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solvent control  (Eppendorf AG)


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    Structured Review

    Eppendorf AG solvent control
    Solvent Control, supplied by Eppendorf AG, used in various techniques. Bioz Stars score: 99/100, based on 205264 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/control+solvent/Eppendorf/pmc11779754-85-32-38
    Average 99 stars, based on 205264 article reviews
    solvent control - by Bioz Stars, 2026-10
    99/100 stars

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    Related Articles

    Isolation:

    Article Title: Four Neurotoxic Insecticides Impair Partner and Host Finding in the Parasitoid Leptopilina heterotoma and Bioactive Doses Can Be Taken up Via the Host
    Article Snippet: .. To examine whether the insecticides influence the host finding ability of females, 7–10 d old L. heterotoma females were isolated from the breeding tubes, treated with an insecticide dose or the pure solvent (control), and transferred to an Eppendorf vial filled with 1 ml DFM and at least 5 D. melanogaster larvae, as experienced females are more successful in host finding (Papaj and Vet ). ..

    Solvent:

    Article Title: Four Neurotoxic Insecticides Impair Partner and Host Finding in the Parasitoid Leptopilina heterotoma and Bioactive Doses Can Be Taken up Via the Host
    Article Snippet: .. To examine whether the insecticides influence the host finding ability of females, 7–10 d old L. heterotoma females were isolated from the breeding tubes, treated with an insecticide dose or the pure solvent (control), and transferred to an Eppendorf vial filled with 1 ml DFM and at least 5 D. melanogaster larvae, as experienced females are more successful in host finding (Papaj and Vet ). ..

    Article Title: Novel Macrocyclic NLRP3 Inhibitors
    Article Snippet: .. Compounds including positive control (diclofenac, troglitazone. nefazodone) and solvent control (DMSO) are incubated using a 96-deep-well plate (Eppendorf) at 20 M (addition of 1 L of 10 mM DMSO stock solution) in 450 L of 0.1 M sodium phosphate buffer at pH 7.4 containing human liver microsomes (HLM). .. nefazodone) and solvent control (DMSO) are incubated using a 96-deep-well plate (Eppendorf) at 20 M (addition of 1 L of 10 mM DMSO stock solution) in 450 L of 0.1 M sodium phosphate buffer at pH 7.4 containing human liver microsomes (HLM).

    Article Title: A Scoping Review on Fungus and Mycotoxin Studies in the Building's Environment: Mycotoxin Analysis by Mass Spectrometry
    Article Snippet: 5 , Finland and Sweden , Settled airborne dust samples were collected from surfaces above floor levels using a conventional vacuum cleaner device and nylon dust collecting socks. To eliminate the coarse fraction, dust bag dust samples were size homogenized by filtering through a sterile strainer. Samples were dried in a desiccator prior to aliquoting and stored at 20°C. Sampling point selected in living room , The raw extracts were diluted and analyzed without further cleaning in a mixture of acetonitrile, water, and acetic acid (79/20/1), and the raw extracts were diluted and analyzed without further cleaning , A method for determining multimycotoxins in food and feed was created, and it was expanded to include a list of 159 fungal and 27 bacterial metabolites for the examination of naturally infected indoor samples. Its purpose is to demonstrate the usefulness of a multianalyte LC-MS/MS-based spiking at many levels for determining extraction performance parameters, matrix effects, and recoveries. Since dust samples absorb a substantial quantity of solvent relative to food and feed matrixes, the fraction of extraction solvent has been increased. In order to completely utilize instrument capacity for data gathering, each analyte's availability time was defined in the sMRM mode, where retention time and dwell time were fiercely generated for each point in time from the target scan time, for each analyte , When compared to pure methanol and ethyl acetate, the acidified mixture of acetonitrile and water provided the optimum compromise for extracting chosen metabolites. Compared to mortar, carton-gypsum board and coarse-soil-containing splints, settled house dust caused severe matrix effects and incomplete extraction led to low recoveries of analytes due to complex composition from cell fragments, and many other organic compounds accumulated on particulate matter HPLC-MS-MS and GC-MS-MS have both been shown to be useful analytical methods for detecting some of the most toxic mycotoxins produced by molds that are commonly found in moist indoor environments. These technologies are sensitive that they can identify STRG, VER, and TRID in both mold-affected building materials and house dust , [ , ]; Bloom et al. 2007; [ ] . .. 8 , Croatia , Using a MAS-100 Eco air sampler (Merck, Darmstadt, Germany) with 400 holes (hole to agar impactor) and dichloran 18 percent glycerol agar (DG18) plates, airborne fungi were collected in two-month intervals at apartments (APs), basements (BS), grain mill (GM), and open air (ODA) over a one-year period , Growth aspergilli were cut at 3 plugs of 6 mm diameter by using cylindrical drill and transferred into Eppendorf tubes containing 1000 μ l of solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% (v/v) formic acid. The clean extracted sample was sonicated. Ultrasonically extraction was transferred into clean vials using syringe with 0.45 μ m filters (Sartorius, Germany). Then, the extracted samples were dried under stream of nitrogen gas before kept at −20°C. The dried samples were redissolved in 500 μ l of methanol/water (3/1) mixture and filtered through 0.45 μ m filters into new vials. Collected dust samples were extracted with solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% formic acid. The sample mixture was shaken for 1 hour at room temperature and centrifuged. The supernatants were collected and evaporated to dryness. Dried residues were redissolved with ration of 5 mL of methanol/water (3/1). All samples were filtered through 0.45 μ m filters into clean vials , Analysis by using ClassVP 6.2 software and control DGU-14A vacuum degasser, a quaternary LC-10ADVp pump, a CTO-10ASVp column thermostat, an SPD-10ADVp UV-VIS detector, and an SCL-10 system (HPLC Shimadzu). Separation was performed on a LiChroCART Purosphere STAR RP-18 250 mm × 4 mm column with 5 μ m particle size (Merck, Hungary) coupled with a Lichospher 100 RP-18 guard column (Merck, Hungary) at 35°C. Mobile phase with setting of flow rate of 0.5 mL/min, and the injection volume was 20 μ L. The gradient elution was achieved by changing the ratio of methanol and water. STC was quantified by measuring peak areas in an HPLC chromatogram and comparing them to STC calibration standards , Sharp peak of less polar metabolite eluted right before STC in A. jensenii and A. venenatus chromatograms was discovered. This study did not analyze it by LC/MS/MS analyses and considering STC-derived metabolites and/or precursors belonging to 5-methoxy-STC. Another research had compared with this study and found the metabolite detected by HPLC-DAD and TLC with AlCl 3 , [ ] . .. 9 , Poland , Moldy surfaces in form of scrapings and airborne dust from 22 moldy dwellings in winter season , All filters were washed with 4 mL of a solvent ratio of acetonitrile/water/acetic acid (79/20/1). Then, the samples were extracted for 90 min with KL 2 Multipurpose Shaker (Edmund Bühler GmbH, Germany). The samples were centrifuged at 1000 g for 15 min. The supernatant was dried under gentle stream of nitrogen at 40°C. 1 mL of acetonitrile was dissolved into dried residue , HPLC analysis was conducted using a symmetry C18 column (150 × 2.1 mm 5 μ m) with column temperature set at 40°C and 10 μ L of sample injection. Gradient elution using mixture of methanol: acetate buffer 0.1 mol/L pH 4.6 serves as mobile phase. Simultaneous determination was performed at an absorbance of 247 nm and 326 nm. UV spectra at an absorbance of 210–500 nm and retention time of the standards were used to analyze the samples , The method collection like scraping and airborne dust did not indicate quantities exceeding the limit of determination of the method. However, the study revealed that ST and RC were present in the fungi cultivated from scrapings. This demonstrates that toxinogenic strains of Aspergillus versicolor and Penicillium chrysogenum display this feature when cultivated on MEA medium in the laboratory. All the studies, including this study, used the HPLC approach; therefore, it is unclear why this study was not able to demonstrate the presence of mycotoxins in the air dust and scrape samples from flats , [ ] .

    Article Title: Hydroxylated benzo[c]phenanthrene metabolites cause osteoblast apoptosis and skeletal abnormalities in fish.
    Article Snippet: Syringes were filled with triolein (solvent control), BcP (0.1, 1, 10, and 100 nM) (Kanto Chemical Co., Inc., Tokyo, Japan), and 3-OHBcP (0.001, 0.01, 0.1, 1, and 10 nM) (Kanto Chemical Co., Inc., Tokyo, Japan) solutions. .. A micromanipulator (SZX12, Olympus, Tokyo, Japan) and microinjector (Eppendorf FemtoJet, Hamburg, Germany) were set up to inject 0.5 nL of either the solvent control or a contaminant into one of the oil droplets in the embryo yolk (Fig. S2). .. Afterward, embryos were transferred into six-well culture plates (Becton, Dickinson and Company, Franklin Lakes, NJ, USA).

    Control:

    Article Title: Four Neurotoxic Insecticides Impair Partner and Host Finding in the Parasitoid Leptopilina heterotoma and Bioactive Doses Can Be Taken up Via the Host
    Article Snippet: .. To examine whether the insecticides influence the host finding ability of females, 7–10 d old L. heterotoma females were isolated from the breeding tubes, treated with an insecticide dose or the pure solvent (control), and transferred to an Eppendorf vial filled with 1 ml DFM and at least 5 D. melanogaster larvae, as experienced females are more successful in host finding (Papaj and Vet ). ..

