rabbit polyclonal histone h2b  (Bio-Techne corporation)


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    Bio-Techne corporation rabbit polyclonal histone h2b
    Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and <t>H2b.</t> (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.
    Rabbit Polyclonal Histone H2b, supplied by Bio-Techne corporation, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit polyclonal histone h2b/product/Bio-Techne corporation
    Average 93 stars, based on 1 article reviews
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    Images

    1) Product Images from "Cathepsin V regulates cell cycle progression and histone stability in the nucleus of breast cancer cells"

    Article Title: Cathepsin V regulates cell cycle progression and histone stability in the nucleus of breast cancer cells

    Journal: Frontiers in Pharmacology

    doi: 10.3389/fphar.2023.1271435

    Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and H2b. (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.
    Figure Legend Snippet: Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and H2b. (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.

    Techniques Used: Expressing, Western Blot


    Structured Review

    Proteintech histone h2b anti rabbit antibody
    (A) Steady-state chromatin organization predicted by numerical simulations showing phase separation into compacted heterochromatin domains (red) and loosely packed euchromatin domains (blue) and the formation of heterochromatin-rich LADs at the nuclear periphery. (B) Representative Voronoi density rendering of <t>H2B</t> STORM images, color-coded to indicate density levels (blue for low density and red for high density). (C) Numerical simulations showing the synergistic effects of chromatin-lamin affinity and methylation rates on LADs and inner heterochromatin domain morphology. At low levels of chromatin-lamina affinity, as the methylation level increases, the radius of the discrete LADs increases at a fixed value of the contact angle . The morphology of LADs is determined by both the level of methylation and chromatin-lamin affinity. Low affinity results in the formation of isolated LADs, while at greater levels of affinity LAD spread along the lamina. (D) Kinetic balance determines the steady-state size of interior HC domains. The diffusion of methylate histones from the EC region towards the HC domains and histone methylation drive their growth, counteracted by the opposing kinetics of histone acetylation. (E) The scaling relationship between the size of interior HC domains and the level of methylation. (F) (Left) At the interface of HC-rich LAD, EC-rich environment, and lamina, a balance of interfacial interaction between the two phases of chromatin ( γ he ) and the strength of chromatin-lamina affinities ( γ lh ) gives rise to a stable morphology of LADs, which have a characteristic contact angle with the lamina( θ ). (Right) The formation of LADs in steady state requires a balance between diffusion-driven heterochromatin influx (into the LAD) and acetylation-driven conversion of heterochromatin into euchromatin. (G) Schematics illustrating the morphology of LAD at varying levels of chromatin-lamina affinity. (H) The scaling relationship between the thickness of LAD and chromatin-lamina affinity at a given methylation level. The inset shows the scaling relation at varying methylation levels.
    Histone H2b Anti Rabbit Antibody, supplied by Proteintech, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Revealing the Biophysics of Lamina-Associated Domain Formation by Integrating Theoretical Modeling and High-Resolution Imaging"

    Article Title: Revealing the Biophysics of Lamina-Associated Domain Formation by Integrating Theoretical Modeling and High-Resolution Imaging

    Journal: bioRxiv

    doi: 10.1101/2024.06.24.600310

    (A) Steady-state chromatin organization predicted by numerical simulations showing phase separation into compacted heterochromatin domains (red) and loosely packed euchromatin domains (blue) and the formation of heterochromatin-rich LADs at the nuclear periphery. (B) Representative Voronoi density rendering of H2B STORM images, color-coded to indicate density levels (blue for low density and red for high density). (C) Numerical simulations showing the synergistic effects of chromatin-lamin affinity and methylation rates on LADs and inner heterochromatin domain morphology. At low levels of chromatin-lamina affinity, as the methylation level increases, the radius of the discrete LADs increases at a fixed value of the contact angle . The morphology of LADs is determined by both the level of methylation and chromatin-lamin affinity. Low affinity results in the formation of isolated LADs, while at greater levels of affinity LAD spread along the lamina. (D) Kinetic balance determines the steady-state size of interior HC domains. The diffusion of methylate histones from the EC region towards the HC domains and histone methylation drive their growth, counteracted by the opposing kinetics of histone acetylation. (E) The scaling relationship between the size of interior HC domains and the level of methylation. (F) (Left) At the interface of HC-rich LAD, EC-rich environment, and lamina, a balance of interfacial interaction between the two phases of chromatin ( γ he ) and the strength of chromatin-lamina affinities ( γ lh ) gives rise to a stable morphology of LADs, which have a characteristic contact angle with the lamina( θ ). (Right) The formation of LADs in steady state requires a balance between diffusion-driven heterochromatin influx (into the LAD) and acetylation-driven conversion of heterochromatin into euchromatin. (G) Schematics illustrating the morphology of LAD at varying levels of chromatin-lamina affinity. (H) The scaling relationship between the thickness of LAD and chromatin-lamina affinity at a given methylation level. The inset shows the scaling relation at varying methylation levels.
    Figure Legend Snippet: (A) Steady-state chromatin organization predicted by numerical simulations showing phase separation into compacted heterochromatin domains (red) and loosely packed euchromatin domains (blue) and the formation of heterochromatin-rich LADs at the nuclear periphery. (B) Representative Voronoi density rendering of H2B STORM images, color-coded to indicate density levels (blue for low density and red for high density). (C) Numerical simulations showing the synergistic effects of chromatin-lamin affinity and methylation rates on LADs and inner heterochromatin domain morphology. At low levels of chromatin-lamina affinity, as the methylation level increases, the radius of the discrete LADs increases at a fixed value of the contact angle . The morphology of LADs is determined by both the level of methylation and chromatin-lamin affinity. Low affinity results in the formation of isolated LADs, while at greater levels of affinity LAD spread along the lamina. (D) Kinetic balance determines the steady-state size of interior HC domains. The diffusion of methylate histones from the EC region towards the HC domains and histone methylation drive their growth, counteracted by the opposing kinetics of histone acetylation. (E) The scaling relationship between the size of interior HC domains and the level of methylation. (F) (Left) At the interface of HC-rich LAD, EC-rich environment, and lamina, a balance of interfacial interaction between the two phases of chromatin ( γ he ) and the strength of chromatin-lamina affinities ( γ lh ) gives rise to a stable morphology of LADs, which have a characteristic contact angle with the lamina( θ ). (Right) The formation of LADs in steady state requires a balance between diffusion-driven heterochromatin influx (into the LAD) and acetylation-driven conversion of heterochromatin into euchromatin. (G) Schematics illustrating the morphology of LAD at varying levels of chromatin-lamina affinity. (H) The scaling relationship between the thickness of LAD and chromatin-lamina affinity at a given methylation level. The inset shows the scaling relation at varying methylation levels.

