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Characterization of γ -secretase in vitro assay with guinea pig brain enzyme. ~1 μ g of purified recombinant C100-3XFLAG was incubated with 2.75 μ g of CHAPSO solubilised membranes of guinea pig brain in 20 mM HEPES buffer, pH 7.3, plus 3 mM CaCl 2 , 3 mM MgCl 2 and 150 mM KCl. The reactions were stopped by adding Laemmli buffer, boiled, and separated on Tris-Tricine gels. M2 (anti-FLAG) antibody and WO2 (anti-A β 1–16) were used for western blot detection. (a) Production of an AICD fragment in the assay is inhibited by the γ -secretase inhibitors, L-685,458 and DAPT. (b) Both AICD and A β are produced in the reaction and inhibited by L-685,458. AICD signal increases in a time dependent manner over 20 h. A β signal is increased at 4 h compared to 2 h, but decreased at 20 h, possibly due to degradation. (Inc, incubation at 37°C). (c) Positive effect of phospholipids on AICD production in the γ -secretase assay. PC, phosphatidylcholine; PE, phosphatidylethanolamine. (d) Positive effect of ATP on the γ -secretase assay. ATP was added 1.25 mM concentration. (e) Quantitation of three separate experiments using <t>GeneTools</t> Syngene software shows ~1.6 fold enhancement of γ -secretase activity in the presence of 1.25 mM ATP. The error bars represent SEM.
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1) Product Images from "Effect of Metal Chelators on γ-Secretase Indicates That Calcium and Magnesium Ions Facilitate Cleavage of Alzheimer Amyloid Precursor Substrate"

Article Title: Effect of Metal Chelators on γ-Secretase Indicates That Calcium and Magnesium Ions Facilitate Cleavage of Alzheimer Amyloid Precursor Substrate

Journal: International Journal of Alzheimer's Disease

doi: 10.4061/2011/950932

Characterization of γ -secretase in vitro assay with guinea pig brain enzyme. ~1 μ g of purified recombinant C100-3XFLAG was incubated with 2.75 μ g of CHAPSO solubilised membranes of guinea pig brain in 20 mM HEPES buffer, pH 7.3, plus 3 mM CaCl 2 , 3 mM MgCl 2 and 150 mM KCl. The reactions were stopped by adding Laemmli buffer, boiled, and separated on Tris-Tricine gels. M2 (anti-FLAG) antibody and WO2 (anti-A β 1–16) were used for western blot detection. (a) Production of an AICD fragment in the assay is inhibited by the γ -secretase inhibitors, L-685,458 and DAPT. (b) Both AICD and A β are produced in the reaction and inhibited by L-685,458. AICD signal increases in a time dependent manner over 20 h. A β signal is increased at 4 h compared to 2 h, but decreased at 20 h, possibly due to degradation. (Inc, incubation at 37°C). (c) Positive effect of phospholipids on AICD production in the γ -secretase assay. PC, phosphatidylcholine; PE, phosphatidylethanolamine. (d) Positive effect of ATP on the γ -secretase assay. ATP was added 1.25 mM concentration. (e) Quantitation of three separate experiments using GeneTools Syngene software shows ~1.6 fold enhancement of γ -secretase activity in the presence of 1.25 mM ATP. The error bars represent SEM.
Figure Legend Snippet: Characterization of γ -secretase in vitro assay with guinea pig brain enzyme. ~1 μ g of purified recombinant C100-3XFLAG was incubated with 2.75 μ g of CHAPSO solubilised membranes of guinea pig brain in 20 mM HEPES buffer, pH 7.3, plus 3 mM CaCl 2 , 3 mM MgCl 2 and 150 mM KCl. The reactions were stopped by adding Laemmli buffer, boiled, and separated on Tris-Tricine gels. M2 (anti-FLAG) antibody and WO2 (anti-A β 1–16) were used for western blot detection. (a) Production of an AICD fragment in the assay is inhibited by the γ -secretase inhibitors, L-685,458 and DAPT. (b) Both AICD and A β are produced in the reaction and inhibited by L-685,458. AICD signal increases in a time dependent manner over 20 h. A β signal is increased at 4 h compared to 2 h, but decreased at 20 h, possibly due to degradation. (Inc, incubation at 37°C). (c) Positive effect of phospholipids on AICD production in the γ -secretase assay. PC, phosphatidylcholine; PE, phosphatidylethanolamine. (d) Positive effect of ATP on the γ -secretase assay. ATP was added 1.25 mM concentration. (e) Quantitation of three separate experiments using GeneTools Syngene software shows ~1.6 fold enhancement of γ -secretase activity in the presence of 1.25 mM ATP. The error bars represent SEM.

