Structured Review

Agilent technologies c18 column
Optimized chromatogram of flupirtine maleate (10.3 min) on a <t>C18</t> column
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1) Product Images from "Identification of Degradation Products and a Stability-Indicating RP-HPLC Method for the Determination of Flupirtine Maleate in Pharmaceutical Dosage Forms"

Article Title: Identification of Degradation Products and a Stability-Indicating RP-HPLC Method for the Determination of Flupirtine Maleate in Pharmaceutical Dosage Forms

Journal: Scientia Pharmaceutica

doi: 10.3797/scipharm.1310-01

Optimized chromatogram of flupirtine maleate (10.3 min) on a C18 column
Figure Legend Snippet: Optimized chromatogram of flupirtine maleate (10.3 min) on a C18 column

Techniques Used:

2) Product Images from "Identification of a dioxin-responsive oxylipin signature in roots of date palm: involvement of a 9-hydroperoxide fatty acid reductase, caleosin/peroxygenase PdPXG2"

Article Title: Identification of a dioxin-responsive oxylipin signature in roots of date palm: involvement of a 9-hydroperoxide fatty acid reductase, caleosin/peroxygenase PdPXG2

Journal: Scientific Reports

doi: 10.1038/s41598-018-31342-4

Catalytic properities of PdPXG2. ( A ) Fatty acid epoxidation activity of PdPXG2 as a function of carbon chain length and unsaturation degree of fatty acids. ( B ) Stereoselectivity of PdPXG2 towards the cis -double bond configuration in C16:1 or C18:1. PdPXG2 exhibited a strong stereoselectivity since no epoxidation was detected with UFAs having the double bond in trans -configuration regardless of the position (6, 9 or 11) of the cis -double bond in the carbon chain. ( C ) Epoxidation of [ 14 C]-labelled palmitic acid (C16:1) and oleic acid (C18:1) ( Cis -Δ9 for both) by recombinant PdPXG2 in the presence of various hydroperoxides; i.e. H 2 O 2 , 7-HpHxTrE, 11-HpHxTrE, 9-HpODE, 13-HpODE, 9-HpOTrE and 13-HpOTrE compared with cumene hydroperoxide (Cu-OOH). ( D ) The reductase activity of purified recombinant PdPXG2 against fatty acid hydroperoxides, 7-HpHxTrE, 11-HpHxTrE, 9-HpODE, 13-HpODE, 9-HpOTrE and 13-HpOTrE using a HPLC-UV-detector system. All measurements were in triplicate. Values are the means ± S.D. ( n = 3). * P
Figure Legend Snippet: Catalytic properities of PdPXG2. ( A ) Fatty acid epoxidation activity of PdPXG2 as a function of carbon chain length and unsaturation degree of fatty acids. ( B ) Stereoselectivity of PdPXG2 towards the cis -double bond configuration in C16:1 or C18:1. PdPXG2 exhibited a strong stereoselectivity since no epoxidation was detected with UFAs having the double bond in trans -configuration regardless of the position (6, 9 or 11) of the cis -double bond in the carbon chain. ( C ) Epoxidation of [ 14 C]-labelled palmitic acid (C16:1) and oleic acid (C18:1) ( Cis -Δ9 for both) by recombinant PdPXG2 in the presence of various hydroperoxides; i.e. H 2 O 2 , 7-HpHxTrE, 11-HpHxTrE, 9-HpODE, 13-HpODE, 9-HpOTrE and 13-HpOTrE compared with cumene hydroperoxide (Cu-OOH). ( D ) The reductase activity of purified recombinant PdPXG2 against fatty acid hydroperoxides, 7-HpHxTrE, 11-HpHxTrE, 9-HpODE, 13-HpODE, 9-HpOTrE and 13-HpOTrE using a HPLC-UV-detector system. All measurements were in triplicate. Values are the means ± S.D. ( n = 3). * P

Techniques Used: Activity Assay, Recombinant, Purification, High Performance Liquid Chromatography

3) Product Images from "Organ-Specific Analysis of Morus alba Using a Gel-Free/Label-Free Proteomic Technique"

Article Title: Organ-Specific Analysis of Morus alba Using a Gel-Free/Label-Free Proteomic Technique

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms20020365

Analysis of the metabolites in Morus leaf, branch, and root and their antioxidant activities. The methanol extracts from Morus leaf, branch, and root were analyzed by HPLC ( A ). A C18 column was used with a flow rate of 1 mL min −1 . The peaks were determined at a wavelength of 320 nm. For the determination of the antioxidant activities of Morus leaf, branch, and root, ABTS + scavenging, hydroxyl free radical, and O 2 − scavenging activities were analyzed ( B ). The data are shown as the mean ± SD from three independent biological replicates. Means with the same letter are not significantly different according to the one-way ANOVA test ( p
Figure Legend Snippet: Analysis of the metabolites in Morus leaf, branch, and root and their antioxidant activities. The methanol extracts from Morus leaf, branch, and root were analyzed by HPLC ( A ). A C18 column was used with a flow rate of 1 mL min −1 . The peaks were determined at a wavelength of 320 nm. For the determination of the antioxidant activities of Morus leaf, branch, and root, ABTS + scavenging, hydroxyl free radical, and O 2 − scavenging activities were analyzed ( B ). The data are shown as the mean ± SD from three independent biological replicates. Means with the same letter are not significantly different according to the one-way ANOVA test ( p

Techniques Used: High Performance Liquid Chromatography, Flow Cytometry

4) Product Images from "High-level expression of a novel liver-targeting fusion interferon with preferred Escherichia coli codon preference and its anti-hepatitis B virus activity in vivo"

Article Title: High-level expression of a novel liver-targeting fusion interferon with preferred Escherichia coli codon preference and its anti-hepatitis B virus activity in vivo