    Article Title: Novel Macrocyclic NLRP3 Inhibitors
    Article Snippet: .. Compounds including positive control (diclofenac, troglitazone. nefazodone) and solvent control (DMSO) are incubated using a 96-deep-well plate (Eppendorf) at 20 M (addition of 1 L of 10 mM DMSO stock solution) in 450 L of 0.1 M sodium phosphate buffer at pH 7.4 containing human liver microsomes (HLM). .. nefazodone) and solvent control (DMSO) are incubated using a 96-deep-well plate (Eppendorf) at 20 M (addition of 1 L of 10 mM DMSO stock solution) in 450 L of 0.1 M sodium phosphate buffer at pH 7.4 containing human liver microsomes (HLM).

    Article Title: A Scoping Review on Fungus and Mycotoxin Studies in the Building's Environment: Mycotoxin Analysis by Mass Spectrometry
    Article Snippet: 5 , Finland and Sweden , Settled airborne dust samples were collected from surfaces above floor levels using a conventional vacuum cleaner device and nylon dust collecting socks. To eliminate the coarse fraction, dust bag dust samples were size homogenized by filtering through a sterile strainer. Samples were dried in a desiccator prior to aliquoting and stored at 20°C. Sampling point selected in living room , The raw extracts were diluted and analyzed without further cleaning in a mixture of acetonitrile, water, and acetic acid (79/20/1), and the raw extracts were diluted and analyzed without further cleaning , A method for determining multimycotoxins in food and feed was created, and it was expanded to include a list of 159 fungal and 27 bacterial metabolites for the examination of naturally infected indoor samples. Its purpose is to demonstrate the usefulness of a multianalyte LC-MS/MS-based spiking at many levels for determining extraction performance parameters, matrix effects, and recoveries. Since dust samples absorb a substantial quantity of solvent relative to food and feed matrixes, the fraction of extraction solvent has been increased. In order to completely utilize instrument capacity for data gathering, each analyte's availability time was defined in the sMRM mode, where retention time and dwell time were fiercely generated for each point in time from the target scan time, for each analyte , When compared to pure methanol and ethyl acetate, the acidified mixture of acetonitrile and water provided the optimum compromise for extracting chosen metabolites. Compared to mortar, carton-gypsum board and coarse-soil-containing splints, settled house dust caused severe matrix effects and incomplete extraction led to low recoveries of analytes due to complex composition from cell fragments, and many other organic compounds accumulated on particulate matter HPLC-MS-MS and GC-MS-MS have both been shown to be useful analytical methods for detecting some of the most toxic mycotoxins produced by molds that are commonly found in moist indoor environments. These technologies are sensitive that they can identify STRG, VER, and TRID in both mold-affected building materials and house dust , [ , ]; Bloom et al. 2007; [ ] . .. 8 , Croatia , Using a MAS-100 Eco air sampler (Merck, Darmstadt, Germany) with 400 holes (hole to agar impactor) and dichloran 18 percent glycerol agar (DG18) plates, airborne fungi were collected in two-month intervals at apartments (APs), basements (BS), grain mill (GM), and open air (ODA) over a one-year period , Growth aspergilli were cut at 3 plugs of 6 mm diameter by using cylindrical drill and transferred into Eppendorf tubes containing 1000 μ l of solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% (v/v) formic acid. The clean extracted sample was sonicated. Ultrasonically extraction was transferred into clean vials using syringe with 0.45 μ m filters (Sartorius, Germany). Then, the extracted samples were dried under stream of nitrogen gas before kept at −20°C. The dried samples were redissolved in 500 μ l of methanol/water (3/1) mixture and filtered through 0.45 μ m filters into new vials. Collected dust samples were extracted with solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% formic acid. The sample mixture was shaken for 1 hour at room temperature and centrifuged. The supernatants were collected and evaporated to dryness. Dried residues were redissolved with ration of 5 mL of methanol/water (3/1). All samples were filtered through 0.45 μ m filters into clean vials , Analysis by using ClassVP 6.2 software and control DGU-14A vacuum degasser, a quaternary LC-10ADVp pump, a CTO-10ASVp column thermostat, an SPD-10ADVp UV-VIS detector, and an SCL-10 system (HPLC Shimadzu). Separation was performed on a LiChroCART Purosphere STAR RP-18 250 mm × 4 mm column with 5 μ m particle size (Merck, Hungary) coupled with a Lichospher 100 RP-18 guard column (Merck, Hungary) at 35°C. Mobile phase with setting of flow rate of 0.5 mL/min, and the injection volume was 20 μ L. The gradient elution was achieved by changing the ratio of methanol and water. STC was quantified by measuring peak areas in an HPLC chromatogram and comparing them to STC calibration standards , Sharp peak of less polar metabolite eluted right before STC in A. jensenii and A. venenatus chromatograms was discovered. This study did not analyze it by LC/MS/MS analyses and considering STC-derived metabolites and/or precursors belonging to 5-methoxy-STC. Another research had compared with this study and found the metabolite detected by HPLC-DAD and TLC with AlCl 3 , [ ] . .. 9 , Poland , Moldy surfaces in form of scrapings and airborne dust from 22 moldy dwellings in winter season , All filters were washed with 4 mL of a solvent ratio of acetonitrile/water/acetic acid (79/20/1). Then, the samples were extracted for 90 min with KL 2 Multipurpose Shaker (Edmund Bühler GmbH, Germany). The samples were centrifuged at 1000 g for 15 min. The supernatant was dried under gentle stream of nitrogen at 40°C. 1 mL of acetonitrile was dissolved into dried residue , HPLC analysis was conducted using a symmetry C18 column (150 × 2.1 mm 5 μ m) with column temperature set at 40°C and 10 μ L of sample injection. Gradient elution using mixture of methanol: acetate buffer 0.1 mol/L pH 4.6 serves as mobile phase. Simultaneous determination was performed at an absorbance of 247 nm and 326 nm. UV spectra at an absorbance of 210–500 nm and retention time of the standards were used to analyze the samples , The method collection like scraping and airborne dust did not indicate quantities exceeding the limit of determination of the method. However, the study revealed that ST and RC were present in the fungi cultivated from scrapings. This demonstrates that toxinogenic strains of Aspergillus versicolor and Penicillium chrysogenum display this feature when cultivated on MEA medium in the laboratory. All the studies, including this study, used the HPLC approach; therefore, it is unclear why this study was not able to demonstrate the presence of mycotoxins in the air dust and scrape samples from flats , [ ] .

    Article Title: Hydroxylated benzo[c]phenanthrene metabolites cause osteoblast apoptosis and skeletal abnormalities in fish.
    Article Snippet: Syringes were filled with triolein (solvent control), BcP (0.1, 1, 10, and 100 nM) (Kanto Chemical Co., Inc., Tokyo, Japan), and 3-OHBcP (0.001, 0.01, 0.1, 1, and 10 nM) (Kanto Chemical Co., Inc., Tokyo, Japan) solutions. .. A micromanipulator (SZX12, Olympus, Tokyo, Japan) and microinjector (Eppendorf FemtoJet, Hamburg, Germany) were set up to inject 0.5 nL of either the solvent control or a contaminant into one of the oil droplets in the embryo yolk (Fig. S2). .. Afterward, embryos were transferred into six-well culture plates (Becton, Dickinson and Company, Franklin Lakes, NJ, USA).

    Positive Control:

    Article Title: Novel Macrocyclic NLRP3 Inhibitors
    Article Snippet: .. Compounds including positive control (diclofenac, troglitazone. nefazodone) and solvent control (DMSO) are incubated using a 96-deep-well plate (Eppendorf) at 20 M (addition of 1 L of 10 mM DMSO stock solution) in 450 L of 0.1 M sodium phosphate buffer at pH 7.4 containing human liver microsomes (HLM). .. nefazodone) and solvent control (DMSO) are incubated using a 96-deep-well plate (Eppendorf) at 20 M (addition of 1 L of 10 mM DMSO stock solution) in 450 L of 0.1 M sodium phosphate buffer at pH 7.4 containing human liver microsomes (HLM).

    Incubation:

    Article Title: Novel Macrocyclic NLRP3 Inhibitors
    Article Snippet: .. Compounds including positive control (diclofenac, troglitazone. nefazodone) and solvent control (DMSO) are incubated using a 96-deep-well plate (Eppendorf) at 20 M (addition of 1 L of 10 mM DMSO stock solution) in 450 L of 0.1 M sodium phosphate buffer at pH 7.4 containing human liver microsomes (HLM). .. nefazodone) and solvent control (DMSO) are incubated using a 96-deep-well plate (Eppendorf) at 20 M (addition of 1 L of 10 mM DMSO stock solution) in 450 L of 0.1 M sodium phosphate buffer at pH 7.4 containing human liver microsomes (HLM).

    Article Title: PGP-14 establishes a polar lipid permeability barrier within the C . elegans pharyngeal cuticle
    Article Snippet: .. For the duo Eosin Y + wact-469 incubation, 50uL of worm pellet was added to 430uL of NGM+ 15uL of 5mg/mL Eosin Y + 60uM wact-469 in 1% DMSO in 1.5mL Eppendorf tube (final volume 500uL). ..