    Techniques Used: Methylation, Isolation, Diffusion-based Assay

    ubiquityl histone h2b lys120 d11 rabbit mab  (Protein Simple Inc)


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    Protein Simple Inc ubiquityl histone h2b lys120 d11 rabbit mab
    a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and <t>H2B.</t> Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.
    Ubiquityl Histone H2b Lys120 D11 Rabbit Mab, supplied by Protein Simple Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ubiquityl histone h2b lys120 d11 rabbit mab/product/Protein Simple Inc
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    Images

    1) Product Images from "Structure of the human Bre1 complex bound to the nucleosome"

    Article Title: Structure of the human Bre1 complex bound to the nucleosome

    Journal: Nature Communications

    doi: 10.1038/s41467-024-46910-8

    a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and H2B. Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.
    Figure Legend Snippet: a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and H2B. Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.

    Techniques Used: Binding Assay

    ubiquityl histone h2b lys120 d11 rabbit mab  (Cell Signaling Technology Inc)


    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
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    Cell Signaling Technology Inc ubiquityl histone h2b lys120 d11 rabbit mab
    a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and <t>H2B.</t> Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.
    Ubiquityl Histone H2b Lys120 D11 Rabbit Mab, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ubiquityl histone h2b lys120 d11 rabbit mab/product/Cell Signaling Technology Inc
    Average 86 stars, based on 1 article reviews
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    Images

    1) Product Images from "Structure of the human Bre1 complex bound to the nucleosome"

    Article Title: Structure of the human Bre1 complex bound to the nucleosome

    Journal: Nature Communications

    doi: 10.1038/s41467-024-46910-8

    a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and H2B. Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.
    Figure Legend Snippet: a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and H2B. Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.

    Techniques Used: Binding Assay

    rabbit anti acetyl histone h2b lys5  (Cell Signaling Technology Inc)


    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
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    Cell Signaling Technology Inc rabbit anti acetyl histone h2b lys5

    Rabbit Anti Acetyl Histone H2b Lys5, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit anti acetyl histone h2b lys5/product/Cell Signaling Technology Inc
    Average 86 stars, based on 1 article reviews
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    Images

    1) Product Images from "Mof plays distinct roles in hepatic lipid metabolism under healthy or non-alcoholic fatty liver conditions"

    Article Title: Mof plays distinct roles in hepatic lipid metabolism under healthy or non-alcoholic fatty liver conditions

    Journal: iScience

    doi: 10.1016/j.isci.2023.108446


    Figure Legend Snippet:

    Techniques Used: Labeling, Affinity Purification, Recombinant, Injection, Lysis, Staining, Transfection, Cell Culture, Modification, Cholesterol Assay, Polymer, Enzyme-linked Immunosorbent Assay, Western Blot, SYBR Green Assay, Mass Spectrometry, Sequencing, Software

    rabbit anti acetyl histone h2b lys20  (Cell Signaling Technology Inc)


    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
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    Cell Signaling Technology Inc rabbit anti acetyl histone h2b lys20

    Rabbit Anti Acetyl Histone H2b Lys20, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit anti acetyl histone h2b lys20/product/Cell Signaling Technology Inc
    Average 86 stars, based on 1 article reviews
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    rabbit anti acetyl histone h2b lys20 - by Bioz Stars, 2024-07
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    Images

    1) Product Images from "Mof plays distinct roles in hepatic lipid metabolism under healthy or non-alcoholic fatty liver conditions"

    Article Title: Mof plays distinct roles in hepatic lipid metabolism under healthy or non-alcoholic fatty liver conditions

    Journal: iScience

    doi: 10.1016/j.isci.2023.108446


    Figure Legend Snippet:

    Techniques Used: Labeling, Affinity Purification, Recombinant, Injection, Lysis, Staining, Transfection, Cell Culture, Modification, Cholesterol Assay, Polymer, Enzyme-linked Immunosorbent Assay, Western Blot, SYBR Green Assay, Mass Spectrometry, Sequencing, Software

    rabbit polyclonal histone h2b  (Bio-Techne corporation)


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    Bio-Techne corporation rabbit polyclonal histone h2b
    Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and <t>H2b.</t> (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.
    Rabbit Polyclonal Histone H2b, supplied by Bio-Techne corporation, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit polyclonal histone h2b/product/Bio-Techne corporation
    Average 93 stars, based on 1 article reviews
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    Images

    1) Product Images from "Cathepsin V regulates cell cycle progression and histone stability in the nucleus of breast cancer cells"

    Article Title: Cathepsin V regulates cell cycle progression and histone stability in the nucleus of breast cancer cells

    Journal: Frontiers in Pharmacology

    doi: 10.3389/fphar.2023.1271435

    Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and H2b. (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.
    Figure Legend Snippet: Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and H2b. (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.

    Techniques Used: Expressing, Western Blot


    Structured Review

    Abcam rabbit polyclonal anti histone h2b
    a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and <t>H2B</t> display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.
    Rabbit Polyclonal Anti Histone H2b, supplied by Abcam, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit polyclonal anti histone h2b/product/Abcam
    Average 86 stars, based on 1 article reviews
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    86/100 stars

    Images

    1) Product Images from "Chromatin organization drives the search mechanism of nuclear factors"

    Article Title: Chromatin organization drives the search mechanism of nuclear factors

    Journal: Nature Communications

    doi: 10.1038/s41467-023-42133-5

    a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and H2B display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.
    Figure Legend Snippet: a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and H2B display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.

    Techniques Used: Microscopy, Diffusion-based Assay

    recombinant anti histone h2b htb2 rabbit igg  (Danaher Inc)


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    Danaher Inc recombinant anti histone h2b htb2 rabbit igg
    (A) Schematic representation of Rim4 variants, featuring three RNA recognition motifs (RRMs) and a C-terminal low-complexity domain (LCD). (B) (Left) Representative prophase I cell FM images of EGFP-Rim4 (green) with (top) mScarlet-Nup49 (red) or (bottom) mScarlet-Pab1 (red). White dashed circle outlines potential nuclear membrane; blue dashed circle indicates vacuole area. (Right) EGFP-Rim4 fluorescence signals along the line traversing the cell (3× zoom) were plotted against distance, with bracket marking nucleus. (C) Prophase I cell lysates were fractionated into nuclear and cytosolic parts and immunoblotted using indicated antibodies. Histone <t>H2B</t> <t>(Htb2)</t> and Nup49 (Nup49-EGFP) served as nuclear markers. Shown are representative IB images from two independent experiments. (D) Recovery of nuclear mScarlet-Rim4 following photobleaching, assessed by FRAP. (Top) Schematic showing the entire nucleus being photobleached in cells at prophase I (12 h in sporulation medium [SPM]), followed by recovery. (Bottom) The nuclear/cytoplasmic mScarlet-Rim4 ratio plotted to recovery time. The green dot represents the initial ratio, while the red dot represents the first recording (3 s) after photobleaching (n = 4, mean [solid line] ± standard error [SE, dashed line]). shows representative cells examined by FRAP. (E) (Left) Representative FM images showing the intracellular distribution of indicated EGFP-Rim4 variants and EGFP, expressed under Rim4 promoter (green). Nup49-mScarlet (red) marks the nucleus. (Right) Quantification as described in (B). (F) Quantitative analysis of (E), showing the nuclear/cytoplasmic EGFP-Rim4 variants ratio (median ± 95% confidence interval [CI]) from three independent experiments with the number of analyzed cells listed under each column (Dunn’s test; ns, no significance; ***p < 0.001). Strain details in . Scale bars, 5 μm.
    Recombinant Anti Histone H2b Htb2 Rabbit Igg, supplied by Danaher Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Autophagy-mediated surveillance of Rim4-mRNA interaction safeguards programmed meiotic translation"

    Article Title: Autophagy-mediated surveillance of Rim4-mRNA interaction safeguards programmed meiotic translation