Journal: BMC Biotechnology

doi: 10.1186/s12896-015-0177-1

Characterization of recombinant protein by SDS-PAGE, western blot, RP-HPLC and MALDI-MS. a : Purification of IFN-CSP. Lane M: Protein molecular weight marker, Lane 1–2: Total proteins of E. coli BL21/pET-21b-IFN-CSP before and after induction, Lane 3–4: Supernatant and precipitation after ultrasonication and centrifugation. Lane 5: Purified IFN-CSP using trion and urea wash. Lane 6: Purified IFN-CSP using HiTrap affinity chromatography. b : IFN-CSP was analyzed by western blot. Lane M: Protein molecular weight marker. Lane 1–2: Total proteins of E. coli BL21/pET-21b-IFN-CSP before and after induction. c : Analysis of purified IFN-CSP by RP-HPLC with a C18 column. d : Mass spectrum of purified IFN-CSP recorded on an Applied Biosytems Voyager MALDI-TOF mass spectrometry
Figure Legend Snippet: Characterization of recombinant protein by SDS-PAGE, western blot, RP-HPLC and MALDI-MS. a : Purification of IFN-CSP. Lane M: Protein molecular weight marker, Lane 1–2: Total proteins of E. coli BL21/pET-21b-IFN-CSP before and after induction, Lane 3–4: Supernatant and precipitation after ultrasonication and centrifugation. Lane 5: Purified IFN-CSP using trion and urea wash. Lane 6: Purified IFN-CSP using HiTrap affinity chromatography. b : IFN-CSP was analyzed by western blot. Lane M: Protein molecular weight marker. Lane 1–2: Total proteins of E. coli BL21/pET-21b-IFN-CSP before and after induction. c : Analysis of purified IFN-CSP by RP-HPLC with a C18 column. d : Mass spectrum of purified IFN-CSP recorded on an Applied Biosytems Voyager MALDI-TOF mass spectrometry

Techniques Used: Recombinant, SDS Page, Western Blot, High Performance Liquid Chromatography, Mass Spectrometry, Purification, Molecular Weight, Marker, Positron Emission Tomography, Centrifugation, Affinity Chromatography

5) Product Images from "Differential tissue accumulation of 2,3,7,8-Tetrachlorinated dibenzo-p-dioxin in Arabidopsis thaliana affects plant chronology, lipid metabolism and seed yield"

Article Title: Differential tissue accumulation of 2,3,7,8-Tetrachlorinated dibenzo-p-dioxin in Arabidopsis thaliana affects plant chronology, lipid metabolism and seed yield

Journal: BMC Plant Biology

doi: 10.1186/s12870-015-0583-5

Lipid peroxidation as response to TCDD-exposure. a . Content of major C18-fatty acids (%) in Arabidopsis shoot on day 36 after exposure to TCDD at indicated doses. b . Total hydroperoxides produced by untreated and TCDD-treated Arabidopsis tissues was monitored using FOX-1 assay at various stage of development. Three independent plants were examined at each concentration of TCDD. Three measurements were taken per extract. Data are mean values ± SD ( n = 6). FW: fresh weight. Statistical significance of the data was evaluated by ANOVA analysis. Asterisks indicate significant differences in lipid peroxides according to the plant age compared to germination stage (6 days): * P
Figure Legend Snippet: Lipid peroxidation as response to TCDD-exposure. a . Content of major C18-fatty acids (%) in Arabidopsis shoot on day 36 after exposure to TCDD at indicated doses. b . Total hydroperoxides produced by untreated and TCDD-treated Arabidopsis tissues was monitored using FOX-1 assay at various stage of development. Three independent plants were examined at each concentration of TCDD. Three measurements were taken per extract. Data are mean values ± SD ( n = 6). FW: fresh weight. Statistical significance of the data was evaluated by ANOVA analysis. Asterisks indicate significant differences in lipid peroxides according to the plant age compared to germination stage (6 days): * P

Techniques Used: Produced, Concentration Assay

6) Product Images from "Identification of a dioxin-responsive oxylipin signature in roots of date palm: involvement of a 9-hydroperoxide fatty acid reductase, caleosin/peroxygenase PdPXG2"

Article Title: Identification of a dioxin-responsive oxylipin signature in roots of date palm: involvement of a 9-hydroperoxide fatty acid reductase, caleosin/peroxygenase PdPXG2

Journal: Scientific Reports

doi: 10.1038/s41598-018-31342-4

Catalytic properities of PdPXG2. ( A ) Fatty acid epoxidation activity of PdPXG2 as a function of carbon chain length and unsaturation degree of fatty acids. ( B ) Stereoselectivity of PdPXG2 towards the cis -double bond configuration in C16:1 or C18:1. PdPXG2 exhibited a strong stereoselectivity since no epoxidation was detected with UFAs having the double bond in trans -configuration regardless of the position (6, 9 or 11) of the cis -double bond in the carbon chain. ( C ) Epoxidation of [ 14 C]-labelled palmitic acid (C16:1) and oleic acid (C18:1) ( Cis -Δ9 for both) by recombinant PdPXG2 in the presence of various hydroperoxides; i.e. H 2 O 2 , 7-HpHxTrE, 11-HpHxTrE, 9-HpODE, 13-HpODE, 9-HpOTrE and 13-HpOTrE compared with cumene hydroperoxide (Cu-OOH). ( D ) The reductase activity of purified recombinant PdPXG2 against fatty acid hydroperoxides, 7-HpHxTrE, 11-HpHxTrE, 9-HpODE, 13-HpODE, 9-HpOTrE and 13-HpOTrE using a HPLC-UV-detector system. All measurements were in triplicate. Values are the means ± S.D. ( n = 3). * P
Figure Legend Snippet: Catalytic properities of PdPXG2. ( A ) Fatty acid epoxidation activity of PdPXG2 as a function of carbon chain length and unsaturation degree of fatty acids. ( B ) Stereoselectivity of PdPXG2 towards the cis -double bond configuration in C16:1 or C18:1. PdPXG2 exhibited a strong stereoselectivity since no epoxidation was detected with UFAs having the double bond in trans -configuration regardless of the position (6, 9 or 11) of the cis -double bond in the carbon chain. ( C ) Epoxidation of [ 14 C]-labelled palmitic acid (C16:1) and oleic acid (C18:1) ( Cis -Δ9 for both) by recombinant PdPXG2 in the presence of various hydroperoxides; i.e. H 2 O 2 , 7-HpHxTrE, 11-HpHxTrE, 9-HpODE, 13-HpODE, 9-HpOTrE and 13-HpOTrE compared with cumene hydroperoxide (Cu-OOH). ( D ) The reductase activity of purified recombinant PdPXG2 against fatty acid hydroperoxides, 7-HpHxTrE, 11-HpHxTrE, 9-HpODE, 13-HpODE, 9-HpOTrE and 13-HpOTrE using a HPLC-UV-detector system. All measurements were in triplicate. Values are the means ± S.D. ( n = 3). * P