    Sonication:

    Article Title: A Scoping Review on Fungus and Mycotoxin Studies in the Building's Environment: Mycotoxin Analysis by Mass Spectrometry
    Article Snippet: 5 , Finland and Sweden , Settled airborne dust samples were collected from surfaces above floor levels using a conventional vacuum cleaner device and nylon dust collecting socks. To eliminate the coarse fraction, dust bag dust samples were size homogenized by filtering through a sterile strainer. Samples were dried in a desiccator prior to aliquoting and stored at 20°C. Sampling point selected in living room , The raw extracts were diluted and analyzed without further cleaning in a mixture of acetonitrile, water, and acetic acid (79/20/1), and the raw extracts were diluted and analyzed without further cleaning , A method for determining multimycotoxins in food and feed was created, and it was expanded to include a list of 159 fungal and 27 bacterial metabolites for the examination of naturally infected indoor samples. Its purpose is to demonstrate the usefulness of a multianalyte LC-MS/MS-based spiking at many levels for determining extraction performance parameters, matrix effects, and recoveries. Since dust samples absorb a substantial quantity of solvent relative to food and feed matrixes, the fraction of extraction solvent has been increased. In order to completely utilize instrument capacity for data gathering, each analyte's availability time was defined in the sMRM mode, where retention time and dwell time were fiercely generated for each point in time from the target scan time, for each analyte , When compared to pure methanol and ethyl acetate, the acidified mixture of acetonitrile and water provided the optimum compromise for extracting chosen metabolites. Compared to mortar, carton-gypsum board and coarse-soil-containing splints, settled house dust caused severe matrix effects and incomplete extraction led to low recoveries of analytes due to complex composition from cell fragments, and many other organic compounds accumulated on particulate matter HPLC-MS-MS and GC-MS-MS have both been shown to be useful analytical methods for detecting some of the most toxic mycotoxins produced by molds that are commonly found in moist indoor environments. These technologies are sensitive that they can identify STRG, VER, and TRID in both mold-affected building materials and house dust , [ , ]; Bloom et al. 2007; [ ] . .. 8 , Croatia , Using a MAS-100 Eco air sampler (Merck, Darmstadt, Germany) with 400 holes (hole to agar impactor) and dichloran 18 percent glycerol agar (DG18) plates, airborne fungi were collected in two-month intervals at apartments (APs), basements (BS), grain mill (GM), and open air (ODA) over a one-year period , Growth aspergilli were cut at 3 plugs of 6 mm diameter by using cylindrical drill and transferred into Eppendorf tubes containing 1000 μ l of solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% (v/v) formic acid. The clean extracted sample was sonicated. Ultrasonically extraction was transferred into clean vials using syringe with 0.45 μ m filters (Sartorius, Germany). Then, the extracted samples were dried under stream of nitrogen gas before kept at −20°C. The dried samples were redissolved in 500 μ l of methanol/water (3/1) mixture and filtered through 0.45 μ m filters into new vials. Collected dust samples were extracted with solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% formic acid. The sample mixture was shaken for 1 hour at room temperature and centrifuged. The supernatants were collected and evaporated to dryness. Dried residues were redissolved with ration of 5 mL of methanol/water (3/1). All samples were filtered through 0.45 μ m filters into clean vials , Analysis by using ClassVP 6.2 software and control DGU-14A vacuum degasser, a quaternary LC-10ADVp pump, a CTO-10ASVp column thermostat, an SPD-10ADVp UV-VIS detector, and an SCL-10 system (HPLC Shimadzu). Separation was performed on a LiChroCART Purosphere STAR RP-18 250 mm × 4 mm column with 5 μ m particle size (Merck, Hungary) coupled with a Lichospher 100 RP-18 guard column (Merck, Hungary) at 35°C. Mobile phase with setting of flow rate of 0.5 mL/min, and the injection volume was 20 μ L. The gradient elution was achieved by changing the ratio of methanol and water. STC was quantified by measuring peak areas in an HPLC chromatogram and comparing them to STC calibration standards , Sharp peak of less polar metabolite eluted right before STC in A. jensenii and A. venenatus chromatograms was discovered. This study did not analyze it by LC/MS/MS analyses and considering STC-derived metabolites and/or precursors belonging to 5-methoxy-STC. Another research had compared with this study and found the metabolite detected by HPLC-DAD and TLC with AlCl 3 , [ ] . .. 9 , Poland , Moldy surfaces in form of scrapings and airborne dust from 22 moldy dwellings in winter season , All filters were washed with 4 mL of a solvent ratio of acetonitrile/water/acetic acid (79/20/1). Then, the samples were extracted for 90 min with KL 2 Multipurpose Shaker (Edmund Bühler GmbH, Germany). The samples were centrifuged at 1000 g for 15 min. The supernatant was dried under gentle stream of nitrogen at 40°C. 1 mL of acetonitrile was dissolved into dried residue , HPLC analysis was conducted using a symmetry C18 column (150 × 2.1 mm 5 μ m) with column temperature set at 40°C and 10 μ L of sample injection. Gradient elution using mixture of methanol: acetate buffer 0.1 mol/L pH 4.6 serves as mobile phase. Simultaneous determination was performed at an absorbance of 247 nm and 326 nm. UV spectra at an absorbance of 210–500 nm and retention time of the standards were used to analyze the samples , The method collection like scraping and airborne dust did not indicate quantities exceeding the limit of determination of the method. However, the study revealed that ST and RC were present in the fungi cultivated from scrapings. This demonstrates that toxinogenic strains of Aspergillus versicolor and Penicillium chrysogenum display this feature when cultivated on MEA medium in the laboratory. All the studies, including this study, used the HPLC approach; therefore, it is unclear why this study was not able to demonstrate the presence of mycotoxins in the air dust and scrape samples from flats , [ ] .

    Extraction:

    Article Title: A Scoping Review on Fungus and Mycotoxin Studies in the Building's Environment: Mycotoxin Analysis by Mass Spectrometry
    Article Snippet: 5 , Finland and Sweden , Settled airborne dust samples were collected from surfaces above floor levels using a conventional vacuum cleaner device and nylon dust collecting socks. To eliminate the coarse fraction, dust bag dust samples were size homogenized by filtering through a sterile strainer. Samples were dried in a desiccator prior to aliquoting and stored at 20°C. Sampling point selected in living room , The raw extracts were diluted and analyzed without further cleaning in a mixture of acetonitrile, water, and acetic acid (79/20/1), and the raw extracts were diluted and analyzed without further cleaning , A method for determining multimycotoxins in food and feed was created, and it was expanded to include a list of 159 fungal and 27 bacterial metabolites for the examination of naturally infected indoor samples. Its purpose is to demonstrate the usefulness of a multianalyte LC-MS/MS-based spiking at many levels for determining extraction performance parameters, matrix effects, and recoveries. Since dust samples absorb a substantial quantity of solvent relative to food and feed matrixes, the fraction of extraction solvent has been increased. In order to completely utilize instrument capacity for data gathering, each analyte's availability time was defined in the sMRM mode, where retention time and dwell time were fiercely generated for each point in time from the target scan time, for each analyte , When compared to pure methanol and ethyl acetate, the acidified mixture of acetonitrile and water provided the optimum compromise for extracting chosen metabolites. Compared to mortar, carton-gypsum board and coarse-soil-containing splints, settled house dust caused severe matrix effects and incomplete extraction led to low recoveries of analytes due to complex composition from cell fragments, and many other organic compounds accumulated on particulate matter HPLC-MS-MS and GC-MS-MS have both been shown to be useful analytical methods for detecting some of the most toxic mycotoxins produced by molds that are commonly found in moist indoor environments. These technologies are sensitive that they can identify STRG, VER, and TRID in both mold-affected building materials and house dust , [ , ]; Bloom et al. 2007; [ ] . .. 8 , Croatia , Using a MAS-100 Eco air sampler (Merck, Darmstadt, Germany) with 400 holes (hole to agar impactor) and dichloran 18 percent glycerol agar (DG18) plates, airborne fungi were collected in two-month intervals at apartments (APs), basements (BS), grain mill (GM), and open air (ODA) over a one-year period , Growth aspergilli were cut at 3 plugs of 6 mm diameter by using cylindrical drill and transferred into Eppendorf tubes containing 1000 μ l of solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% (v/v) formic acid. The clean extracted sample was sonicated. Ultrasonically extraction was transferred into clean vials using syringe with 0.45 μ m filters (Sartorius, Germany). Then, the extracted samples were dried under stream of nitrogen gas before kept at −20°C. The dried samples were redissolved in 500 μ l of methanol/water (3/1) mixture and filtered through 0.45 μ m filters into new vials. Collected dust samples were extracted with solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% formic acid. The sample mixture was shaken for 1 hour at room temperature and centrifuged. The supernatants were collected and evaporated to dryness. Dried residues were redissolved with ration of 5 mL of methanol/water (3/1). All samples were filtered through 0.45 μ m filters into clean vials , Analysis by using ClassVP 6.2 software and control DGU-14A vacuum degasser, a quaternary LC-10ADVp pump, a CTO-10ASVp column thermostat, an SPD-10ADVp UV-VIS detector, and an SCL-10 system (HPLC Shimadzu). Separation was performed on a LiChroCART Purosphere STAR RP-18 250 mm × 4 mm column with 5 μ m particle size (Merck, Hungary) coupled with a Lichospher 100 RP-18 guard column (Merck, Hungary) at 35°C. Mobile phase with setting of flow rate of 0.5 mL/min, and the injection volume was 20 μ L. The gradient elution was achieved by changing the ratio of methanol and water. STC was quantified by measuring peak areas in an HPLC chromatogram and comparing them to STC calibration standards , Sharp peak of less polar metabolite eluted right before STC in A. jensenii and A. venenatus chromatograms was discovered. This study did not analyze it by LC/MS/MS analyses and considering STC-derived metabolites and/or precursors belonging to 5-methoxy-STC. Another research had compared with this study and found the metabolite detected by HPLC-DAD and TLC with AlCl 3 , [ ] . .. 9 , Poland , Moldy surfaces in form of scrapings and airborne dust from 22 moldy dwellings in winter season , All filters were washed with 4 mL of a solvent ratio of acetonitrile/water/acetic acid (79/20/1). Then, the samples were extracted for 90 min with KL 2 Multipurpose Shaker (Edmund Bühler GmbH, Germany). The samples were centrifuged at 1000 g for 15 min. The supernatant was dried under gentle stream of nitrogen at 40°C. 1 mL of acetonitrile was dissolved into dried residue , HPLC analysis was conducted using a symmetry C18 column (150 × 2.1 mm 5 μ m) with column temperature set at 40°C and 10 μ L of sample injection. Gradient elution using mixture of methanol: acetate buffer 0.1 mol/L pH 4.6 serves as mobile phase. Simultaneous determination was performed at an absorbance of 247 nm and 326 nm. UV spectra at an absorbance of 210–500 nm and retention time of the standards were used to analyze the samples , The method collection like scraping and airborne dust did not indicate quantities exceeding the limit of determination of the method. However, the study revealed that ST and RC were present in the fungi cultivated from scrapings. This demonstrates that toxinogenic strains of Aspergillus versicolor and Penicillium chrysogenum display this feature when cultivated on MEA medium in the laboratory. All the studies, including this study, used the HPLC approach; therefore, it is unclear why this study was not able to demonstrate the presence of mycotoxins in the air dust and scrape samples from flats , [ ] .