    Journal: Cell reports

    doi: 10.1016/j.celrep.2023.113051

    (A) Schematic representation of Rim4 variants, featuring three RNA recognition motifs (RRMs) and a C-terminal low-complexity domain (LCD). (B) (Left) Representative prophase I cell FM images of EGFP-Rim4 (green) with (top) mScarlet-Nup49 (red) or (bottom) mScarlet-Pab1 (red). White dashed circle outlines potential nuclear membrane; blue dashed circle indicates vacuole area. (Right) EGFP-Rim4 fluorescence signals along the line traversing the cell (3× zoom) were plotted against distance, with bracket marking nucleus. (C) Prophase I cell lysates were fractionated into nuclear and cytosolic parts and immunoblotted using indicated antibodies. Histone H2B (Htb2) and Nup49 (Nup49-EGFP) served as nuclear markers. Shown are representative IB images from two independent experiments. (D) Recovery of nuclear mScarlet-Rim4 following photobleaching, assessed by FRAP. (Top) Schematic showing the entire nucleus being photobleached in cells at prophase I (12 h in sporulation medium [SPM]), followed by recovery. (Bottom) The nuclear/cytoplasmic mScarlet-Rim4 ratio plotted to recovery time. The green dot represents the initial ratio, while the red dot represents the first recording (3 s) after photobleaching (n = 4, mean [solid line] ± standard error [SE, dashed line]). shows representative cells examined by FRAP. (E) (Left) Representative FM images showing the intracellular distribution of indicated EGFP-Rim4 variants and EGFP, expressed under Rim4 promoter (green). Nup49-mScarlet (red) marks the nucleus. (Right) Quantification as described in (B). (F) Quantitative analysis of (E), showing the nuclear/cytoplasmic EGFP-Rim4 variants ratio (median ± 95% confidence interval [CI]) from three independent experiments with the number of analyzed cells listed under each column (Dunn’s test; ns, no significance; ***p < 0.001). Strain details in . Scale bars, 5 μm.
    Figure Legend Snippet: (A) Schematic representation of Rim4 variants, featuring three RNA recognition motifs (RRMs) and a C-terminal low-complexity domain (LCD). (B) (Left) Representative prophase I cell FM images of EGFP-Rim4 (green) with (top) mScarlet-Nup49 (red) or (bottom) mScarlet-Pab1 (red). White dashed circle outlines potential nuclear membrane; blue dashed circle indicates vacuole area. (Right) EGFP-Rim4 fluorescence signals along the line traversing the cell (3× zoom) were plotted against distance, with bracket marking nucleus. (C) Prophase I cell lysates were fractionated into nuclear and cytosolic parts and immunoblotted using indicated antibodies. Histone H2B (Htb2) and Nup49 (Nup49-EGFP) served as nuclear markers. Shown are representative IB images from two independent experiments. (D) Recovery of nuclear mScarlet-Rim4 following photobleaching, assessed by FRAP. (Top) Schematic showing the entire nucleus being photobleached in cells at prophase I (12 h in sporulation medium [SPM]), followed by recovery. (Bottom) The nuclear/cytoplasmic mScarlet-Rim4 ratio plotted to recovery time. The green dot represents the initial ratio, while the red dot represents the first recording (3 s) after photobleaching (n = 4, mean [solid line] ± standard error [SE, dashed line]). shows representative cells examined by FRAP. (E) (Left) Representative FM images showing the intracellular distribution of indicated EGFP-Rim4 variants and EGFP, expressed under Rim4 promoter (green). Nup49-mScarlet (red) marks the nucleus. (Right) Quantification as described in (B). (F) Quantitative analysis of (E), showing the nuclear/cytoplasmic EGFP-Rim4 variants ratio (median ± 95% confidence interval [CI]) from three independent experiments with the number of analyzed cells listed under each column (Dunn’s test; ns, no significance; ***p < 0.001). Strain details in . Scale bars, 5 μm.

    Techniques Used: Membrane, Fluorescence

    KEY RESOURCES TABLE
    Figure Legend Snippet: KEY RESOURCES TABLE

    Techniques Used: Recombinant, Labeling, Protease Inhibitor, Staining, Transformation Assay, Plasmid Preparation, Gel Extraction, Purification, SYBR Green Assay, Luciferase, Software, Imaging

    polyclonal rabbit antibodies against human histone 2b  (Abcam)

     
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    Abcam polyclonal rabbit antibodies against human histone 2b

    Polyclonal Rabbit Antibodies Against Human Histone 2b, supplied by Abcam, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Selective protein aggregation confines and inhibits endotoxins in wounds: Linking host defense to amyloid formation"

    Article Title: Selective protein aggregation confines and inhibits endotoxins in wounds: Linking host defense to amyloid formation

    Journal: iScience

    doi: 10.1016/j.isci.2023.107951


    Figure Legend Snippet:

    Techniques Used: Virus, Sterility, Recombinant, Mass Spectrometry, Activation Assay, Software

    rabbit anti histone h2b  (Cell Signaling Technology Inc)