Techniques Used: Activity Assay, Recombinant, Purification, High Performance Liquid Chromatography

Quantification of PdPXG2-derivatives oxylipins in the date palm root after exposure to TCDD. ( A ) Amounts of fatty acid hydroperoxides (-OOH), expressed as ng mg −1 FW (fresh weight), resulting from oxygenation of C16:3, C18:2 and C18:3 under the action of 9-LOX, 13-LOX or α-DIOX in roots of date palm after exposure to TCDD at 10 ng.L −1 (light-red columns) or 50 ng.L −1 (dark -red columns) compared with control (light-green columns). ( B ) Amounts of fatty acid hydroxides (-OH) resulting from reduction of the indicated hydroperoxides in root tissues after exposure to TCDD compared with controls. ( C ) Amounts of mono- and di-epoxy fatty acids formed from C14:1, C16:1, C16:3, C18:1, C18:2 and C18:3 in root tissues in response to TCDD-exposure. ( D ) Amounts of di- and tri-hydroxy of C16:1, C16:3, C18:1, C18:2 and C18:3 in the same samples. ( E ) Overall evaluation of the quantitative areas covered by TCDD-induced oxylipin congeners after administration of a high (dark -red) or a low dose (light-red) of TCDD. All measurements were done in triplicate. Values are the means ± S.D. ( n = 3). * P
Figure Legend Snippet: Quantification of PdPXG2-derivatives oxylipins in the date palm root after exposure to TCDD. ( A ) Amounts of fatty acid hydroperoxides (-OOH), expressed as ng mg −1 FW (fresh weight), resulting from oxygenation of C16:3, C18:2 and C18:3 under the action of 9-LOX, 13-LOX or α-DIOX in roots of date palm after exposure to TCDD at 10 ng.L −1 (light-red columns) or 50 ng.L −1 (dark -red columns) compared with control (light-green columns). ( B ) Amounts of fatty acid hydroxides (-OH) resulting from reduction of the indicated hydroperoxides in root tissues after exposure to TCDD compared with controls. ( C ) Amounts of mono- and di-epoxy fatty acids formed from C14:1, C16:1, C16:3, C18:1, C18:2 and C18:3 in root tissues in response to TCDD-exposure. ( D ) Amounts of di- and tri-hydroxy of C16:1, C16:3, C18:1, C18:2 and C18:3 in the same samples. ( E ) Overall evaluation of the quantitative areas covered by TCDD-induced oxylipin congeners after administration of a high (dark -red) or a low dose (light-red) of TCDD. All measurements were done in triplicate. Values are the means ± S.D. ( n = 3). * P

Techniques Used:

7) Product Images from "Clove Extract Inhibits Tumor Growth and Promotes Cell Cycle Arrest and Apoptosis"

Article Title: Clove Extract Inhibits Tumor Growth and Promotes Cell Cycle Arrest and Apoptosis

Journal: Oncology research

doi: 10.3727/096504014X13946388748910

HPLC-UV analysis of EAEC. EAEC (A) and a mixture of analytical standards (B) were resuspended in 60% methanol, injected onto an Agilent Zorbax Eclipse XDB-C18 column, and detected at 210 nm. Retention times for eugenol, OA, and UA were 5.39, 36.3, and
Figure Legend Snippet: HPLC-UV analysis of EAEC. EAEC (A) and a mixture of analytical standards (B) were resuspended in 60% methanol, injected onto an Agilent Zorbax Eclipse XDB-C18 column, and detected at 210 nm. Retention times for eugenol, OA, and UA were 5.39, 36.3, and

Techniques Used: High Performance Liquid Chromatography, Injection

8) Product Images from "Smart Method for Carotenoids Characterization in Haematococcus pluvialis Red Phase and Evaluation of Astaxanthin Thermal Stability"

Article Title: Smart Method for Carotenoids Characterization in Haematococcus pluvialis Red Phase and Evaluation of Astaxanthin Thermal Stability

Journal: Antioxidants

doi: 10.3390/antiox9050422

Chromatogram of the H. pluvialis sample analyzed and related absorption spectra of all-trans-astaxanthin, 9-cis astaxanthin, 13-cis astaxanthin, lutein, and β-carotene. Operative condition: Zorbax reverse phase C18 column with 0.4 mL/min of methanol/water (95:5, v/v ) as a mobile phase.
Figure Legend Snippet: Chromatogram of the H. pluvialis sample analyzed and related absorption spectra of all-trans-astaxanthin, 9-cis astaxanthin, 13-cis astaxanthin, lutein, and β-carotene. Operative condition: Zorbax reverse phase C18 column with 0.4 mL/min of methanol/water (95:5, v/v ) as a mobile phase.

Techniques Used:

9) Product Images from "Construction of a Novel Liver-Targeting Fusion Interferon by Incorporation of a Plasmodium Region I-Plus Peptide"

Article Title: Construction of a Novel Liver-Targeting Fusion Interferon by Incorporation of a Plasmodium Region I-Plus Peptide

Journal: BioMed Research International

doi: 10.1155/2014/261631

RP-HPLC analysis of purified fusion protein IFN-CSP with a C18 column.
Figure Legend Snippet: RP-HPLC analysis of purified fusion protein IFN-CSP with a C18 column.