Techniques Used: In Vitro, Purification, Recombinant, Incubation, Western Blot, Produced, Concentration Assay, Quantitation Assay, Software, Activity Assay

Effect of metalloprotease inhibitors, and metal chelators on γ -secretase. Chelators and inhibitors were added as DMSO solutions (final DMSO concentration 2.5%) to the guinea pig brain γ -secretase/C100-3XFLAG reactions. (a) Representative western blot of γ -secretase assay in the presence of various inhibitors. Phpm, phosphoramidon; Ilmst, ilomastat; Pht, phenanthroline; CQ, clioquinol; γ -inh, L-685,458, used at 10 nM (lane 6) and 100 nM (lane 7). (b) Effect of metalloprotease inhibitors on the γ -secretase assay. Activity is expressed as the % of substrate converted into AICD, as determined from band density analysis with GeneTools software. The error bars represent SEM. Inhibitor concentrations were selected as follows: thiorphan, 250 nM; phosphoramidon, 25 μ M; ilomastat, 250 nM; phenanthroline, 5 mM; clioquinol, 100 μ M.
Figure Legend Snippet: Effect of metalloprotease inhibitors, and metal chelators on γ -secretase. Chelators and inhibitors were added as DMSO solutions (final DMSO concentration 2.5%) to the guinea pig brain γ -secretase/C100-3XFLAG reactions. (a) Representative western blot of γ -secretase assay in the presence of various inhibitors. Phpm, phosphoramidon; Ilmst, ilomastat; Pht, phenanthroline; CQ, clioquinol; γ -inh, L-685,458, used at 10 nM (lane 6) and 100 nM (lane 7). (b) Effect of metalloprotease inhibitors on the γ -secretase assay. Activity is expressed as the % of substrate converted into AICD, as determined from band density analysis with GeneTools software. The error bars represent SEM. Inhibitor concentrations were selected as follows: thiorphan, 250 nM; phosphoramidon, 25 μ M; ilomastat, 250 nM; phenanthroline, 5 mM; clioquinol, 100 μ M.

Techniques Used: Concentration Assay, Western Blot, Activity Assay, Software

2) Product Images from "Effect of GA3 Treatment on Seed Development and Seed-Related Gene Expression in Grape "

Article Title: Effect of GA3 Treatment on Seed Development and Seed-Related Gene Expression in Grape

Journal: PLoS ONE

doi: 10.1371/journal.pone.0080044

Hierarchical clustering of antioxidant gene expression in the flowers of three grape cultivars following GA 3 treatment. Results of semi-quantitative RT-PCR assays were quantified using GeneTools software, and log-transformed values of the relative expression levels of genes encoding antioxidant enzymes following GA 3 treatment compared to untreated controls were used for hierarchical cluster analysis. The color scale represents relative expression levels with red denoting up-regulation and green denoting down-regulation. Sampling times are indicated at the top of the figure; F represents floral tissue; K represents the ‘Kyoho’ cultivar; R represents the ‘Red Globe’ cultivar; T represents the ‘Thompson seedless’ cultivar.
Figure Legend Snippet: Hierarchical clustering of antioxidant gene expression in the flowers of three grape cultivars following GA 3 treatment. Results of semi-quantitative RT-PCR assays were quantified using GeneTools software, and log-transformed values of the relative expression levels of genes encoding antioxidant enzymes following GA 3 treatment compared to untreated controls were used for hierarchical cluster analysis. The color scale represents relative expression levels with red denoting up-regulation and green denoting down-regulation. Sampling times are indicated at the top of the figure; F represents floral tissue; K represents the ‘Kyoho’ cultivar; R represents the ‘Red Globe’ cultivar; T represents the ‘Thompson seedless’ cultivar.