    Bioz Manufacturer Symbol Cell Signaling Technology Inc manufactures this product  
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    Cell Signaling Technology Inc rabbit anti histone h2b
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    Bio-Techne corporation rabbit polyclonal histone h2b
    Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and <t>H2b.</t> (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.
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    (A) Steady-state chromatin organization predicted by numerical simulations showing phase separation into compacted heterochromatin domains (red) and loosely packed euchromatin domains (blue) and the formation of heterochromatin-rich LADs at the nuclear periphery. (B) Representative Voronoi density rendering of <t>H2B</t> STORM images, color-coded to indicate density levels (blue for low density and red for high density). (C) Numerical simulations showing the synergistic effects of chromatin-lamin affinity and methylation rates on LADs and inner heterochromatin domain morphology. At low levels of chromatin-lamina affinity, as the methylation level increases, the radius of the discrete LADs increases at a fixed value of the contact angle . The morphology of LADs is determined by both the level of methylation and chromatin-lamin affinity. Low affinity results in the formation of isolated LADs, while at greater levels of affinity LAD spread along the lamina. (D) Kinetic balance determines the steady-state size of interior HC domains. The diffusion of methylate histones from the EC region towards the HC domains and histone methylation drive their growth, counteracted by the opposing kinetics of histone acetylation. (E) The scaling relationship between the size of interior HC domains and the level of methylation. (F) (Left) At the interface of HC-rich LAD, EC-rich environment, and lamina, a balance of interfacial interaction between the two phases of chromatin ( γ he ) and the strength of chromatin-lamina affinities ( γ lh ) gives rise to a stable morphology of LADs, which have a characteristic contact angle with the lamina( θ ). (Right) The formation of LADs in steady state requires a balance between diffusion-driven heterochromatin influx (into the LAD) and acetylation-driven conversion of heterochromatin into euchromatin. (G) Schematics illustrating the morphology of LAD at varying levels of chromatin-lamina affinity. (H) The scaling relationship between the thickness of LAD and chromatin-lamina affinity at a given methylation level. The inset shows the scaling relation at varying methylation levels.
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    a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and <t>H2B.</t> Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.
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    Abcam rabbit polyclonal anti histone h2b
    a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and <t>H2B</t> display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.
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    Danaher Inc recombinant anti histone h2b htb2 rabbit igg
    (A) Schematic representation of Rim4 variants, featuring three RNA recognition motifs (RRMs) and a C-terminal low-complexity domain (LCD). (B) (Left) Representative prophase I cell FM images of EGFP-Rim4 (green) with (top) mScarlet-Nup49 (red) or (bottom) mScarlet-Pab1 (red). White dashed circle outlines potential nuclear membrane; blue dashed circle indicates vacuole area. (Right) EGFP-Rim4 fluorescence signals along the line traversing the cell (3× zoom) were plotted against distance, with bracket marking nucleus. (C) Prophase I cell lysates were fractionated into nuclear and cytosolic parts and immunoblotted using indicated antibodies. Histone <t>H2B</t> <t>(Htb2)</t> and Nup49 (Nup49-EGFP) served as nuclear markers. Shown are representative IB images from two independent experiments. (D) Recovery of nuclear mScarlet-Rim4 following photobleaching, assessed by FRAP. (Top) Schematic showing the entire nucleus being photobleached in cells at prophase I (12 h in sporulation medium [SPM]), followed by recovery. (Bottom) The nuclear/cytoplasmic mScarlet-Rim4 ratio plotted to recovery time. The green dot represents the initial ratio, while the red dot represents the first recording (3 s) after photobleaching (n = 4, mean [solid line] ± standard error [SE, dashed line]). shows representative cells examined by FRAP. (E) (Left) Representative FM images showing the intracellular distribution of indicated EGFP-Rim4 variants and EGFP, expressed under Rim4 promoter (green). Nup49-mScarlet (red) marks the nucleus. (Right) Quantification as described in (B). (F) Quantitative analysis of (E), showing the nuclear/cytoplasmic EGFP-Rim4 variants ratio (median ± 95% confidence interval [CI]) from three independent experiments with the number of analyzed cells listed under each column (Dunn’s test; ns, no significance; ***p < 0.001). Strain details in . Scale bars, 5 μm.
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    Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and H2b. (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.

    Journal: Frontiers in Pharmacology

    Article Title: Cathepsin V regulates cell cycle progression and histone stability in the nucleus of breast cancer cells

    doi: 10.3389/fphar.2023.1271435

    Figure Lengend Snippet: Histone H3 and H4 protein expression is regulated by CTSV. ( A) Western blotting analysis of histone protein expression shows a reduction in histone H3 and H4 in CTSV depleted cells, with no impact on histones H1, H2a and H2b. (B) Confirmation of CTSV impact on histone H3 and H4 was ascertained using rescue experiments and the re-expression of CTSV in shCTSV-1 cells. GAPDH expression was used as an internal loading control and data presented is representative of at least three independent experiments.

    Article Snippet: The following antibodies were used in this study; goat polyclonal CTSV (BioTechne, AF1080), goat polyclonal cyclin D1/D2 (AF4196, BioTechne), mouse monoclonal cyclin E1 (MAB68101, BioTechne), rabbit monoclonal cyclin B1 (MAB60001, BioTechne), rabbit polyclonal HDAC1 (2062S, Cell Signaling), mouse monoclonal histone H1 (NBP2-45184, BioTechne), rabbit polyclonal histone H2a (NB100-56346, BioTechne), rabbit polyclonal histone H2b (NB100-56633, BioTechne), rabbit monoclonal histone H3 (4499S, Cell Signaling), rabbit monoclonal histone H4 (NBP2-80444, BioTechne), mouse monoclonal Hsc70 (MAB4148, BioTechne), mouse monoclonal Hsp90 (ab13492, Abcam), mouse monoclonal Asf1b (NBP2-61684, BioTechne), rabbit monoclonal NASP (ab181169, Abcam), mouse monoclonal GATA3 (BioTechne, MAB6330), goat polyclonal GAPDH (BioTechne, AF5718), mouse monoclonal CTSL (BioTechne, MAB9521) and rat monoclonal α-Tubulin (ab6160, Abcam).

