with components of the SUMOylation pathway in the presence or absence of ATP. Anti-V5 antibody coupled Protein G dynabeads were added to the mixture, washed thoroughly and incubated with extract from sgo1 Δ or sgo1 Δ RTS1-9MYC (AMy8832). Levels of Sgo1 and Rts1 bound to beads were probed by anti-V5 and anti-Myc western blotting, respectively. (C) Rts1 preferentially binds to unsumoylated Sgo1. Rts1-9MYC was immunoprecipitated from sgo1 Δ RTS1-9MYC (AMy8832) using anti-MYC antibody coupled to Protein G dynabeads. Beads were incubated with in vitro SUMOylation reaction mixture containing Sgo1. Levels of Sgo1 and Rts1 bound to beads were probed by anti-V5 and anti-Myc western blotting, respectively. (D-F) Biorientation is unstable when Rts1 is tethered to wild type Sgo1 or Sgo1-4R. Strains used contained CEN4-mNeonGreen MET-CDC20 and SPC42-tdTOMATO and were SGO1-GBP (AMy28389), SGO1-GBP RTS1-non-fluorescent GFP (AMy28092), sgo1-4R-GBP (AMy28417) and sgo1-4R-GBP RTS1-non-fluorescent GFP (AMy28416). The assay was performed as described in Figure 5C . (D) Tethering Rts1 to wild type Sgo1 or Sgo1-4R does not affect the initial establishment of biorientation. (E) Increased reassociation of CEN4-mNeonGreen dots was observed when Rts1 was tethered to wild type Sgo1 or Sgo1-4R. (F) Mis-segregation is only modestly increased when Rts1 is tethered to wild type Sgo1 or Sgo1-4R. (G) Schematic model of how Sgo1 SUMOylation may alter the kinase-phosphatase balance to initiate error correction silencing and promote anaphase onset. For details, see text

    Article Snippet: Sheared chromatin was incubated with the relevant antibody and protein G dynabeads (Thermofisher) at 4°C overnight.

    Techniques: Binding Assay, Mutagenesis, In Vivo, Recombinant, Incubation, Western Blot, Immunoprecipitation, In Vitro

    TCTP interacts with components of DNA damage sensing and repair. ( A ) Benzonase-treated chromatin-enriched fractions that were isolated from confluent U2OS cells 30 min after no (−) or acute [50 cGy, (+)] irradiation (IR) were immunoprecipitated

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Role of the translationally controlled tumor protein in DNA damage sensing and repair

    doi: 10.1073/pnas.1106300109

    Figure Lengend Snippet: TCTP interacts with components of DNA damage sensing and repair. ( A ) Benzonase-treated chromatin-enriched fractions that were isolated from confluent U2OS cells 30 min after no (−) or acute [50 cGy, (+)] irradiation (IR) were immunoprecipitated

    Article Snippet: Then 100 U/mL Benzonase (EMD Millipore) was added and incubated for 1 h at room temperature to release chromatin-bound proteins.

    Techniques: Isolation, Irradiation, Immunoprecipitation