Techniques Used: Expressing, Quantitative RT-PCR, Software, Transformation Assay, Sampling

Hierarchical clustering of genes related to seed development in three grape cultivars following GA 3 treatment. Results of semi-quantitative RT-PCR assays were quantified using GeneTools software, and log-transformed values of the relative expression levels of genes involved in seed development following GA 3 treatments compared to untreated controls were used for hierarchical cluster analysis. The color scale represents relative expression levels with red denoting up-regulation and green denoting down-regulation. Sampling times are indicated at the top of the figure; F represents floral tissue; K represents the ‘Kyoho’ cultivar; S represents seed tissue; R represents the ‘Red Globe’ cultivar; T represents the ‘Thompson seedless’ cultivar.
Figure Legend Snippet: Hierarchical clustering of genes related to seed development in three grape cultivars following GA 3 treatment. Results of semi-quantitative RT-PCR assays were quantified using GeneTools software, and log-transformed values of the relative expression levels of genes involved in seed development following GA 3 treatments compared to untreated controls were used for hierarchical cluster analysis. The color scale represents relative expression levels with red denoting up-regulation and green denoting down-regulation. Sampling times are indicated at the top of the figure; F represents floral tissue; K represents the ‘Kyoho’ cultivar; S represents seed tissue; R represents the ‘Red Globe’ cultivar; T represents the ‘Thompson seedless’ cultivar.

Techniques Used: Quantitative RT-PCR, Software, Transformation Assay, Expressing, Sampling

3) Product Images from "Bixin protects against particle-induced long-term lung injury in an NRF2-dependent manner protects against particle-induced long-term lung injury in an NRF2-dependent manner †Electronic supplementary information (ESI) available: S1 – The relative changes of body weight (A) and the relative changes of lung weight of the mice with the indicated treatments (B). See DOI: 10.1039/c7tx00304h"

Article Title: Bixin protects against particle-induced long-term lung injury in an NRF2-dependent manner protects against particle-induced long-term lung injury in an NRF2-dependent manner †Electronic supplementary information (ESI) available: S1 – The relative changes of body weight (A) and the relative changes of lung weight of the mice with the indicated treatments (B). See DOI: 10.1039/c7tx00304h

Journal: Toxicology Research

doi: 10.1039/c7tx00304h

Bixin activates the NRF2 signaling pathway by decreasing NRF2 ubiquitination and increasing NRF2 protein stability. (A) THP-1 cells were cotransfected with plasmids encoding the indicated proteins for 24 h. The transfected cells were treated with SF (5 μM), tBHQ (40 μM) or bixin (40 μM) along with MG132 (10 μM) for 4 h. Anti-NRF2 immunoprecipitates were analyzed by immunoblotting with anti-HA antibody for the detection of ubiquitin-conjugated NRF2. (B) THP-1 cells were treated with bixin (40 μM) along with MG132 (10 μM) for 4 h. Anti-NRF2 immunoprecipitates were analyzed by immunoblotting with ubiquitin antibody for the detection of endogenous unbiquitin-conjugated NRF2. (C) THP-1 cells were either left untreated or treated with bixin (40 μM) for 4 h. Cycloheximide (CHX, 50 μM) was added and the cells were lysed at the indicated time points. Cell lysates were subjected to immunoblot analysis using anti-NRF2 and anti-GAPDH antibodies. The intensities of the bands were quantified using the GeneTools software and plotted against time after CHX treatment to obtain the half-life values.
Figure Legend Snippet: Bixin activates the NRF2 signaling pathway by decreasing NRF2 ubiquitination and increasing NRF2 protein stability. (A) THP-1 cells were cotransfected with plasmids encoding the indicated proteins for 24 h. The transfected cells were treated with SF (5 μM), tBHQ (40 μM) or bixin (40 μM) along with MG132 (10 μM) for 4 h. Anti-NRF2 immunoprecipitates were analyzed by immunoblotting with anti-HA antibody for the detection of ubiquitin-conjugated NRF2. (B) THP-1 cells were treated with bixin (40 μM) along with MG132 (10 μM) for 4 h. Anti-NRF2 immunoprecipitates were analyzed by immunoblotting with ubiquitin antibody for the detection of endogenous unbiquitin-conjugated NRF2. (C) THP-1 cells were either left untreated or treated with bixin (40 μM) for 4 h. Cycloheximide (CHX, 50 μM) was added and the cells were lysed at the indicated time points. Cell lysates were subjected to immunoblot analysis using anti-NRF2 and anti-GAPDH antibodies. The intensities of the bands were quantified using the GeneTools software and plotted against time after CHX treatment to obtain the half-life values.