    Techniques: Expressing, Western Blot

    (A) Steady-state chromatin organization predicted by numerical simulations showing phase separation into compacted heterochromatin domains (red) and loosely packed euchromatin domains (blue) and the formation of heterochromatin-rich LADs at the nuclear periphery. (B) Representative Voronoi density rendering of H2B STORM images, color-coded to indicate density levels (blue for low density and red for high density). (C) Numerical simulations showing the synergistic effects of chromatin-lamin affinity and methylation rates on LADs and inner heterochromatin domain morphology. At low levels of chromatin-lamina affinity, as the methylation level increases, the radius of the discrete LADs increases at a fixed value of the contact angle . The morphology of LADs is determined by both the level of methylation and chromatin-lamin affinity. Low affinity results in the formation of isolated LADs, while at greater levels of affinity LAD spread along the lamina. (D) Kinetic balance determines the steady-state size of interior HC domains. The diffusion of methylate histones from the EC region towards the HC domains and histone methylation drive their growth, counteracted by the opposing kinetics of histone acetylation. (E) The scaling relationship between the size of interior HC domains and the level of methylation. (F) (Left) At the interface of HC-rich LAD, EC-rich environment, and lamina, a balance of interfacial interaction between the two phases of chromatin ( γ he ) and the strength of chromatin-lamina affinities ( γ lh ) gives rise to a stable morphology of LADs, which have a characteristic contact angle with the lamina( θ ). (Right) The formation of LADs in steady state requires a balance between diffusion-driven heterochromatin influx (into the LAD) and acetylation-driven conversion of heterochromatin into euchromatin. (G) Schematics illustrating the morphology of LAD at varying levels of chromatin-lamina affinity. (H) The scaling relationship between the thickness of LAD and chromatin-lamina affinity at a given methylation level. The inset shows the scaling relation at varying methylation levels.

    Journal: bioRxiv

    Article Title: Revealing the Biophysics of Lamina-Associated Domain Formation by Integrating Theoretical Modeling and High-Resolution Imaging

    doi: 10.1101/2024.06.24.600310

    Figure Lengend Snippet: (A) Steady-state chromatin organization predicted by numerical simulations showing phase separation into compacted heterochromatin domains (red) and loosely packed euchromatin domains (blue) and the formation of heterochromatin-rich LADs at the nuclear periphery. (B) Representative Voronoi density rendering of H2B STORM images, color-coded to indicate density levels (blue for low density and red for high density). (C) Numerical simulations showing the synergistic effects of chromatin-lamin affinity and methylation rates on LADs and inner heterochromatin domain morphology. At low levels of chromatin-lamina affinity, as the methylation level increases, the radius of the discrete LADs increases at a fixed value of the contact angle . The morphology of LADs is determined by both the level of methylation and chromatin-lamin affinity. Low affinity results in the formation of isolated LADs, while at greater levels of affinity LAD spread along the lamina. (D) Kinetic balance determines the steady-state size of interior HC domains. The diffusion of methylate histones from the EC region towards the HC domains and histone methylation drive their growth, counteracted by the opposing kinetics of histone acetylation. (E) The scaling relationship between the size of interior HC domains and the level of methylation. (F) (Left) At the interface of HC-rich LAD, EC-rich environment, and lamina, a balance of interfacial interaction between the two phases of chromatin ( γ he ) and the strength of chromatin-lamina affinities ( γ lh ) gives rise to a stable morphology of LADs, which have a characteristic contact angle with the lamina( θ ). (Right) The formation of LADs in steady state requires a balance between diffusion-driven heterochromatin influx (into the LAD) and acetylation-driven conversion of heterochromatin into euchromatin. (G) Schematics illustrating the morphology of LAD at varying levels of chromatin-lamina affinity. (H) The scaling relationship between the thickness of LAD and chromatin-lamina affinity at a given methylation level. The inset shows the scaling relation at varying methylation levels.

    Article Snippet: Subsequently, the cells were subjected to overnight incubation at 4°C with a 1:50 dilution of histone H2B anti-rabbit antibody (ProteinTech, #15857-1-AP).

    Techniques: Methylation, Isolation, Diffusion-based Assay

    a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and H2B. Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.

    Journal: Nature Communications

    Article Title: Structure of the human Bre1 complex bound to the nucleosome

    doi: 10.1038/s41467-024-46910-8

    Figure Lengend Snippet: a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and H2B. Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.

    Article Snippet: For Wes analysis, Ubiquityl-Histone H2B (Lys120) (D11) Rabbit mAb was used as the primary antibody (1:250 dilution), and Anti-Rabbit Detection Module (DM-001; ProteinSimple) was used without dilution following the manufacturer’s protocol.

    Techniques: Binding Assay

    a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and H2B. Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.

    Journal: Nature Communications

    Article Title: Structure of the human Bre1 complex bound to the nucleosome

    doi: 10.1038/s41467-024-46910-8

    Figure Lengend Snippet: a Model structure of the RINGA-RINGB-Rad6A-ubiquitin complex bound to the nucleosome in two views. b Close-up view of ubiquitin and H2B. Two lysine residues (H2BK120 and H2BK116) near G76 of ubiquitin are shown. H2BS112, whose GlcNAcylation stimulates H2BK120 ubiquitination, is also shown. c Proposed mechanistic model. The wild-type Bre1 complex can bind to the nucleosome in two orientations, but H2BK120 ubiquitination occurs only when Bre1A binds to the acidic patch, as RING A , but not RING B , can recruit Rad6A and ubiquitin. Bre1B with G974T B -A978T B double substitution can recruit Rad6A and ubiquitin; thus, H2BK120 ubiquitination occurs in both binding modes.