    Software:

    Article Title: A Scoping Review on Fungus and Mycotoxin Studies in the Building's Environment: Mycotoxin Analysis by Mass Spectrometry
    Article Snippet: 5 , Finland and Sweden , Settled airborne dust samples were collected from surfaces above floor levels using a conventional vacuum cleaner device and nylon dust collecting socks. To eliminate the coarse fraction, dust bag dust samples were size homogenized by filtering through a sterile strainer. Samples were dried in a desiccator prior to aliquoting and stored at 20°C. Sampling point selected in living room , The raw extracts were diluted and analyzed without further cleaning in a mixture of acetonitrile, water, and acetic acid (79/20/1), and the raw extracts were diluted and analyzed without further cleaning , A method for determining multimycotoxins in food and feed was created, and it was expanded to include a list of 159 fungal and 27 bacterial metabolites for the examination of naturally infected indoor samples. Its purpose is to demonstrate the usefulness of a multianalyte LC-MS/MS-based spiking at many levels for determining extraction performance parameters, matrix effects, and recoveries. Since dust samples absorb a substantial quantity of solvent relative to food and feed matrixes, the fraction of extraction solvent has been increased. In order to completely utilize instrument capacity for data gathering, each analyte's availability time was defined in the sMRM mode, where retention time and dwell time were fiercely generated for each point in time from the target scan time, for each analyte , When compared to pure methanol and ethyl acetate, the acidified mixture of acetonitrile and water provided the optimum compromise for extracting chosen metabolites. Compared to mortar, carton-gypsum board and coarse-soil-containing splints, settled house dust caused severe matrix effects and incomplete extraction led to low recoveries of analytes due to complex composition from cell fragments, and many other organic compounds accumulated on particulate matter HPLC-MS-MS and GC-MS-MS have both been shown to be useful analytical methods for detecting some of the most toxic mycotoxins produced by molds that are commonly found in moist indoor environments. These technologies are sensitive that they can identify STRG, VER, and TRID in both mold-affected building materials and house dust , [ , ]; Bloom et al. 2007; [ ] . .. 8 , Croatia , Using a MAS-100 Eco air sampler (Merck, Darmstadt, Germany) with 400 holes (hole to agar impactor) and dichloran 18 percent glycerol agar (DG18) plates, airborne fungi were collected in two-month intervals at apartments (APs), basements (BS), grain mill (GM), and open air (ODA) over a one-year period , Growth aspergilli were cut at 3 plugs of 6 mm diameter by using cylindrical drill and transferred into Eppendorf tubes containing 1000 μ l of solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% (v/v) formic acid. The clean extracted sample was sonicated. Ultrasonically extraction was transferred into clean vials using syringe with 0.45 μ m filters (Sartorius, Germany). Then, the extracted samples were dried under stream of nitrogen gas before kept at −20°C. The dried samples were redissolved in 500 μ l of methanol/water (3/1) mixture and filtered through 0.45 μ m filters into new vials. Collected dust samples were extracted with solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% formic acid. The sample mixture was shaken for 1 hour at room temperature and centrifuged. The supernatants were collected and evaporated to dryness. Dried residues were redissolved with ration of 5 mL of methanol/water (3/1). All samples were filtered through 0.45 μ m filters into clean vials , Analysis by using ClassVP 6.2 software and control DGU-14A vacuum degasser, a quaternary LC-10ADVp pump, a CTO-10ASVp column thermostat, an SPD-10ADVp UV-VIS detector, and an SCL-10 system (HPLC Shimadzu). Separation was performed on a LiChroCART Purosphere STAR RP-18 250 mm × 4 mm column with 5 μ m particle size (Merck, Hungary) coupled with a Lichospher 100 RP-18 guard column (Merck, Hungary) at 35°C. Mobile phase with setting of flow rate of 0.5 mL/min, and the injection volume was 20 μ L. The gradient elution was achieved by changing the ratio of methanol and water. STC was quantified by measuring peak areas in an HPLC chromatogram and comparing them to STC calibration standards , Sharp peak of less polar metabolite eluted right before STC in A. jensenii and A. venenatus chromatograms was discovered. This study did not analyze it by LC/MS/MS analyses and considering STC-derived metabolites and/or precursors belonging to 5-methoxy-STC. Another research had compared with this study and found the metabolite detected by HPLC-DAD and TLC with AlCl 3 , [ ] . .. 9 , Poland , Moldy surfaces in form of scrapings and airborne dust from 22 moldy dwellings in winter season , All filters were washed with 4 mL of a solvent ratio of acetonitrile/water/acetic acid (79/20/1). Then, the samples were extracted for 90 min with KL 2 Multipurpose Shaker (Edmund Bühler GmbH, Germany). The samples were centrifuged at 1000 g for 15 min. The supernatant was dried under gentle stream of nitrogen at 40°C. 1 mL of acetonitrile was dissolved into dried residue , HPLC analysis was conducted using a symmetry C18 column (150 × 2.1 mm 5 μ m) with column temperature set at 40°C and 10 μ L of sample injection. Gradient elution using mixture of methanol: acetate buffer 0.1 mol/L pH 4.6 serves as mobile phase. Simultaneous determination was performed at an absorbance of 247 nm and 326 nm. UV spectra at an absorbance of 210–500 nm and retention time of the standards were used to analyze the samples , The method collection like scraping and airborne dust did not indicate quantities exceeding the limit of determination of the method. However, the study revealed that ST and RC were present in the fungi cultivated from scrapings. This demonstrates that toxinogenic strains of Aspergillus versicolor and Penicillium chrysogenum display this feature when cultivated on MEA medium in the laboratory. All the studies, including this study, used the HPLC approach; therefore, it is unclear why this study was not able to demonstrate the presence of mycotoxins in the air dust and scrape samples from flats , [ ] .

    High Performance Liquid Chromatography:

    Article Title: A Scoping Review on Fungus and Mycotoxin Studies in the Building's Environment: Mycotoxin Analysis by Mass Spectrometry
    Article Snippet: 5 , Finland and Sweden , Settled airborne dust samples were collected from surfaces above floor levels using a conventional vacuum cleaner device and nylon dust collecting socks. To eliminate the coarse fraction, dust bag dust samples were size homogenized by filtering through a sterile strainer. Samples were dried in a desiccator prior to aliquoting and stored at 20°C. Sampling point selected in living room , The raw extracts were diluted and analyzed without further cleaning in a mixture of acetonitrile, water, and acetic acid (79/20/1), and the raw extracts were diluted and analyzed without further cleaning , A method for determining multimycotoxins in food and feed was created, and it was expanded to include a list of 159 fungal and 27 bacterial metabolites for the examination of naturally infected indoor samples. Its purpose is to demonstrate the usefulness of a multianalyte LC-MS/MS-based spiking at many levels for determining extraction performance parameters, matrix effects, and recoveries. Since dust samples absorb a substantial quantity of solvent relative to food and feed matrixes, the fraction of extraction solvent has been increased. In order to completely utilize instrument capacity for data gathering, each analyte's availability time was defined in the sMRM mode, where retention time and dwell time were fiercely generated for each point in time from the target scan time, for each analyte , When compared to pure methanol and ethyl acetate, the acidified mixture of acetonitrile and water provided the optimum compromise for extracting chosen metabolites. Compared to mortar, carton-gypsum board and coarse-soil-containing splints, settled house dust caused severe matrix effects and incomplete extraction led to low recoveries of analytes due to complex composition from cell fragments, and many other organic compounds accumulated on particulate matter HPLC-MS-MS and GC-MS-MS have both been shown to be useful analytical methods for detecting some of the most toxic mycotoxins produced by molds that are commonly found in moist indoor environments. These technologies are sensitive that they can identify STRG, VER, and TRID in both mold-affected building materials and house dust , [ , ]; Bloom et al. 2007; [ ] . .. 8 , Croatia , Using a MAS-100 Eco air sampler (Merck, Darmstadt, Germany) with 400 holes (hole to agar impactor) and dichloran 18 percent glycerol agar (DG18) plates, airborne fungi were collected in two-month intervals at apartments (APs), basements (BS), grain mill (GM), and open air (ODA) over a one-year period , Growth aspergilli were cut at 3 plugs of 6 mm diameter by using cylindrical drill and transferred into Eppendorf tubes containing 1000 μ l of solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% (v/v) formic acid. The clean extracted sample was sonicated. Ultrasonically extraction was transferred into clean vials using syringe with 0.45 μ m filters (Sartorius, Germany). Then, the extracted samples were dried under stream of nitrogen gas before kept at −20°C. The dried samples were redissolved in 500 μ l of methanol/water (3/1) mixture and filtered through 0.45 μ m filters into new vials. Collected dust samples were extracted with solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% formic acid. The sample mixture was shaken for 1 hour at room temperature and centrifuged. The supernatants were collected and evaporated to dryness. Dried residues were redissolved with ration of 5 mL of methanol/water (3/1). All samples were filtered through 0.45 μ m filters into clean vials , Analysis by using ClassVP 6.2 software and control DGU-14A vacuum degasser, a quaternary LC-10ADVp pump, a CTO-10ASVp column thermostat, an SPD-10ADVp UV-VIS detector, and an SCL-10 system (HPLC Shimadzu). Separation was performed on a LiChroCART Purosphere STAR RP-18 250 mm × 4 mm column with 5 μ m particle size (Merck, Hungary) coupled with a Lichospher 100 RP-18 guard column (Merck, Hungary) at 35°C. Mobile phase with setting of flow rate of 0.5 mL/min, and the injection volume was 20 μ L. The gradient elution was achieved by changing the ratio of methanol and water. STC was quantified by measuring peak areas in an HPLC chromatogram and comparing them to STC calibration standards , Sharp peak of less polar metabolite eluted right before STC in A. jensenii and A. venenatus chromatograms was discovered. This study did not analyze it by LC/MS/MS analyses and considering STC-derived metabolites and/or precursors belonging to 5-methoxy-STC. Another research had compared with this study and found the metabolite detected by HPLC-DAD and TLC with AlCl 3 , [ ] . .. 9 , Poland , Moldy surfaces in form of scrapings and airborne dust from 22 moldy dwellings in winter season , All filters were washed with 4 mL of a solvent ratio of acetonitrile/water/acetic acid (79/20/1). Then, the samples were extracted for 90 min with KL 2 Multipurpose Shaker (Edmund Bühler GmbH, Germany). The samples were centrifuged at 1000 g for 15 min. The supernatant was dried under gentle stream of nitrogen at 40°C. 1 mL of acetonitrile was dissolved into dried residue , HPLC analysis was conducted using a symmetry C18 column (150 × 2.1 mm 5 μ m) with column temperature set at 40°C and 10 μ L of sample injection. Gradient elution using mixture of methanol: acetate buffer 0.1 mol/L pH 4.6 serves as mobile phase. Simultaneous determination was performed at an absorbance of 247 nm and 326 nm. UV spectra at an absorbance of 210–500 nm and retention time of the standards were used to analyze the samples , The method collection like scraping and airborne dust did not indicate quantities exceeding the limit of determination of the method. However, the study revealed that ST and RC were present in the fungi cultivated from scrapings. This demonstrates that toxinogenic strains of Aspergillus versicolor and Penicillium chrysogenum display this feature when cultivated on MEA medium in the laboratory. All the studies, including this study, used the HPLC approach; therefore, it is unclear why this study was not able to demonstrate the presence of mycotoxins in the air dust and scrape samples from flats , [ ] .

    Injection:

    Article Title: A Scoping Review on Fungus and Mycotoxin Studies in the Building's Environment: Mycotoxin Analysis by Mass Spectrometry
    Article Snippet: 5 , Finland and Sweden , Settled airborne dust samples were collected from surfaces above floor levels using a conventional vacuum cleaner device and nylon dust collecting socks. To eliminate the coarse fraction, dust bag dust samples were size homogenized by filtering through a sterile strainer. Samples were dried in a desiccator prior to aliquoting and stored at 20°C. Sampling point selected in living room , The raw extracts were diluted and analyzed without further cleaning in a mixture of acetonitrile, water, and acetic acid (79/20/1), and the raw extracts were diluted and analyzed without further cleaning , A method for determining multimycotoxins in food and feed was created, and it was expanded to include a list of 159 fungal and 27 bacterial metabolites for the examination of naturally infected indoor samples. Its purpose is to demonstrate the usefulness of a multianalyte LC-MS/MS-based spiking at many levels for determining extraction performance parameters, matrix effects, and recoveries. Since dust samples absorb a substantial quantity of solvent relative to food and feed matrixes, the fraction of extraction solvent has been increased. In order to completely utilize instrument capacity for data gathering, each analyte's availability time was defined in the sMRM mode, where retention time and dwell time were fiercely generated for each point in time from the target scan time, for each analyte , When compared to pure methanol and ethyl acetate, the acidified mixture of acetonitrile and water provided the optimum compromise for extracting chosen metabolites. Compared to mortar, carton-gypsum board and coarse-soil-containing splints, settled house dust caused severe matrix effects and incomplete extraction led to low recoveries of analytes due to complex composition from cell fragments, and many other organic compounds accumulated on particulate matter HPLC-MS-MS and GC-MS-MS have both been shown to be useful analytical methods for detecting some of the most toxic mycotoxins produced by molds that are commonly found in moist indoor environments. These technologies are sensitive that they can identify STRG, VER, and TRID in both mold-affected building materials and house dust , [ , ]; Bloom et al. 2007; [ ] . .. 8 , Croatia , Using a MAS-100 Eco air sampler (Merck, Darmstadt, Germany) with 400 holes (hole to agar impactor) and dichloran 18 percent glycerol agar (DG18) plates, airborne fungi were collected in two-month intervals at apartments (APs), basements (BS), grain mill (GM), and open air (ODA) over a one-year period , Growth aspergilli were cut at 3 plugs of 6 mm diameter by using cylindrical drill and transferred into Eppendorf tubes containing 1000 μ l of solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% (v/v) formic acid. The clean extracted sample was sonicated. Ultrasonically extraction was transferred into clean vials using syringe with 0.45 μ m filters (Sartorius, Germany). Then, the extracted samples were dried under stream of nitrogen gas before kept at −20°C. The dried samples were redissolved in 500 μ l of methanol/water (3/1) mixture and filtered through 0.45 μ m filters into new vials. Collected dust samples were extracted with solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% formic acid. The sample mixture was shaken for 1 hour at room temperature and centrifuged. The supernatants were collected and evaporated to dryness. Dried residues were redissolved with ration of 5 mL of methanol/water (3/1). All samples were filtered through 0.45 μ m filters into clean vials , Analysis by using ClassVP 6.2 software and control DGU-14A vacuum degasser, a quaternary LC-10ADVp pump, a CTO-10ASVp column thermostat, an SPD-10ADVp UV-VIS detector, and an SCL-10 system (HPLC Shimadzu). Separation was performed on a LiChroCART Purosphere STAR RP-18 250 mm × 4 mm column with 5 μ m particle size (Merck, Hungary) coupled with a Lichospher 100 RP-18 guard column (Merck, Hungary) at 35°C. Mobile phase with setting of flow rate of 0.5 mL/min, and the injection volume was 20 μ L. The gradient elution was achieved by changing the ratio of methanol and water. STC was quantified by measuring peak areas in an HPLC chromatogram and comparing them to STC calibration standards , Sharp peak of less polar metabolite eluted right before STC in A. jensenii and A. venenatus chromatograms was discovered. This study did not analyze it by LC/MS/MS analyses and considering STC-derived metabolites and/or precursors belonging to 5-methoxy-STC. Another research had compared with this study and found the metabolite detected by HPLC-DAD and TLC with AlCl 3 , [ ] . .. 9 , Poland , Moldy surfaces in form of scrapings and airborne dust from 22 moldy dwellings in winter season , All filters were washed with 4 mL of a solvent ratio of acetonitrile/water/acetic acid (79/20/1). Then, the samples were extracted for 90 min with KL 2 Multipurpose Shaker (Edmund Bühler GmbH, Germany). The samples were centrifuged at 1000 g for 15 min. The supernatant was dried under gentle stream of nitrogen at 40°C. 1 mL of acetonitrile was dissolved into dried residue , HPLC analysis was conducted using a symmetry C18 column (150 × 2.1 mm 5 μ m) with column temperature set at 40°C and 10 μ L of sample injection. Gradient elution using mixture of methanol: acetate buffer 0.1 mol/L pH 4.6 serves as mobile phase. Simultaneous determination was performed at an absorbance of 247 nm and 326 nm. UV spectra at an absorbance of 210–500 nm and retention time of the standards were used to analyze the samples , The method collection like scraping and airborne dust did not indicate quantities exceeding the limit of determination of the method. However, the study revealed that ST and RC were present in the fungi cultivated from scrapings. This demonstrates that toxinogenic strains of Aspergillus versicolor and Penicillium chrysogenum display this feature when cultivated on MEA medium in the laboratory. All the studies, including this study, used the HPLC approach; therefore, it is unclear why this study was not able to demonstrate the presence of mycotoxins in the air dust and scrape samples from flats , [ ] .