Techniques Used: Transfection, Software

4) Product Images from "Phosphorylation of Ser78 of Hsp27 correlated with HER-2/neu status and lymph node positivity in breast cancer"

Article Title: Phosphorylation of Ser78 of Hsp27 correlated with HER-2/neu status and lymph node positivity in breast cancer

Journal: Molecular Cancer

doi: 10.1186/1476-4598-6-52

Western blotting of Hsp27, pSer 15 , pSer 78 and pSer 82 . Twenty μg proteins from each of 4 HER-2/ neu positive and 4 -negative tumour samples were separated by 10% SDS-PAGE and transferred onto PVDF membranes. After blocking, the membranes were incubated with the respective primary antibodies (anti-Hsp27, anti-pSer 15 , anti-pSer 78 and anti-pSer 82 ), followed by hybridization to HRP-conjugated secondary antibody. The chemiluminescent signals emitted were captured with the MULTI-GENIUS Bio-Imaging System and signal intensities were analyzed using the GeneTools software (Syngene). The relative phosphorylation levels of pSer 15 , pSer 78 and pSer 82 presented (histograms, right) are the respective ratios of signal intensity probed with phosphorylation site-specific antibody to signal intensity probed with anti-Hsp27, for each of the three pSer residues. Data with ± SD (standard deviation) are expressed as the average of triplicate experiments. * p
Figure Legend Snippet: Western blotting of Hsp27, pSer 15 , pSer 78 and pSer 82 . Twenty μg proteins from each of 4 HER-2/ neu positive and 4 -negative tumour samples were separated by 10% SDS-PAGE and transferred onto PVDF membranes. After blocking, the membranes were incubated with the respective primary antibodies (anti-Hsp27, anti-pSer 15 , anti-pSer 78 and anti-pSer 82 ), followed by hybridization to HRP-conjugated secondary antibody. The chemiluminescent signals emitted were captured with the MULTI-GENIUS Bio-Imaging System and signal intensities were analyzed using the GeneTools software (Syngene). The relative phosphorylation levels of pSer 15 , pSer 78 and pSer 82 presented (histograms, right) are the respective ratios of signal intensity probed with phosphorylation site-specific antibody to signal intensity probed with anti-Hsp27, for each of the three pSer residues. Data with ± SD (standard deviation) are expressed as the average of triplicate experiments. * p

Techniques Used: Western Blot, SDS Page, Blocking Assay, Incubation, Hybridization, Imaging, Software, Standard Deviation

5) Product Images from "GADD45? inhibition of DNMT1 dependent DNA methylation during homology directed DNA repair"

Article Title: GADD45? inhibition of DNMT1 dependent DNA methylation during homology directed DNA repair