    Article Snippet: For Western blotting, Ubiquityl-Histone H2B (Lys120) (D11) Rabbit mAb (No. 5546; Cell Signaling) was used as the primary antibody (1:1000 dilution), goat anti-rabbit IgG-HRP (sc-2004; Santa Cruz Biotechnology) as the secondary antibody (1:2000 dilution), and ECL Prime (Cytiva) as the chemiluminescent reagent.

    Techniques: Binding Assay

    Journal: iScience

    Article Title: Mof plays distinct roles in hepatic lipid metabolism under healthy or non-alcoholic fatty liver conditions

    doi: 10.1016/j.isci.2023.108446

    Figure Lengend Snippet:

    Article Snippet: Rabbit anti-Acetyl-Histone H2B (Lys5) , Cell Signaling Technology , Cat#2574S; RRID: AB_331553.

    Techniques: Labeling, Affinity Purification, Recombinant, Injection, Lysis, Staining, Transfection, Cell Culture, Modification, Cholesterol Assay, Polymer, Enzyme-linked Immunosorbent Assay, Western Blot, SYBR Green Assay, Mass Spectrometry, Sequencing, Software

    Journal: iScience

    Article Title: Mof plays distinct roles in hepatic lipid metabolism under healthy or non-alcoholic fatty liver conditions

    doi: 10.1016/j.isci.2023.108446

    Figure Lengend Snippet:

    Article Snippet: Rabbit anti-Acetyl-Histone H2B (Lys20) , Cell Signaling Technology , Cat#2571S; RRID: AB_331546.

    Techniques: Labeling, Affinity Purification, Recombinant, Injection, Lysis, Staining, Transfection, Cell Culture, Modification, Cholesterol Assay, Polymer, Enzyme-linked Immunosorbent Assay, Western Blot, SYBR Green Assay, Mass Spectrometry, Sequencing, Software

    a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and H2B display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: Chromatin organization drives the search mechanism of nuclear factors

    doi: 10.1038/s41467-023-42133-5

    Figure Lengend Snippet: a paSMT is carried out using highly inclined laminated optical sheet (HILO) microscopy (top left) by labelling the endogenous HaloTag-p53 with the photoactivatable dye PA-JF 549 (bottom left). Movies, acquired at a framerate of 100 fps highlight quasi-immobile chromatin-bound molecules (cyan arrowhead) and diffusing (purple arrowhead) ones (max proj = maximal projection over the entire movie; cyan dotted line indicates the cell nucleus, scale bar: 5 µm). b We use vbSPT to classify track segments into bound and diffusing components, and then focus on diffusing molecules, by computing diffusional anisotropy, by calculating the distributions of angles \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta$$\end{document} θ between consecutive jumps, and the fold-anisotropy metric, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 , calculated as the probability of observing a backward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(150^\circ \le \theta \le 210^\circ )$$\end{document} p ( 15 0 ∘ ≤ θ ≤ 21 0 ∘ ) over the probability of observing a forward displacement \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p(-30^\circ \le \theta \le 30^\circ )$$\end{document} p ( − 3 0 ∘ ≤ θ ≤ 3 0 ∘ ) . c Different NFs display different diffusional anisotropy, with factors poorly localized in DNA-dense regions displaying lower anisotropy than factors enriched in DNA-dense regions. d Fold-anisotropy metric \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${f}_{180/0}$$\end{document} f 180 / 0 as function of the distance run by the molecules. p53, CTCF, and H2B display high diffusional anisotropy at a spatial scale of ~100–150 nm, a signature of transient trapping of these molecules in traps of similar size ( n cells = 30, 30, 29, 14, 31, n angles = 59470, 62813, 180414, 26052, 26566 for HaloTag, p565, p53, CTCF, and Histone H2B respectively, error bars: s.e.m. estimated through boot-strapping). e Analysis of diffusional anisotropy in our SMT/mSIM data allows us to identify that the highest diffusional anisotropy occurs for molecules with slow instantaneous diffusion coefficients in regions at high chromatin density (same data as in Fig. ). Source data are provided as a Source Data file.

    Article Snippet: The antibodies employed in this study were: mouse monoclonal anti-p53 DO-1 (Santa Cruz Biotechnology, cat. sc-126; 1:3000 dilution, incubated 1 h at RT), rabbit monoclonal anti-p21 (Abcam, cat. ab109520; 1:1000 dilution, incubated overnight at 4 °C), rabbit monoclonal anti-GAPDH (Abcam, cat. ab128915; 1:50,000 dilution, incubated 1 h at RT), rabbit monoclonal anti-NF-κB p65 (Cell Signaling cat. D14E12 XP®; dilution 1:1000), rabbit polyclonal anti-Histone H2B (Abcam cat. ab1790, dilution 1:5000), mouse monoclonal anti-HaloTag (Promega G921A, dilution 1:1000), mouse monoclonal anti-vinculin (Thermo-Fisher, cat. MA5-11690; 1:4000 dilution, incubated 1 h at RT).