    Thin Layer Chromatography:

    Article Title: A Scoping Review on Fungus and Mycotoxin Studies in the Building's Environment: Mycotoxin Analysis by Mass Spectrometry
    Article Snippet: 5 , Finland and Sweden , Settled airborne dust samples were collected from surfaces above floor levels using a conventional vacuum cleaner device and nylon dust collecting socks. To eliminate the coarse fraction, dust bag dust samples were size homogenized by filtering through a sterile strainer. Samples were dried in a desiccator prior to aliquoting and stored at 20°C. Sampling point selected in living room , The raw extracts were diluted and analyzed without further cleaning in a mixture of acetonitrile, water, and acetic acid (79/20/1), and the raw extracts were diluted and analyzed without further cleaning , A method for determining multimycotoxins in food and feed was created, and it was expanded to include a list of 159 fungal and 27 bacterial metabolites for the examination of naturally infected indoor samples. Its purpose is to demonstrate the usefulness of a multianalyte LC-MS/MS-based spiking at many levels for determining extraction performance parameters, matrix effects, and recoveries. Since dust samples absorb a substantial quantity of solvent relative to food and feed matrixes, the fraction of extraction solvent has been increased. In order to completely utilize instrument capacity for data gathering, each analyte's availability time was defined in the sMRM mode, where retention time and dwell time were fiercely generated for each point in time from the target scan time, for each analyte , When compared to pure methanol and ethyl acetate, the acidified mixture of acetonitrile and water provided the optimum compromise for extracting chosen metabolites. Compared to mortar, carton-gypsum board and coarse-soil-containing splints, settled house dust caused severe matrix effects and incomplete extraction led to low recoveries of analytes due to complex composition from cell fragments, and many other organic compounds accumulated on particulate matter HPLC-MS-MS and GC-MS-MS have both been shown to be useful analytical methods for detecting some of the most toxic mycotoxins produced by molds that are commonly found in moist indoor environments. These technologies are sensitive that they can identify STRG, VER, and TRID in both mold-affected building materials and house dust , [ , ]; Bloom et al. 2007; [ ] . .. 8 , Croatia , Using a MAS-100 Eco air sampler (Merck, Darmstadt, Germany) with 400 holes (hole to agar impactor) and dichloran 18 percent glycerol agar (DG18) plates, airborne fungi were collected in two-month intervals at apartments (APs), basements (BS), grain mill (GM), and open air (ODA) over a one-year period , Growth aspergilli were cut at 3 plugs of 6 mm diameter by using cylindrical drill and transferred into Eppendorf tubes containing 1000 μ l of solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% (v/v) formic acid. The clean extracted sample was sonicated. Ultrasonically extraction was transferred into clean vials using syringe with 0.45 μ m filters (Sartorius, Germany). Then, the extracted samples were dried under stream of nitrogen gas before kept at −20°C. The dried samples were redissolved in 500 μ l of methanol/water (3/1) mixture and filtered through 0.45 μ m filters into new vials. Collected dust samples were extracted with solvent mixture methanol-DCM-ethyl acetate with a ratio (1/2/3) supplemented with 1% formic acid. The sample mixture was shaken for 1 hour at room temperature and centrifuged. The supernatants were collected and evaporated to dryness. Dried residues were redissolved with ration of 5 mL of methanol/water (3/1). All samples were filtered through 0.45 μ m filters into clean vials , Analysis by using ClassVP 6.2 software and control DGU-14A vacuum degasser, a quaternary LC-10ADVp pump, a CTO-10ASVp column thermostat, an SPD-10ADVp UV-VIS detector, and an SCL-10 system (HPLC Shimadzu). Separation was performed on a LiChroCART Purosphere STAR RP-18 250 mm × 4 mm column with 5 μ m particle size (Merck, Hungary) coupled with a Lichospher 100 RP-18 guard column (Merck, Hungary) at 35°C. Mobile phase with setting of flow rate of 0.5 mL/min, and the injection volume was 20 μ L. The gradient elution was achieved by changing the ratio of methanol and water. STC was quantified by measuring peak areas in an HPLC chromatogram and comparing them to STC calibration standards , Sharp peak of less polar metabolite eluted right before STC in A. jensenii and A. venenatus chromatograms was discovered. This study did not analyze it by LC/MS/MS analyses and considering STC-derived metabolites and/or precursors belonging to 5-methoxy-STC. Another research had compared with this study and found the metabolite detected by HPLC-DAD and TLC with AlCl 3 , [ ] . .. 9 , Poland , Moldy surfaces in form of scrapings and airborne dust from 22 moldy dwellings in winter season , All filters were washed with 4 mL of a solvent ratio of acetonitrile/water/acetic acid (79/20/1). Then, the samples were extracted for 90 min with KL 2 Multipurpose Shaker (Edmund Bühler GmbH, Germany). The samples were centrifuged at 1000 g for 15 min. The supernatant was dried under gentle stream of nitrogen at 40°C. 1 mL of acetonitrile was dissolved into dried residue , HPLC analysis was conducted using a symmetry C18 column (150 × 2.1 mm 5 μ m) with column temperature set at 40°C and 10 μ L of sample injection. Gradient elution using mixture of methanol: acetate buffer 0.1 mol/L pH 4.6 serves as mobile phase. Simultaneous determination was performed at an absorbance of 247 nm and 326 nm. UV spectra at an absorbance of 210–500 nm and retention time of the standards were used to analyze the samples , The method collection like scraping and airborne dust did not indicate quantities exceeding the limit of determination of the method. However, the study revealed that ST and RC were present in the fungi cultivated from scrapings. This demonstrates that toxinogenic strains of Aspergillus versicolor and Penicillium chrysogenum display this feature when cultivated on MEA medium in the laboratory. All the studies, including this study, used the HPLC approach; therefore, it is unclear why this study was not able to demonstrate the presence of mycotoxins in the air dust and scrape samples from flats , [ ] .

    other:

    Article Title: The Incorporation of CBD into Biodegradable DL-Lactide/Glycolide Copolymers Creates a Persistent Antibacterial Environment: An In Vitro Study on Streptococcus mutans and Staphylococcus aureus
    Article Snippet: In the first approach, 100 mg of PURASORB 5010 or PURASORB 7510 was allowed to dissolve in 500 μL dimethyl sulfoxide (DMSO) in Eppendorf tubes (Axygen brand products, Corning Inc., Reynosa, Mexico) overnight at room temperature with constant mixing.

    Article Title: Compounds containing benzosultam
    Article Snippet: 1.3 Other Reagent Information Name Manufacturer Article number Save condition Fetal bovine serum Hyclone SV30087.03 −20° C. Trypsin Gibco 25200-072 −20° C. EMEM culture medium ATCC ATCC30-2003 2-8° C. 1.4 Instrument Information Name Manufacturer Model Carbon dioxide incubator Thermo Fisher Heracell240i Low-temperature, Eppendorf 5810R high-speed centrifuge Analytical balance Sartorius SECURA225D-1CN Ordinary balance Changzhou Tianzhiping EL-2KJ Instruments Co., LTD Digital vernier caliper Mitutoyo 0-150 mm Experimental Methods and Steps: 2.1 Tumor Cell Inoculation Cell inoculation: 0.2 mL of Calu-6 cell (mixed in a ratio of 1:1 with matrix gel) was subcutaneously inoculated on the right back of each mouse, and group administration was started when the average tumor volume reached 173 mm, 2.2 Grouping TABLE 1 Experimental animal grouping and administration regimen volume Compound Dosage parameters Route of Administration Group N1 treatment (mg/kg) (μL/g)2 administration frequency 1 6 Solvent control — 10 Oral (PO) Once a day (QD) group 3 2 6 Compound 1 50 10 Oral (PO) Once a day (QD) 3 6 Compound 3 50 10 Oral (PO) Once a day (QD) 4 6 Compound 4 50 10 Oral (PO) Once a day (QD) 5 6 Compound 9 50 10 Oral (PO) Once a day (QD) 6 6 Compound 11 50 10 Oral (PO) Once a day (QD) Note: 1number of mice in each group; 2administration volume parameters: 10 μL/g according to mouse body weight.