Techniques Used: High Performance Liquid Chromatography, Purification

10) Product Images from "Zanthoxylum alkylamides ameliorate protein metabolism disorder in STZ-induced diabetic rats"

Article Title: Zanthoxylum alkylamides ameliorate protein metabolism disorder in STZ-induced diabetic rats

Journal: Journal of Molecular Endocrinology

doi: 10.1530/JME-16-0218

HPLC analysis of Zanthoxylum alkylamides. Exactly 0.05 mg alkylamides dried by nitrogen was dissolved in methanol at a volume of 5 mL and filtered through 0.45 µm microporous membrane. The samples were applied to a C18 column (4.6 mm × 250 mm, 5 µm, Agilent). Mobile phase A had 50% water, and mobile phase B had 50% methanol. The flow rate was 1 mL/min, sample volume 10 µL, column temperature 40°C and ultraviolet detection wavelength 254 nm.
Figure Legend Snippet: HPLC analysis of Zanthoxylum alkylamides. Exactly 0.05 mg alkylamides dried by nitrogen was dissolved in methanol at a volume of 5 mL and filtered through 0.45 µm microporous membrane. The samples were applied to a C18 column (4.6 mm × 250 mm, 5 µm, Agilent). Mobile phase A had 50% water, and mobile phase B had 50% methanol. The flow rate was 1 mL/min, sample volume 10 µL, column temperature 40°C and ultraviolet detection wavelength 254 nm.

Techniques Used: High Performance Liquid Chromatography, Flow Cytometry

11) Product Images from "Recombinant Expression and Functional Characterization of Martentoxin: A Selective Inhibitor for BK Channel (? + ?4)"

Article Title: Recombinant Expression and Functional Characterization of Martentoxin: A Selective Inhibitor for BK Channel (? + ?4)

Journal: Toxins

doi: 10.3390/toxins6041419

RP-HPLC chromatography and mass spectra of rMarTX. ( A ) RP-HPLC chromatography of native MarTX on a C18 column using a linear gradient of 5%–95% acetonitrile with 0.1% trifluoroacetic acid (TFA) in 60 min at a constant flow rate of 1 mL/min, and detected at 230 nm; ( B ) RP-HPLC chromatography of rMarTX under the same condition; ( C ) Mass spectra of purified rMarTX. The calculated theoretical molecular weight of rMarTX was 4060 Da [ 17 ] and the measured molecular weight was 4059.06 Da.
Figure Legend Snippet: RP-HPLC chromatography and mass spectra of rMarTX. ( A ) RP-HPLC chromatography of native MarTX on a C18 column using a linear gradient of 5%–95% acetonitrile with 0.1% trifluoroacetic acid (TFA) in 60 min at a constant flow rate of 1 mL/min, and detected at 230 nm; ( B ) RP-HPLC chromatography of rMarTX under the same condition; ( C ) Mass spectra of purified rMarTX. The calculated theoretical molecular weight of rMarTX was 4060 Da [ 17 ] and the measured molecular weight was 4059.06 Da.

Techniques Used: High Performance Liquid Chromatography, Chromatography, Flow Cytometry, Purification, Molecular Weight

12) Product Images from "Interspecies Anticancer and Antimicrobial Activities of Genus Solanum and Estimation of Rutin by Validated UPLC-PDA Method"

Article Title: Interspecies Anticancer and Antimicrobial Activities of Genus Solanum and Estimation of Rutin by Validated UPLC-PDA Method

Journal: Evidence-based Complementary and Alternative Medicine : eCAM

doi: 10.1155/2018/6040815

Representative chromatogram of rutin estimation in the ethanol extracts of Solanum species [Conditions: Eclipse XDB 80Å C18 column (4.6 × 100 mm, 3.5 μ m); mobile phase, acetonitrile: water (gradient system); flow rate, 0.18 mL/min; λ max = 332 nm at temperature (25 ± 1°C)]. (a) Representative chromatogram of SCEE showing rutin at Rt = 4.189 min. (b) Representative chromatogram SGEE showing rutin at Rt = 4.111 min. (c) Representative chromatogram of SIEE showing rutin at Rt = 4.147 min. (d) Representative chromatogram of SSEE showing rutin at Rt = 4.194 min. (e) Representative chromatogram of SNEE showing rutin at Rt = 4.112 min. (f) Representative chromatogram of SVEE showing rutin at Rt = 4.165 min.
Figure Legend Snippet: Representative chromatogram of rutin estimation in the ethanol extracts of Solanum species [Conditions: Eclipse XDB 80Å C18 column (4.6 × 100 mm, 3.5 μ m); mobile phase, acetonitrile: water (gradient system); flow rate, 0.18 mL/min; λ max = 332 nm at temperature (25 ± 1°C)]. (a) Representative chromatogram of SCEE showing rutin at Rt = 4.189 min. (b) Representative chromatogram SGEE showing rutin at Rt = 4.111 min. (c) Representative chromatogram of SIEE showing rutin at Rt = 4.147 min. (d) Representative chromatogram of SSEE showing rutin at Rt = 4.194 min. (e) Representative chromatogram of SNEE showing rutin at Rt = 4.112 min. (f) Representative chromatogram of SVEE showing rutin at Rt = 4.165 min.

Techniques Used: Flow Cytometry

Representative chromatogram of rutin showing retention time at 4.172 min [Conditions: Eclipse XDB 80Å C18 column (4.6 × 100 mm, 3.5 μ m); mobile phase, acetonitrile: water (gradient system); flow rate, 0.18 mL/min; λ max = 332 nm at temperature (25 ± 1°C)].
Figure Legend Snippet: Representative chromatogram of rutin showing retention time at 4.172 min [Conditions: Eclipse XDB 80Å C18 column (4.6 × 100 mm, 3.5 μ m); mobile phase, acetonitrile: water (gradient system); flow rate, 0.18 mL/min; λ max = 332 nm at temperature (25 ± 1°C)].