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkr1115

Analysis of G45a alanine dimerization mutants. Alanine substitution mutations in G45a predicted to disrupt dimer formation ( Supplementary Figure S3 ) were used ( 8 ). The degree of self-association was assayed using cross tag immunoprecipitation (Myc and V5 tags) for each mutation (see Supplementary Figure S5 ). The ability of each mutant to interact with DNMT1 in HeLa cells was assessed by co-transfecting each V5 tagged DNMT1 with Myc-tagged G45a mutant and I-SceI, performing an immunoprecipitation with anti-V5 IgG followed by western probing with anti-Myc IgG (upper blots). The graph below shows the collective digitized data. The shade bars represent the efficiency of DNMT1/G45a binding. The band intensities of co-imunoprecipitated G45a mutants were quantified using the GeneTools program (SynGene, Cambridge, UK). The amount of co-immunoprecipitated G45a was normalized to the amount of immunoprecipitated DNMT1 and plotted as a relative amount against wild-type band intensity. The statistical data are based on three independent experiments. The white bars represent the efficiency of dimer formation (from Supplementary Figure S5 ) and the stippled bars the percent total GFP expression.
Figure Legend Snippet: Analysis of G45a alanine dimerization mutants. Alanine substitution mutations in G45a predicted to disrupt dimer formation ( Supplementary Figure S3 ) were used ( 8 ). The degree of self-association was assayed using cross tag immunoprecipitation (Myc and V5 tags) for each mutation (see Supplementary Figure S5 ). The ability of each mutant to interact with DNMT1 in HeLa cells was assessed by co-transfecting each V5 tagged DNMT1 with Myc-tagged G45a mutant and I-SceI, performing an immunoprecipitation with anti-V5 IgG followed by western probing with anti-Myc IgG (upper blots). The graph below shows the collective digitized data. The shade bars represent the efficiency of DNMT1/G45a binding. The band intensities of co-imunoprecipitated G45a mutants were quantified using the GeneTools program (SynGene, Cambridge, UK). The amount of co-immunoprecipitated G45a was normalized to the amount of immunoprecipitated DNMT1 and plotted as a relative amount against wild-type band intensity. The statistical data are based on three independent experiments. The white bars represent the efficiency of dimer formation (from Supplementary Figure S5 ) and the stippled bars the percent total GFP expression.

Techniques Used: Immunoprecipitation, Mutagenesis, Western Blot, Binding Assay, Expressing

6) Product Images from "Involvement of the Carboxyl-Terminal Region of the Yeast Peroxisomal Half ABC Transporter Pxa2p in Its Interaction with Pxa1p and in Transporter Function"

Article Title: Involvement of the Carboxyl-Terminal Region of the Yeast Peroxisomal Half ABC Transporter Pxa2p in Its Interaction with Pxa1p and in Transporter Function

Journal: PLoS ONE

doi: 10.1371/journal.pone.0104892

Analysis of co-purification of the CT-deleted mutant proteins of Pxa2_NBD-CT with Pxa1_NBD. The various CT-deleted proteins of Pxa2_NBD-CT-His 6 were co-expressed with Pxa1_NBD-HA in yeast strain BJ2168, and yeast cells were disrupted by sonication. The total yeast extracts were subjected to a pull-down assay using Ni 2+ -NTA chromatography. The presence of Pxa2-His 6 or Pxa1-HA in the total extract (T), flow-through (F), wash-one (W1), wash-final (WF), elute-one (E1), elute-two (E2), and elute-three (E3) fractions was revealed by Western blot probed with anti-HA antibody for Pxa1-HA (right panel) and anti-His antibody for Pxa2-His6 (left panel). Protein intensity was analyzed by using GeneTools software (Syngene). Protein intensity of the E2 fraction was normalized to that of the T fraction for each experiment.
Figure Legend Snippet: Analysis of co-purification of the CT-deleted mutant proteins of Pxa2_NBD-CT with Pxa1_NBD. The various CT-deleted proteins of Pxa2_NBD-CT-His 6 were co-expressed with Pxa1_NBD-HA in yeast strain BJ2168, and yeast cells were disrupted by sonication. The total yeast extracts were subjected to a pull-down assay using Ni 2+ -NTA chromatography. The presence of Pxa2-His 6 or Pxa1-HA in the total extract (T), flow-through (F), wash-one (W1), wash-final (WF), elute-one (E1), elute-two (E2), and elute-three (E3) fractions was revealed by Western blot probed with anti-HA antibody for Pxa1-HA (right panel) and anti-His antibody for Pxa2-His6 (left panel). Protein intensity was analyzed by using GeneTools software (Syngene). Protein intensity of the E2 fraction was normalized to that of the T fraction for each experiment.