    Techniques: Microscopy, Diffusion-based Assay

    (A) Schematic representation of Rim4 variants, featuring three RNA recognition motifs (RRMs) and a C-terminal low-complexity domain (LCD). (B) (Left) Representative prophase I cell FM images of EGFP-Rim4 (green) with (top) mScarlet-Nup49 (red) or (bottom) mScarlet-Pab1 (red). White dashed circle outlines potential nuclear membrane; blue dashed circle indicates vacuole area. (Right) EGFP-Rim4 fluorescence signals along the line traversing the cell (3× zoom) were plotted against distance, with bracket marking nucleus. (C) Prophase I cell lysates were fractionated into nuclear and cytosolic parts and immunoblotted using indicated antibodies. Histone H2B (Htb2) and Nup49 (Nup49-EGFP) served as nuclear markers. Shown are representative IB images from two independent experiments. (D) Recovery of nuclear mScarlet-Rim4 following photobleaching, assessed by FRAP. (Top) Schematic showing the entire nucleus being photobleached in cells at prophase I (12 h in sporulation medium [SPM]), followed by recovery. (Bottom) The nuclear/cytoplasmic mScarlet-Rim4 ratio plotted to recovery time. The green dot represents the initial ratio, while the red dot represents the first recording (3 s) after photobleaching (n = 4, mean [solid line] ± standard error [SE, dashed line]). shows representative cells examined by FRAP. (E) (Left) Representative FM images showing the intracellular distribution of indicated EGFP-Rim4 variants and EGFP, expressed under Rim4 promoter (green). Nup49-mScarlet (red) marks the nucleus. (Right) Quantification as described in (B). (F) Quantitative analysis of (E), showing the nuclear/cytoplasmic EGFP-Rim4 variants ratio (median ± 95% confidence interval [CI]) from three independent experiments with the number of analyzed cells listed under each column (Dunn’s test; ns, no significance; ***p < 0.001). Strain details in . Scale bars, 5 μm.

    Journal: Cell reports

    Article Title: Autophagy-mediated surveillance of Rim4-mRNA interaction safeguards programmed meiotic translation

    doi: 10.1016/j.celrep.2023.113051

    Figure Lengend Snippet: (A) Schematic representation of Rim4 variants, featuring three RNA recognition motifs (RRMs) and a C-terminal low-complexity domain (LCD). (B) (Left) Representative prophase I cell FM images of EGFP-Rim4 (green) with (top) mScarlet-Nup49 (red) or (bottom) mScarlet-Pab1 (red). White dashed circle outlines potential nuclear membrane; blue dashed circle indicates vacuole area. (Right) EGFP-Rim4 fluorescence signals along the line traversing the cell (3× zoom) were plotted against distance, with bracket marking nucleus. (C) Prophase I cell lysates were fractionated into nuclear and cytosolic parts and immunoblotted using indicated antibodies. Histone H2B (Htb2) and Nup49 (Nup49-EGFP) served as nuclear markers. Shown are representative IB images from two independent experiments. (D) Recovery of nuclear mScarlet-Rim4 following photobleaching, assessed by FRAP. (Top) Schematic showing the entire nucleus being photobleached in cells at prophase I (12 h in sporulation medium [SPM]), followed by recovery. (Bottom) The nuclear/cytoplasmic mScarlet-Rim4 ratio plotted to recovery time. The green dot represents the initial ratio, while the red dot represents the first recording (3 s) after photobleaching (n = 4, mean [solid line] ± standard error [SE, dashed line]). shows representative cells examined by FRAP. (E) (Left) Representative FM images showing the intracellular distribution of indicated EGFP-Rim4 variants and EGFP, expressed under Rim4 promoter (green). Nup49-mScarlet (red) marks the nucleus. (Right) Quantification as described in (B). (F) Quantitative analysis of (E), showing the nuclear/cytoplasmic EGFP-Rim4 variants ratio (median ± 95% confidence interval [CI]) from three independent experiments with the number of analyzed cells listed under each column (Dunn’s test; ns, no significance; ***p < 0.001). Strain details in . Scale bars, 5 μm.

    Article Snippet: Recombinant Anti-Histone H2B (Htb2) Rabbit IgG [EPR18094] (1:2,500) , Abcam , Cat# ab188291.

    Techniques: Membrane, Fluorescence

    KEY RESOURCES TABLE

    Journal: Cell reports

    Article Title: Autophagy-mediated surveillance of Rim4-mRNA interaction safeguards programmed meiotic translation

    doi: 10.1016/j.celrep.2023.113051

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: Recombinant Anti-Histone H2B (Htb2) Rabbit IgG [EPR18094] (1:2,500) , Abcam , Cat# ab188291.

    Techniques: Recombinant, Labeling, Protease Inhibitor, Staining, Transformation Assay, Plasmid Preparation, Gel Extraction, Purification, SYBR Green Assay, Luciferase, Software, Imaging

    Journal: iScience

    Article Title: Selective protein aggregation confines and inhibits endotoxins in wounds: Linking host defense to amyloid formation

    doi: 10.1016/j.isci.2023.107951

    Figure Lengend Snippet:

    Article Snippet: Polyclonal rabbit antibodies against human histone 2b , Abcam , ab1790.

    Techniques: Virus, Sterility, Recombinant, Mass Spectrometry, Activation Assay, Software