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    p53 is a pioneer factor that increases DNA accessibility. ( A ) ATAC-seq was performed on four biological replicates of Nutlin-3a and <t>DMSO</t> control-treated MCF-7 cells. Accessible sites were identified by peak calling, and their differential accessibility was assessed. ( B ) Enrichment of transcription factor binding sites that overlap sites with increased (left) or decreased (right) accessibility upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) The presence (open) or absence (closed) of an ATAC-seq peak has been assessed at 7705 recurrent p53 binding sites, and changes between the Nutlin-3a and DMSO control conditions are displayed. ( D ) p53 ChIP-seq and ATAC-seq signals are displayed for the groups identified in panel (C). Regions sorted by ATAC-seq signal. Genome browser images displaying p53 ChIP-seq and ATAC-seq data at a p53 binding site ( E ) that became accessible and ( F ) that remained inaccessible upon Nutlin-3a treatment. The predicted p53RE is highlighted. p53 ChIP-seq and nucleosome-free ATAC-seq data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS according to library size and accessible DNA background.
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    p53 is a pioneer factor that increases DNA accessibility. ( A ) ATAC-seq was performed on four biological replicates of Nutlin-3a and <t>DMSO</t> control-treated MCF-7 cells. Accessible sites were identified by peak calling, and their differential accessibility was assessed. ( B ) Enrichment of transcription factor binding sites that overlap sites with increased (left) or decreased (right) accessibility upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) The presence (open) or absence (closed) of an ATAC-seq peak has been assessed at 7705 recurrent p53 binding sites, and changes between the Nutlin-3a and DMSO control conditions are displayed. ( D ) p53 ChIP-seq and ATAC-seq signals are displayed for the groups identified in panel (C). Regions sorted by ATAC-seq signal. Genome browser images displaying p53 ChIP-seq and ATAC-seq data at a p53 binding site ( E ) that became accessible and ( F ) that remained inaccessible upon Nutlin-3a treatment. The predicted p53RE is highlighted. p53 ChIP-seq and nucleosome-free ATAC-seq data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS according to library size and accessible DNA background.
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    p53 is a pioneer factor that increases DNA accessibility. ( A ) ATAC-seq was performed on four biological replicates of Nutlin-3a and <t>DMSO</t> control-treated MCF-7 cells. Accessible sites were identified by peak calling, and their differential accessibility was assessed. ( B ) Enrichment of transcription factor binding sites that overlap sites with increased (left) or decreased (right) accessibility upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) The presence (open) or absence (closed) of an ATAC-seq peak has been assessed at 7705 recurrent p53 binding sites, and changes between the Nutlin-3a and DMSO control conditions are displayed. ( D ) p53 ChIP-seq and ATAC-seq signals are displayed for the groups identified in panel (C). Regions sorted by ATAC-seq signal. Genome browser images displaying p53 ChIP-seq and ATAC-seq data at a p53 binding site ( E ) that became accessible and ( F ) that remained inaccessible upon Nutlin-3a treatment. The predicted p53RE is highlighted. p53 ChIP-seq and nucleosome-free ATAC-seq data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS according to library size and accessible DNA background.
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    p53 is a pioneer factor that increases DNA accessibility. ( A ) ATAC-seq was performed on four biological replicates of Nutlin-3a and <t>DMSO</t> control-treated MCF-7 cells. Accessible sites were identified by peak calling, and their differential accessibility was assessed. ( B ) Enrichment of transcription factor binding sites that overlap sites with increased (left) or decreased (right) accessibility upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) The presence (open) or absence (closed) of an ATAC-seq peak has been assessed at 7705 recurrent p53 binding sites, and changes between the Nutlin-3a and DMSO control conditions are displayed. ( D ) p53 ChIP-seq and ATAC-seq signals are displayed for the groups identified in panel (C). Regions sorted by ATAC-seq signal. Genome browser images displaying p53 ChIP-seq and ATAC-seq data at a p53 binding site ( E ) that became accessible and ( F ) that remained inaccessible upon Nutlin-3a treatment. The predicted p53RE is highlighted. p53 ChIP-seq and nucleosome-free ATAC-seq data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS according to library size and accessible DNA background.
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    p53 is a pioneer factor that increases DNA accessibility. ( A ) ATAC-seq was performed on four biological replicates of Nutlin-3a and <t>DMSO</t> control-treated MCF-7 cells. Accessible sites were identified by peak calling, and their differential accessibility was assessed. ( B ) Enrichment of transcription factor binding sites that overlap sites with increased (left) or decreased (right) accessibility upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) The presence (open) or absence (closed) of an ATAC-seq peak has been assessed at 7705 recurrent p53 binding sites, and changes between the Nutlin-3a and DMSO control conditions are displayed. ( D ) p53 ChIP-seq and ATAC-seq signals are displayed for the groups identified in panel (C). Regions sorted by ATAC-seq signal. Genome browser images displaying p53 ChIP-seq and ATAC-seq data at a p53 binding site ( E ) that became accessible and ( F ) that remained inaccessible upon Nutlin-3a treatment. The predicted p53RE is highlighted. p53 ChIP-seq and nucleosome-free ATAC-seq data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS according to library size and accessible DNA background.
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    Image Search Results


    circTACC3 m 6 A modification is associated with its intracellular localization. (A) Representative image of H&E staining of MASH‐related HCC tumor and paired peritumoral normal tissue derived organoids with relatively low (#1) and high (#2) circTACC3 expression, treated with or without PA + OA. (B) 3D fluorescence scanning of 3‐OH BrDU probe (green), anti‐Ki‐67 antibody (magenta), and DAPI (blue) indicated tissue derived organoids, treated with or without PA + OA; maximum projection of signals is shown. (C‐D) Assays of fluorescence staining with the 3‐OH BrDU probe were conducted on the cell lines with different nuclear circTACC3 level (C, n = 6) and circTACC3 knockout cell strains or negative controls (D, n = 9). The numbers on the Y‐axis represent the apoptotic rate normalized to baseline of 1. ** P < 0.01; *** P < 0.001; NS , not significant. (E) MeRIP assay shows an enrichment of m 6 A‐modified circTACC3 in cytoplasmic and nuclear fraction of HCCLM3 cells. (F) Representation of predicted m 6 A modification motif of circTACC3 (predicted using the SRAMP website). (G) Absolute quantitative RT‐qPCR of m 6 A RNA shows m 6 A modification ratio of intra‐nuclear circTACC3 in the individual motif scale. (H) The m 6 A modification levels of circTACC3 were evaluated by MeRIP in m 6 A inhibitor treated group compared to control (DMSO) group, and in PA + OA treated group compared to control (Mock) group, respectively ( n = 3). *** P < 0.001. (I) Nucleo‐plasmic fractionation to evaluate circTACC3 expression after indicated treatment ( n = 4). *** P < 0.001. (J) 3D‐FISH conducted on MASH‐related HCC tumor tissue derived organoids demonstrates the 3D distribution of circTACC3 (red) in nuclei (blue). (K) H&E staining of MASH‐related HCC tumor tissue derived organoids treated with PA + OA and/or m 6 A intervention. Abbreviations: PA, palmitic acid; OA, oleic acid; T, tumor tissues; PT, peritumoral normal tissue; H&E, hematoxylin and eosin; MeRIP, methylated RNA immunoprecipitation; m 6 A, N6‐methyladenosine; NAS, Non‐alcoholic fatty liver disease activity score; SAH, S‐adenosylhomocysteine; DAA, 3‐deazaadenosine; FISH, fluorescence i n situ hybridization.

    Journal: Cancer Communications

    Article Title: Intranuclear paraspeckle‐circular RNA TACC3 assembly forms RNA‐DNA hybrids to facilitate MASH‐related hepatocellular carcinoma growth in an m 6 A‐dependent manner

    doi: 10.1002/cac2.70061

    Figure Lengend Snippet: circTACC3 m 6 A modification is associated with its intracellular localization. (A) Representative image of H&E staining of MASH‐related HCC tumor and paired peritumoral normal tissue derived organoids with relatively low (#1) and high (#2) circTACC3 expression, treated with or without PA + OA. (B) 3D fluorescence scanning of 3‐OH BrDU probe (green), anti‐Ki‐67 antibody (magenta), and DAPI (blue) indicated tissue derived organoids, treated with or without PA + OA; maximum projection of signals is shown. (C‐D) Assays of fluorescence staining with the 3‐OH BrDU probe were conducted on the cell lines with different nuclear circTACC3 level (C, n = 6) and circTACC3 knockout cell strains or negative controls (D, n = 9). The numbers on the Y‐axis represent the apoptotic rate normalized to baseline of 1. ** P < 0.01; *** P < 0.001; NS , not significant. (E) MeRIP assay shows an enrichment of m 6 A‐modified circTACC3 in cytoplasmic and nuclear fraction of HCCLM3 cells. (F) Representation of predicted m 6 A modification motif of circTACC3 (predicted using the SRAMP website). (G) Absolute quantitative RT‐qPCR of m 6 A RNA shows m 6 A modification ratio of intra‐nuclear circTACC3 in the individual motif scale. (H) The m 6 A modification levels of circTACC3 were evaluated by MeRIP in m 6 A inhibitor treated group compared to control (DMSO) group, and in PA + OA treated group compared to control (Mock) group, respectively ( n = 3). *** P < 0.001. (I) Nucleo‐plasmic fractionation to evaluate circTACC3 expression after indicated treatment ( n = 4). *** P < 0.001. (J) 3D‐FISH conducted on MASH‐related HCC tumor tissue derived organoids demonstrates the 3D distribution of circTACC3 (red) in nuclei (blue). (K) H&E staining of MASH‐related HCC tumor tissue derived organoids treated with PA + OA and/or m 6 A intervention. Abbreviations: PA, palmitic acid; OA, oleic acid; T, tumor tissues; PT, peritumoral normal tissue; H&E, hematoxylin and eosin; MeRIP, methylated RNA immunoprecipitation; m 6 A, N6‐methyladenosine; NAS, Non‐alcoholic fatty liver disease activity score; SAH, S‐adenosylhomocysteine; DAA, 3‐deazaadenosine; FISH, fluorescence i n situ hybridization.

    Article Snippet: STM2457, S‐adenosylhomocysteine (SAH), 3‐deazaadenosine (DAA) or the solvent control DMSO (v/v = 1/1000, #HY‐Y0320, MedChemExpress, NJ, US) was added on Day 4.

    Techniques: Modification, Staining, Derivative Assay, Expressing, Fluorescence, Knock-Out, Quantitative RT-PCR, Control, Fractionation, Methylation, RNA Immunoprecipitation, Activity Assay, Hybridization

    p53 is a pioneer factor that increases DNA accessibility. ( A ) ATAC-seq was performed on four biological replicates of Nutlin-3a and DMSO control-treated MCF-7 cells. Accessible sites were identified by peak calling, and their differential accessibility was assessed. ( B ) Enrichment of transcription factor binding sites that overlap sites with increased (left) or decreased (right) accessibility upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) The presence (open) or absence (closed) of an ATAC-seq peak has been assessed at 7705 recurrent p53 binding sites, and changes between the Nutlin-3a and DMSO control conditions are displayed. ( D ) p53 ChIP-seq and ATAC-seq signals are displayed for the groups identified in panel (C). Regions sorted by ATAC-seq signal. Genome browser images displaying p53 ChIP-seq and ATAC-seq data at a p53 binding site ( E ) that became accessible and ( F ) that remained inaccessible upon Nutlin-3a treatment. The predicted p53RE is highlighted. p53 ChIP-seq and nucleosome-free ATAC-seq data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS according to library size and accessible DNA background.