Techniques Used: Copurification, Mutagenesis, Sonication, Pull Down Assay, Chromatography, Flow Cytometry, Western Blot, Software

7) Product Images from "Avian Influenza A Virus Polymerase Association with Nucleoprotein, but Not Polymerase Assembly, Is Impaired in Human Cells during the Course of Infection ▿"

Article Title: Avian Influenza A Virus Polymerase Association with Nucleoprotein, but Not Polymerase Assembly, Is Impaired in Human Cells during the Course of Infection ▿

Journal: Journal of Virology

doi: 10.1128/JVI.00977-08

Western blot analysis of P908-Cstrep-WSN- or MZ-Cstrep-WSN-infected cell lysates before and after purification on Strep-tactin beads. (A and B) Analysis of protein complexes eluted from Strep-tactin beads. 293T or DF1 cells were infected at an MOI of 2 with MZ-WSN (MZ), MZ-Cstrep-WSN (MZ-Cstrep), P908-WSN (P908), or P908-Cstrep-WSN (P908-Cstrep) virus and incubated at 37 or 33°C for 6 h. Whole-cell lysates were prepared, and a fraction was incubated with Strep-tactin beads as described in Materials and Methods. Protein complexes were eluted and serially diluted in Laemmli buffer, loaded on a 4 to 12% sodium dodecyl sulfate-polyacrylamide gel, and analyzed by Western blotting as described in Materials and Methods, using either polyclonal antibodies directed against the PB2, PB1, PA, or NP protein or a monoclonal antibody specific for the cellular RNA Pol II, as indicated. (C and D) Analysis of the levels of NP protein before and after purification on Strep-tactin beads. The whole-cell lysates and the Strep-tactin eluates prepared from infected 293T or DF1 cells were serially diluted in whole-cell lysates prepared from uninfected cells and in Laemmli buffer, respectively, loaded on a 4 to 12% sodium dodecyl sulfate-polyacrylamide gel, and analyzed by Western blotting, as described in Materials and Methods, using a polyclonal antibody recognizing the NP protein. The samples are from the same experiment as shown in panels A and B, respectively. The sample dilution factors are indicated using the following notation: 1, undiluted; 1/2, diluted twofold, 1/4, diluted fourfold, and so on. (E to H) Graphic representation of the results of Western blot quantification. After the membranes were scanned using a G-Box (SynGene), the signals corresponding to the PB2, PB1, PA, NP, or RNA Pol II proteins were quantified using the GeneTools software (SynGene). The signals measured in samples derived from MZ-Cstrep-WSN-infected cells were compared to those measured in samples derived from P908-Cstrep-WSN-infected cells, taking into account the sample dilution factor. The MZ/P908 ratios measured in total cell extracts (black bars) and in Strep-tactin eluates (gray bars) are expressed as percentages. The percentage indicated by the asterisk is overestimated due to the fact that the MZ-NP signal was at background levels. The results of one representative experiment out of three are shown.
Figure Legend Snippet: Western blot analysis of P908-Cstrep-WSN- or MZ-Cstrep-WSN-infected cell lysates before and after purification on Strep-tactin beads. (A and B) Analysis of protein complexes eluted from Strep-tactin beads. 293T or DF1 cells were infected at an MOI of 2 with MZ-WSN (MZ), MZ-Cstrep-WSN (MZ-Cstrep), P908-WSN (P908), or P908-Cstrep-WSN (P908-Cstrep) virus and incubated at 37 or 33°C for 6 h. Whole-cell lysates were prepared, and a fraction was incubated with Strep-tactin beads as described in Materials and Methods. Protein complexes were eluted and serially diluted in Laemmli buffer, loaded on a 4 to 12% sodium dodecyl sulfate-polyacrylamide gel, and analyzed by Western blotting as described in Materials and Methods, using either polyclonal antibodies directed against the PB2, PB1, PA, or NP protein or a monoclonal antibody specific for the cellular RNA Pol II, as indicated. (C and D) Analysis of the levels of NP protein before and after purification on Strep-tactin beads. The whole-cell lysates and the Strep-tactin eluates prepared from infected 293T or DF1 cells were serially diluted in whole-cell lysates prepared from uninfected cells and in Laemmli buffer, respectively, loaded on a 4 to 12% sodium dodecyl sulfate-polyacrylamide gel, and analyzed by Western blotting, as described in Materials and Methods, using a polyclonal antibody recognizing the NP protein. The samples are from the same experiment as shown in panels A and B, respectively. The sample dilution factors are indicated using the following notation: 1, undiluted; 1/2, diluted twofold, 1/4, diluted fourfold, and so on. (E to H) Graphic representation of the results of Western blot quantification. After the membranes were scanned using a G-Box (SynGene), the signals corresponding to the PB2, PB1, PA, NP, or RNA Pol II proteins were quantified using the GeneTools software (SynGene). The signals measured in samples derived from MZ-Cstrep-WSN-infected cells were compared to those measured in samples derived from P908-Cstrep-WSN-infected cells, taking into account the sample dilution factor. The MZ/P908 ratios measured in total cell extracts (black bars) and in Strep-tactin eluates (gray bars) are expressed as percentages. The percentage indicated by the asterisk is overestimated due to the fact that the MZ-NP signal was at background levels. The results of one representative experiment out of three are shown.