Techniques Used: Flow Cytometry

13) Product Images from "Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity"

Article Title: Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity

Journal: bioRxiv

doi: 10.1101/2020.08.11.243204

Schematic overview of the cryo-EM single particle data processing workflow. For an accompanying detailed description, please see the Methods. Blue text indicates the software used for each step. (A) 8120 frame stacks were aligned and dose filtered ( Zheng et al., 2017 ), subjected to CTF estimation ( Zhang, 2016 ), and then ~337,000 particles (Dataset-A) were extracted by deep learning-based automated picking ( Wagner et al., 2019 ). One round of 2D classification reduced the dataset to ~263,000 particles (Dataset-B). (B) Stochastic gradient decent (SGD) and 3D classification were applied to a subset of Dataset-B to generate C15 and C17 starting maps ab initio , without prior reference ( Zivanov et al., 2018 ). (C) 3D classification of the full Dataset-B using these ab initio references and enforced symmetry split the dataset into C15 and C17 classes. (D) Subsequent rounds of 3D classification yielded classes for C14-C18 symmetries. (E) These were refined to produce final averages for Dataset-B. (F-G) The Dataset-B maps of five symmetries were used for several iterative rounds of 3D classification on Dataset-A, yielding classes of C14-C18 with more particles. (H) 3D refinement of these classes included iterative rounds of RELION 3D auto-refinement ( Scheres, 2012 ), per-particle defocus estimation (CTF refinement) ( Zivanov et al., 2018 ), and per-particle motion correction and dose-weighting (Bayesian polishing) ( Zivanov et al., 2019 ). (I) The resulting final EM density maps of C14-C18 rings had resolutions ranging from 3.8 Å to 5.0 Å, as judged by “gold standard” Fourier shell correlation (FSC) comparing independently refined half-maps (see Fig. S3A ).
Figure Legend Snippet: Schematic overview of the cryo-EM single particle data processing workflow. For an accompanying detailed description, please see the Methods. Blue text indicates the software used for each step. (A) 8120 frame stacks were aligned and dose filtered ( Zheng et al., 2017 ), subjected to CTF estimation ( Zhang, 2016 ), and then ~337,000 particles (Dataset-A) were extracted by deep learning-based automated picking ( Wagner et al., 2019 ). One round of 2D classification reduced the dataset to ~263,000 particles (Dataset-B). (B) Stochastic gradient decent (SGD) and 3D classification were applied to a subset of Dataset-B to generate C15 and C17 starting maps ab initio , without prior reference ( Zivanov et al., 2018 ). (C) 3D classification of the full Dataset-B using these ab initio references and enforced symmetry split the dataset into C15 and C17 classes. (D) Subsequent rounds of 3D classification yielded classes for C14-C18 symmetries. (E) These were refined to produce final averages for Dataset-B. (F-G) The Dataset-B maps of five symmetries were used for several iterative rounds of 3D classification on Dataset-A, yielding classes of C14-C18 with more particles. (H) 3D refinement of these classes included iterative rounds of RELION 3D auto-refinement ( Scheres, 2012 ), per-particle defocus estimation (CTF refinement) ( Zivanov et al., 2018 ), and per-particle motion correction and dose-weighting (Bayesian polishing) ( Zivanov et al., 2019 ). (I) The resulting final EM density maps of C14-C18 rings had resolutions ranging from 3.8 Å to 5.0 Å, as judged by “gold standard” Fourier shell correlation (FSC) comparing independently refined half-maps (see Fig. S3A ).

Techniques Used: Software

VIPP1 monomer flexibility across ring layers and symmetries. Accompanies Fig. 1I-K . (A, inset) VIPP1 monomers have four regions of flexibility (F1-F4). (A) All four regions flex to build a ring: VIPP1 monomers from each layer superimposed for rings of each symmetry. In layer 1, part of H4/5 is remodeled into a coil (see Fig. S8 ). The color scheme matches Figs. 1 and S4 . (B) Only F3 flexes to accommodate different symmetries: superposition of VIPP1 monomers from the same layers across all five symmetries (five shades of color, with C14 the darkest and C18 the lightest).
Figure Legend Snippet: VIPP1 monomer flexibility across ring layers and symmetries. Accompanies Fig. 1I-K . (A, inset) VIPP1 monomers have four regions of flexibility (F1-F4). (A) All four regions flex to build a ring: VIPP1 monomers from each layer superimposed for rings of each symmetry. In layer 1, part of H4/5 is remodeled into a coil (see Fig. S8 ). The color scheme matches Figs. 1 and S4 . (B) Only F3 flexes to accommodate different symmetries: superposition of VIPP1 monomers from the same layers across all five symmetries (five shades of color, with C14 the darkest and C18 the lightest).

Techniques Used:

VIPP1 monomers interweave and flex to form basket-like ring structures. (A) Inclined and (B) side views of the cryo-EM density map for a syn VIPP1 ring with C16 symmetry. The ring consists of six layers shown in different colors (layer 1: olive green, layer 6: orange). Two shades of each color highlight the interwoven structure. (C) Cut-open view of the ring reveals how the H1 helices of each monomer align to form vertical columns that face toward the lumen. (D) Inclined and (E) side views of layer 3, shown in isolation to visualize the way VIPP1 monomers (in four shades of blue) extend and interact. (F) Schematic diagram of the VIPP1 monomer’s secondary structure elements (helices H1-H7 in colored rectangles) and (G) the corresponding regions on the VIPP1 molecular model, fit into the EM density (transparent white). The C-terminal domain (dashed line box), which includes H7, was not resolved in the EM density map, likely due to high flexibility. Magnified view of two regions of the monomer structure (H1 and the loop connecting H3 with H4), showing the fit of the VIPP1 model into the EM density map. (H) Cryo-EM VIPP1 ring structures for five symmetries (C14-C18). (I) Comparing the molecular models of these structures (see Figs. S4 , S7 ) revealed four regions of flexibility in the VIPP1 monomer (F1-F4). (J) Superposition of the VIPP1 monomers from each layer of the C16 ring. F1-F4 all flex to assemble the ring. The N-terminal side of H4/5 is remodeled into a coil in layer 1 (see Fig. S8 ). (K) Superposition of the VIPP1 monomers from layer 3 of each symmetry (C14: darkest blue, C18: lightest blues). Only the F3 loop flexes to accommodate different ring symmetries.
Figure Legend Snippet: VIPP1 monomers interweave and flex to form basket-like ring structures. (A) Inclined and (B) side views of the cryo-EM density map for a syn VIPP1 ring with C16 symmetry. The ring consists of six layers shown in different colors (layer 1: olive green, layer 6: orange). Two shades of each color highlight the interwoven structure. (C) Cut-open view of the ring reveals how the H1 helices of each monomer align to form vertical columns that face toward the lumen. (D) Inclined and (E) side views of layer 3, shown in isolation to visualize the way VIPP1 monomers (in four shades of blue) extend and interact. (F) Schematic diagram of the VIPP1 monomer’s secondary structure elements (helices H1-H7 in colored rectangles) and (G) the corresponding regions on the VIPP1 molecular model, fit into the EM density (transparent white). The C-terminal domain (dashed line box), which includes H7, was not resolved in the EM density map, likely due to high flexibility. Magnified view of two regions of the monomer structure (H1 and the loop connecting H3 with H4), showing the fit of the VIPP1 model into the EM density map. (H) Cryo-EM VIPP1 ring structures for five symmetries (C14-C18). (I) Comparing the molecular models of these structures (see Figs. S4 , S7 ) revealed four regions of flexibility in the VIPP1 monomer (F1-F4). (J) Superposition of the VIPP1 monomers from each layer of the C16 ring. F1-F4 all flex to assemble the ring. The N-terminal side of H4/5 is remodeled into a coil in layer 1 (see Fig. S8 ). (K) Superposition of the VIPP1 monomers from layer 3 of each symmetry (C14: darkest blue, C18: lightest blues). Only the F3 loop flexes to accommodate different ring symmetries.

Techniques Used: Isolation

Molecular modeling for VIPP1 rings of each symmetry. (A) Cryo-EM density maps and (B) corresponding molecular models for five different symmetries of VIPP1 rings. Density maps for C14, C15 and C16 have six layers, whereas C17 and C18 have seven layers (only the first six layers from the top could be modeled due to the low resolution of layer 7). (C) One vertical row of monomers is displayed, showing the inclination of H1 (left side) and H6 (right side) for each ring structure. (D-E) For each Vipp1 structure, the inclination of H6 was measured as the angle relative to the horizontal plane of the ring. (E) Plot of the mean (dot) and standard deviation (error bars) from all symmetries. (F) Plot showing the diameter of each layer from the structures of each symmetry. Diameters were measured from the outer walls of the rings. Note that layer 7 was only observed in the C17 and C18 rings.
Figure Legend Snippet: Molecular modeling for VIPP1 rings of each symmetry. (A) Cryo-EM density maps and (B) corresponding molecular models for five different symmetries of VIPP1 rings. Density maps for C14, C15 and C16 have six layers, whereas C17 and C18 have seven layers (only the first six layers from the top could be modeled due to the low resolution of layer 7). (C) One vertical row of monomers is displayed, showing the inclination of H1 (left side) and H6 (right side) for each ring structure. (D-E) For each Vipp1 structure, the inclination of H6 was measured as the angle relative to the horizontal plane of the ring. (E) Plot of the mean (dot) and standard deviation (error bars) from all symmetries. (F) Plot showing the diameter of each layer from the structures of each symmetry. Diameters were measured from the outer walls of the rings. Note that layer 7 was only observed in the C17 and C18 rings.

Techniques Used: Standard Deviation

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Article Snippet: .. The digestion of alkylated GeXXVIIA-L was carried out in 100 mM Tris-HCl, pH 8.5, using 3 μg/mL Asp-N (Sigma, St Louis, MO, USA) at 37 °C for 18 h. The digested products were separated on a ZORBAX C18 HPLC analytical column (4.6 × 250 mm, Agilent). .. Oocyte Two-Electrode-Voltage Clamp Recordings Oocyte preparation, RNA preparation, and expression of nAChR subunits in Xenopus oocytes were performed as described previously [ ].

Article Title: Cancer-targeted design of bioresponsive prodrug with enhanced cellular uptake to achieve precise cancer therapy
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Article Title: Development of a selective agonist for relaxin family peptide receptor 3
Article Snippet: .. Finally, mature R3/I5 mutants were purified by HPLC using an analytical C18 reverse-phase column (Zorbax 300SB-C18, 4.6 × 250 mm, Agilent Technology) and their identity confirmed by electrospray mass spectrometry on a QTRAP mass spectrometer (Applied Biosystems, Foster City, CA, USA). .. Circular dichroism spectroscopy Mature R3/I5 mutants were dissolved in 1.0 mM aqueous hydrochloride solution (pH 3.0) and their concentrations were determined by absorbance at 280 nm using an extinction coefficient (ε280nm ) of 7365 M−1 ·cm−1 .

Article Title: DigiFab Interacts With Endogenous Cardiotonic Steroids and Reverses Preeclampsia-Induced Na/K-ATPase Inhibition
Article Snippet: .. Plasma samples of 250 μL from each group were pooled, extracted on C-18 cartridges as above, dried, reconstituted in 10% acetonitrile, and fractionated on Agilent 1100 series HPLC system using Agilent Zorbax Eclipse XDB-C18 (Agilent Technologies, Palo Alto, California), 4.6 × 150 mm, 5 μm particle size, 80 Å column, flow rate 1 mL/min, in linear (10%-85.5%) gradient of acetonitrile against 0.1% trifluoroacetic acid for 45 minutes. .. Thirty 1.5-minute fractions were collected and analyzed for MBG immunoreactivity using assays based on 4G4 anti-MBG mAb (above) and on 3E9 anti-MBG mAb, an antibody reported previously to reduce blood pressure in experimental hypertension and to ex vivo reverse PE-induced NKA inhibition, and digoxin-like immunoreactivity using assays based on Digibind and DigiFab.