    Journal: Nucleic Acids Research

    Article Title: p53 reveals principles of chromatin remodeling and enhancer activation

    doi: 10.1093/nar/gkaf465

    Figure Lengend Snippet: p53 is a pioneer factor that increases DNA accessibility. ( A ) ATAC-seq was performed on four biological replicates of Nutlin-3a and DMSO control-treated MCF-7 cells. Accessible sites were identified by peak calling, and their differential accessibility was assessed. ( B ) Enrichment of transcription factor binding sites that overlap sites with increased (left) or decreased (right) accessibility upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) The presence (open) or absence (closed) of an ATAC-seq peak has been assessed at 7705 recurrent p53 binding sites, and changes between the Nutlin-3a and DMSO control conditions are displayed. ( D ) p53 ChIP-seq and ATAC-seq signals are displayed for the groups identified in panel (C). Regions sorted by ATAC-seq signal. Genome browser images displaying p53 ChIP-seq and ATAC-seq data at a p53 binding site ( E ) that became accessible and ( F ) that remained inaccessible upon Nutlin-3a treatment. The predicted p53RE is highlighted. p53 ChIP-seq and nucleosome-free ATAC-seq data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS according to library size and accessible DNA background.

    Article Snippet: Cells were treated with Dimethylsulfoxid (DMSO) solvent control (0.15%; Carl Roth, Karlsruhe, Germany) or Nutlin-3a (10 μM; MedChemExpress, Monmouth Junction, NJ, USA) for 24 h.

    Techniques: Control, Binding Assay, ChIP-sequencing

    p53 establishes enhancers. ( A ) p53 binding sites were sorted by local chromatin state (promoter, enhancer, transcription, quiescent). In addition, they were sorted by the presence (open) or absence (closed) of an ATAC-seq peak in Nutlin-3a and DMSO control conditions. ( B ) CUT&Tag for H3K4me1 and H3K27ac was performed on two biological replicates of Nutlin-3a and DMSO control-treated MCF-7 cells. H3K4me1, H3K27ac, ATAC-seq, and p53 ChIP-seq signals are displayed for p53 binding sites that were closed in the DMSO control condition and open ( C ) or closed ( D ) in the Nutlin-3a treatment condition. Regions were sorted by average signal and p53 binding sites located in promoters were removed for visualization purposes because of the small group size and different signal scales. ( E ) p53 occupancy (CPM) at p53 binding sites in the different groups. Significance determined using a two-tailed Kruskal–Wallis test. *** P -value <.001.

    Journal: Nucleic Acids Research

    Article Title: p53 reveals principles of chromatin remodeling and enhancer activation

    doi: 10.1093/nar/gkaf465

    Figure Lengend Snippet: p53 establishes enhancers. ( A ) p53 binding sites were sorted by local chromatin state (promoter, enhancer, transcription, quiescent). In addition, they were sorted by the presence (open) or absence (closed) of an ATAC-seq peak in Nutlin-3a and DMSO control conditions. ( B ) CUT&Tag for H3K4me1 and H3K27ac was performed on two biological replicates of Nutlin-3a and DMSO control-treated MCF-7 cells. H3K4me1, H3K27ac, ATAC-seq, and p53 ChIP-seq signals are displayed for p53 binding sites that were closed in the DMSO control condition and open ( C ) or closed ( D ) in the Nutlin-3a treatment condition. Regions were sorted by average signal and p53 binding sites located in promoters were removed for visualization purposes because of the small group size and different signal scales. ( E ) p53 occupancy (CPM) at p53 binding sites in the different groups. Significance determined using a two-tailed Kruskal–Wallis test. *** P -value <.001.

    Article Snippet: Cells were treated with Dimethylsulfoxid (DMSO) solvent control (0.15%; Carl Roth, Karlsruhe, Germany) or Nutlin-3a (10 μM; MedChemExpress, Monmouth Junction, NJ, USA) for 24 h.

    Techniques: Binding Assay, Control, ChIP-sequencing, Two Tailed Test

    p53-induced transcription correlates with chromatin remodeling and requires high p53 abundance. ( A ) CAGE-seq was performed on four biological replicates of Nutlin-3a and DMSO control-treated MCF-7 cells. Significantly differentially regulated TSSs were identified. ( B ) Enrichment of transcription factor binding sites at sites with increased (left) or decreased (right) TSS activity upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) Comparison of changes in TSS activity (CAGE-seq) and DNA accessibility (ATAC-seq) for all TSSs in accessible DNA regions (determined by ATAC-seq peaks) upon Nutlin-3a treatment. ( D ) Subsets of TSSs/accessible sites that overlap with p53 (top panel), E2F4 (middle panel), and RFX7 binding sites (bottom panel). ( E ) p53 ChIP-seq, ATAC-seq, H3K4me1, and H3K27ac signals at p53 binding sites located in promoter regions. Subgroups were determined by overlaps with an induced TSS (log 2 FC > 0.5), uninduced TSS (log 2 FC < 0.5), and no TSS. Regions sorted by H3K27ac signal. ( F ) Comparison of changes in local transcription (CAGE-seq) and p53 occupancy (CPM from ChIP-seq). Significance determined by two-tailed Spearman correlation. Sigmoidal fit obtained best r 2 . ( G ) The fraction of promoter p53 binding sites with a canonical p53RE, noncanonical p53RE, and no p53RE.

    Journal: Nucleic Acids Research

    Article Title: p53 reveals principles of chromatin remodeling and enhancer activation

    doi: 10.1093/nar/gkaf465

    Figure Lengend Snippet: p53-induced transcription correlates with chromatin remodeling and requires high p53 abundance. ( A ) CAGE-seq was performed on four biological replicates of Nutlin-3a and DMSO control-treated MCF-7 cells. Significantly differentially regulated TSSs were identified. ( B ) Enrichment of transcription factor binding sites at sites with increased (left) or decreased (right) TSS activity upon Nutlin-3a treatment. The top 15 transcription factors are displayed. ( C ) Comparison of changes in TSS activity (CAGE-seq) and DNA accessibility (ATAC-seq) for all TSSs in accessible DNA regions (determined by ATAC-seq peaks) upon Nutlin-3a treatment. ( D ) Subsets of TSSs/accessible sites that overlap with p53 (top panel), E2F4 (middle panel), and RFX7 binding sites (bottom panel). ( E ) p53 ChIP-seq, ATAC-seq, H3K4me1, and H3K27ac signals at p53 binding sites located in promoter regions. Subgroups were determined by overlaps with an induced TSS (log 2 FC > 0.5), uninduced TSS (log 2 FC < 0.5), and no TSS. Regions sorted by H3K27ac signal. ( F ) Comparison of changes in local transcription (CAGE-seq) and p53 occupancy (CPM from ChIP-seq). Significance determined by two-tailed Spearman correlation. Sigmoidal fit obtained best r 2 . ( G ) The fraction of promoter p53 binding sites with a canonical p53RE, noncanonical p53RE, and no p53RE.

    Article Snippet: Cells were treated with Dimethylsulfoxid (DMSO) solvent control (0.15%; Carl Roth, Karlsruhe, Germany) or Nutlin-3a (10 μM; MedChemExpress, Monmouth Junction, NJ, USA) for 24 h.

    Techniques: Control, Binding Assay, Activity Assay, Comparison, ChIP-sequencing, Two Tailed Test

    p53 preferentially directs transcription initiation to the p53RE and other sites within 100 bp. ( A ) Positional p53 motif enrichment relative to the CAGE-seq-detected TSS (CTSS) identified by HOMER2. The density of CTSSs at ±200 bp around canonical p53REs of p53 binding sites in ( B ) Nutlin-3a and DMSO control samples and ( C ) the Nutlin-3a data separated by EpiMap-derived chromatin states. ( D ) Genome browser images displaying CAGE-seq data among p53 ChIP-seq, ATAC-seq, and CUT&Tag (H3K4me1 and H3K27ac) data at two p53 binding sites. The predicted p53RE is highlighted. p53 ChIP-seq, nucleosome-free ATAC-seq, and CUT&Tag data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS. CTSSs were coverage normalized. ( E ) Dynamic p53 binding is required for Pol II initiation after its recruitment to the edges of nucleosome-depleted regions.

    Journal: Nucleic Acids Research

    Article Title: p53 reveals principles of chromatin remodeling and enhancer activation

    doi: 10.1093/nar/gkaf465

    Figure Lengend Snippet: p53 preferentially directs transcription initiation to the p53RE and other sites within 100 bp. ( A ) Positional p53 motif enrichment relative to the CAGE-seq-detected TSS (CTSS) identified by HOMER2. The density of CTSSs at ±200 bp around canonical p53REs of p53 binding sites in ( B ) Nutlin-3a and DMSO control samples and ( C ) the Nutlin-3a data separated by EpiMap-derived chromatin states. ( D ) Genome browser images displaying CAGE-seq data among p53 ChIP-seq, ATAC-seq, and CUT&Tag (H3K4me1 and H3K27ac) data at two p53 binding sites. The predicted p53RE is highlighted. p53 ChIP-seq, nucleosome-free ATAC-seq, and CUT&Tag data were normalized to CPM. Mono-nucleosome ATAC-seq data were normalized by DANPOS. CTSSs were coverage normalized. ( E ) Dynamic p53 binding is required for Pol II initiation after its recruitment to the edges of nucleosome-depleted regions.

    Article Snippet: Cells were treated with Dimethylsulfoxid (DMSO) solvent control (0.15%; Carl Roth, Karlsruhe, Germany) or Nutlin-3a (10 μM; MedChemExpress, Monmouth Junction, NJ, USA) for 24 h.

    Techniques: Binding Assay, Control, Derivative Assay, ChIP-sequencing