Techniques Used: Western Blot, Infection, Purification, Incubation, Software, Derivative Assay

8) Product Images from "Secretion of Fc-amidated peptide fusion proteins by Chinese hamster ovary cells"

Article Title: Secretion of Fc-amidated peptide fusion proteins by Chinese hamster ovary cells

Journal: BMC Biotechnology

doi: 10.1186/s12896-015-0173-5

Characterization of Fc-fusion protein expression in CHO lines expressing PAM. Fc-AP-GLP1 ( a ) and Fc-GS-PYY ( b ) were expressed in PAM1 CHO cells; Fc-AP-NMU ( c ) was expressed in PAM820s CHO cells. Aliquots of cell extract ( a , 5 %; b , 3 %; c , 6 % of total cell extract) and spent medium ( a , 0.7 %; b , 1.3 %; c , 2.3 % of total medium volume) were prepared as described for Fig. 3 . d Using GeneTools, data from several similar analyses were quantified to determine μg Fc/mg cell protein ( d ) and Fc secretion rate ( e )
Figure Legend Snippet: Characterization of Fc-fusion protein expression in CHO lines expressing PAM. Fc-AP-GLP1 ( a ) and Fc-GS-PYY ( b ) were expressed in PAM1 CHO cells; Fc-AP-NMU ( c ) was expressed in PAM820s CHO cells. Aliquots of cell extract ( a , 5 %; b , 3 %; c , 6 % of total cell extract) and spent medium ( a , 0.7 %; b , 1.3 %; c , 2.3 % of total medium volume) were prepared as described for Fig. 3 . d Using GeneTools, data from several similar analyses were quantified to determine μg Fc/mg cell protein ( d ) and Fc secretion rate ( e )

Techniques Used: Expressing

Characterization of Fc-fusion protein expression and secretion in wildtype CHO lines. Samples of cell extract (CE) and spent medium (16 h collection) prepared from CHO lines expressing Fc-AP-GLP1 ( a ) [15 μg (7 %) of CE; 0.9 % of spent medium], Fc-GS-PYY ( b ) [10 μg (8.5 %) of CE; 1.3 % of spent medium) and Fc-AP-NMU ( c ) [10 μg (5.3 %) of CE; 1.3 % of spent medium) were fractionated by SDS-PAGE; samples and a human IgG standard were visualized using antibody to human Fc. d Using GeneTools, data from several similar analyses (n = 3–4) were quantified to determine μg Fc/mg cell protein. e The secretion rate for Fc was calculated for several experiments by quantifying the amount of Fc recovered from the cell extract (CE) and from the medium using GeneTools; for each cell line, secretion rate was expressed as % cell content secreted per hour
Figure Legend Snippet: Characterization of Fc-fusion protein expression and secretion in wildtype CHO lines. Samples of cell extract (CE) and spent medium (16 h collection) prepared from CHO lines expressing Fc-AP-GLP1 ( a ) [15 μg (7 %) of CE; 0.9 % of spent medium], Fc-GS-PYY ( b ) [10 μg (8.5 %) of CE; 1.3 % of spent medium) and Fc-AP-NMU ( c ) [10 μg (5.3 %) of CE; 1.3 % of spent medium) were fractionated by SDS-PAGE; samples and a human IgG standard were visualized using antibody to human Fc. d Using GeneTools, data from several similar analyses (n = 3–4) were quantified to determine μg Fc/mg cell protein. e The secretion rate for Fc was calculated for several experiments by quantifying the amount of Fc recovered from the cell extract (CE) and from the medium using GeneTools; for each cell line, secretion rate was expressed as % cell content secreted per hour