Article Title: Mechanism for insulin-like peptide 5 distinguishing the homologous relaxin family peptide receptor 3 and 4
Article Snippet: .. Thereafter, the purified folded precursors were sequentially treated with endoproteinase Lys-C and carboxypeptidase B (papaya glutaminyl cyclase was also used for the R3/I5 mutants) according to our previous procedure , and the resultant two-chain INSL5 and R3/I5 mutants were purified by HPLC using an analytical C18 reverse-phase column (Zorbax 300SB-C18, 4.6 × 250 mm, from Agilent Technology). .. The fraction of mature mutant eluted by an acidic acetonitrile gradient was manually collected, lyophilized, and subjected to mass spectrometry analysis.

Flow Cytometry:

Article Title: Synthesis of new potent agonistic analogs of growth hormone-releasing hormone (GHRH) and evaluation of their endocrine and cardiac activities
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Article Title: DigiFab Interacts With Endogenous Cardiotonic Steroids and Reverses Preeclampsia-Induced Na/K-ATPase Inhibition
Article Snippet: .. Plasma samples of 250 μL from each group were pooled, extracted on C-18 cartridges as above, dried, reconstituted in 10% acetonitrile, and fractionated on Agilent 1100 series HPLC system using Agilent Zorbax Eclipse XDB-C18 (Agilent Technologies, Palo Alto, California), 4.6 × 150 mm, 5 μm particle size, 80 Å column, flow rate 1 mL/min, in linear (10%-85.5%) gradient of acetonitrile against 0.1% trifluoroacetic acid for 45 minutes. .. Thirty 1.5-minute fractions were collected and analyzed for MBG immunoreactivity using assays based on 4G4 anti-MBG mAb (above) and on 3E9 anti-MBG mAb, an antibody reported previously to reduce blood pressure in experimental hypertension and to ex vivo reverse PE-induced NKA inhibition, and digoxin-like immunoreactivity using assays based on Digibind and DigiFab.

Mass Spectrometry:

Article Title: Development of a selective agonist for relaxin family peptide receptor 3
Article Snippet: .. Finally, mature R3/I5 mutants were purified by HPLC using an analytical C18 reverse-phase column (Zorbax 300SB-C18, 4.6 × 250 mm, Agilent Technology) and their identity confirmed by electrospray mass spectrometry on a QTRAP mass spectrometer (Applied Biosystems, Foster City, CA, USA). .. Circular dichroism spectroscopy Mature R3/I5 mutants were dissolved in 1.0 mM aqueous hydrochloride solution (pH 3.0) and their concentrations were determined by absorbance at 280 nm using an extinction coefficient (ε280nm ) of 7365 M−1 ·cm−1 .

Chromatography:

Article Title: Detection of 7-Dehydrocholesterol and Vitamin D3 Derivatives in Honey
Article Snippet: .. Chromatography for LC-MS was performed using a Zorbax Eclipse Plus C18 column (2.1 × 50 mm, 1.8 μm) (Agilent Technology, Santa Clara, CA, USA), an ACQUITY UPLC BEH C18 column (2.1 × 50 mm, 1.7 μm), an Atlantis C18 column (100 × 4.6 mm, 5 μm) (Waters, Milford, MA, USA) or a Pursuit 200Å PFP column (4.6 × 150 mm, 5 µm) (Agilent Technology, Santa Clara, CA, USA). ..

Purification:

Article Title: Development of a selective agonist for relaxin family peptide receptor 3
Article Snippet: .. Finally, mature R3/I5 mutants were purified by HPLC using an analytical C18 reverse-phase column (Zorbax 300SB-C18, 4.6 × 250 mm, Agilent Technology) and their identity confirmed by electrospray mass spectrometry on a QTRAP mass spectrometer (Applied Biosystems, Foster City, CA, USA). .. Circular dichroism spectroscopy Mature R3/I5 mutants were dissolved in 1.0 mM aqueous hydrochloride solution (pH 3.0) and their concentrations were determined by absorbance at 280 nm using an extinction coefficient (ε280nm ) of 7365 M−1 ·cm−1 .

Article Title: Mechanism for insulin-like peptide 5 distinguishing the homologous relaxin family peptide receptor 3 and 4
Article Snippet: .. Thereafter, the purified folded precursors were sequentially treated with endoproteinase Lys-C and carboxypeptidase B (papaya glutaminyl cyclase was also used for the R3/I5 mutants) according to our previous procedure , and the resultant two-chain INSL5 and R3/I5 mutants were purified by HPLC using an analytical C18 reverse-phase column (Zorbax 300SB-C18, 4.6 × 250 mm, from Agilent Technology). .. The fraction of mature mutant eluted by an acidic acetonitrile gradient was manually collected, lyophilized, and subjected to mass spectrometry analysis.

Liquid Chromatography with Mass Spectroscopy:

Article Title: Detection of 7-Dehydrocholesterol and Vitamin D3 Derivatives in Honey
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  • 90
    Agilent technologies extend c18 column
    Fingerprint analysis of aqueous extract of CS. HPLC of CS aqueous extract is plotted at 265 nm, using an <t>extend-C18</t> column and gradient elution with methanol and 0.1% phosphoric acid. The peak identifications are rutin (A), quercetin (B), and kaempferol (C).
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    93
    Agilent technologies c18 trap column
    HPLC separation in combination with mass spectrometry for Embp identification. The proteins in the culture supernatants of S. epidermidis (ATCC12228) were separated by reversed-phase HPLC using a LUNA <t>C18</t> 5 μm column. ( a ) Twelve fractions were collected after HPLC separation. The HI activity of the eluted proteins (100 μl) in each fraction was tested using A/San Diego/1/09(H1N1 pdm09) as the virus antigen. ( b ) Tryptic digests of proteins in fraction 12 of the HLPC separation, which showed the greatest HI activity, were subjected to Nano-LC-LTQ MS/MS. A sequenced peptide (SINAYNKAIQSLETQITSAKDN) is shown and was identified as an internal peptide of Embp (Q8CP76). The m/z value of each “y” and “b” ion in collision-induced dissociation (CID) spectra is indicated.
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    85
    Agilent technologies c18 rp guard column
    Inhibition of 3CL Pro activity by HPLC assay. Injection of 40 µl of incubation samples for <t>C18</t> reverse phase column analysis. The substrate or product fragment peaks were analyzed by HPLC with UV absorbance detection at 214 nm. The HPLC system is described in Methods.
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    Fingerprint analysis of aqueous extract of CS. HPLC of CS aqueous extract is plotted at 265 nm, using an extend-C18 column and gradient elution with methanol and 0.1% phosphoric acid. The peak identifications are rutin (A), quercetin (B), and kaempferol (C).

    Journal: Evidence-based Complementary and Alternative Medicine : eCAM

    Article Title: Chimonanthus nitens var. salicifolius Aqueous Extract Protects against 5-Fluorouracil Induced Gastrointestinal Mucositis in a Mouse Model

    doi: 10.1155/2013/789263

    Figure Lengend Snippet: Fingerprint analysis of aqueous extract of CS. HPLC of CS aqueous extract is plotted at 265 nm, using an extend-C18 column and gradient elution with methanol and 0.1% phosphoric acid. The peak identifications are rutin (A), quercetin (B), and kaempferol (C).

    Article Snippet: An extend-C18 column (150 nm ∗ 4.6 mm, Agilent, Germany) was used for separation and the temperature was maintained at 25°C.

    Techniques: High Performance Liquid Chromatography

    Optimized chromatogram of flupirtine maleate (10.3 min) on a C18 column

    Journal: Scientia Pharmaceutica

    Article Title: Identification of Degradation Products and a Stability-Indicating RP-HPLC Method for the Determination of Flupirtine Maleate in Pharmaceutical Dosage Forms

    doi: 10.3797/scipharm.1310-01

    Figure Lengend Snippet: Optimized chromatogram of flupirtine maleate (10.3 min) on a C18 column

    Article Snippet: Method Development and Optimization of the Chromatographic Conditions In preliminary experiments, the drug was subjected to the reversed-phase mode using a C18 column (Agilent, 250 × 4.6 mm, 5μ) and mobile phases consisting of water (pH 3.0 adjusted with orthophosphoric acid) and methanol by varying the % aqueous phase from 10% to 30%.

    Techniques:

    HPLC separation in combination with mass spectrometry for Embp identification. The proteins in the culture supernatants of S. epidermidis (ATCC12228) were separated by reversed-phase HPLC using a LUNA C18 5 μm column. ( a ) Twelve fractions were collected after HPLC separation. The HI activity of the eluted proteins (100 μl) in each fraction was tested using A/San Diego/1/09(H1N1 pdm09) as the virus antigen. ( b ) Tryptic digests of proteins in fraction 12 of the HLPC separation, which showed the greatest HI activity, were subjected to Nano-LC-LTQ MS/MS. A sequenced peptide (SINAYNKAIQSLETQITSAKDN) is shown and was identified as an internal peptide of Embp (Q8CP76). The m/z value of each “y” and “b” ion in collision-induced dissociation (CID) spectra is indicated.

    Journal: Scientific Reports

    Article Title: Nasal commensal Staphylococcus epidermidis counteracts influenza virus

    doi: 10.1038/srep27870

    Figure Lengend Snippet: HPLC separation in combination with mass spectrometry for Embp identification. The proteins in the culture supernatants of S. epidermidis (ATCC12228) were separated by reversed-phase HPLC using a LUNA C18 5 μm column. ( a ) Twelve fractions were collected after HPLC separation. The HI activity of the eluted proteins (100 μl) in each fraction was tested using A/San Diego/1/09(H1N1 pdm09) as the virus antigen. ( b ) Tryptic digests of proteins in fraction 12 of the HLPC separation, which showed the greatest HI activity, were subjected to Nano-LC-LTQ MS/MS. A sequenced peptide (SINAYNKAIQSLETQITSAKDN) is shown and was identified as an internal peptide of Embp (Q8CP76). The m/z value of each “y” and “b” ion in collision-induced dissociation (CID) spectra is indicated.

    Article Snippet: The automated Nano-LC-LTQ MS/MS setup consisted of an Eksigent Nano 2D LC system, a switch valve, a C18 trap column (Agilent, Santa Clara, CA), and a capillary reversed-phase column (10 cm in length, 75 mm internal diameter) packed with 5 mm, C18 AQUASIL resin with an integral spray tip (Picofrit, 15 mm tip, New Objective, Woburn, MA).

    Techniques: High Performance Liquid Chromatography, Mass Spectrometry, Activity Assay

    Inhibition of 3CL Pro activity by HPLC assay. Injection of 40 µl of incubation samples for C18 reverse phase column analysis. The substrate or product fragment peaks were analyzed by HPLC with UV absorbance detection at 214 nm. The HPLC system is described in Methods.

    Journal: Evidence-based Complementary and Alternative Medicine

    Article Title: Inhibition of SARS-CoV 3C-like Protease Activity by Theaflavin-3,3?-digallate (TF3)

    doi: 10.1093/ecam/neh081

    Figure Lengend Snippet: Inhibition of 3CL Pro activity by HPLC assay. Injection of 40 µl of incubation samples for C18 reverse phase column analysis. The substrate or product fragment peaks were analyzed by HPLC with UV absorbance detection at 214 nm. The HPLC system is described in Methods.

    Article Snippet: The HPLC analysis condition is: a C18 RP guard column (250 × 4.6 mm × 5 µm, Agilent Zorbax Extend).

    Techniques: Inhibition, Activity Assay, High Performance Liquid Chromatography, Injection, Incubation