Techniques Used: Expressing, SDS Page

9) Product Images from "Plasminogen-Based Capture Combined with Amplification Technology for the Detection of PrPTSE in the Pre-Clinical Phase of Infection"

Article Title: Plasminogen-Based Capture Combined with Amplification Technology for the Detection of PrPTSE in the Pre-Clinical Phase of Infection

Journal: PLoS ONE

doi: 10.1371/journal.pone.0069632

Efficacy of PrP TSE capture. Ten microliters of 10% 127S (lanes 1 and 2) and vCJD IBH (lanes 3 and 4) were diluted in 500 µl of plasma and incubated 2 h with plasminogen-coated beads. PrP TSE bound to the beads were PK-digested and denatured in sample buffer for western blot analysis with 6D11 and 3F4 anti-PrP MAbs. Percentage yield was quantified with Genetools software after acquisition of the chemioluminescent western blot signals with the Genegnome digital imager (Syngene, US) Lanes 1 and 2∶127S IBH capture Lanes 3 and 4: vCJD IBH capture.
Figure Legend Snippet: Efficacy of PrP TSE capture. Ten microliters of 10% 127S (lanes 1 and 2) and vCJD IBH (lanes 3 and 4) were diluted in 500 µl of plasma and incubated 2 h with plasminogen-coated beads. PrP TSE bound to the beads were PK-digested and denatured in sample buffer for western blot analysis with 6D11 and 3F4 anti-PrP MAbs. Percentage yield was quantified with Genetools software after acquisition of the chemioluminescent western blot signals with the Genegnome digital imager (Syngene, US) Lanes 1 and 2∶127S IBH capture Lanes 3 and 4: vCJD IBH capture.

Techniques Used: Incubation, Western Blot, Software

10) Product Images from "Avian Influenza A Virus Polymerase Association with Nucleoprotein, but Not Polymerase Assembly, Is Impaired in Human Cells during the Course of Infection ▿"

Article Title: Avian Influenza A Virus Polymerase Association with Nucleoprotein, but Not Polymerase Assembly, Is Impaired in Human Cells during the Course of Infection ▿

Journal: Journal of Virology

doi: 10.1128/JVI.00977-08

Western blot analysis of P908-Cstrep-WSN- or MZ-Cstrep-WSN-infected cell lysates before and after purification on Strep-tactin beads. (A and B) Analysis of protein complexes eluted from Strep-tactin beads. 293T or DF1 cells were infected at an MOI of 2 with MZ-WSN (MZ), MZ-Cstrep-WSN (MZ-Cstrep), P908-WSN (P908), or P908-Cstrep-WSN (P908-Cstrep) virus and incubated at 37 or 33°C for 6 h. Whole-cell lysates were prepared, and a fraction was incubated with Strep-tactin beads as described in Materials and Methods. Protein complexes were eluted and serially diluted in Laemmli buffer, loaded on a 4 to 12% sodium dodecyl sulfate-polyacrylamide gel, and analyzed by Western blotting as described in Materials and Methods, using either polyclonal antibodies directed against the PB2, PB1, PA, or NP protein or a monoclonal antibody specific for the cellular RNA Pol II, as indicated. (C and D) Analysis of the levels of NP protein before and after purification on Strep-tactin beads. The whole-cell lysates and the Strep-tactin eluates prepared from infected 293T or DF1 cells were serially diluted in whole-cell lysates prepared from uninfected cells and in Laemmli buffer, respectively, loaded on a 4 to 12% sodium dodecyl sulfate-polyacrylamide gel, and analyzed by Western blotting, as described in Materials and Methods, using a polyclonal antibody recognizing the NP protein. The samples are from the same experiment as shown in panels A and B, respectively. The sample dilution factors are indicated using the following notation: 1, undiluted; 1/2, diluted twofold, 1/4, diluted fourfold, and so on. (E to H) Graphic representation of the results of Western blot quantification. After the membranes were scanned using a G-Box (SynGene), the signals corresponding to the PB2, PB1, PA, NP, or RNA Pol II proteins were quantified using the GeneTools software (SynGene). The signals measured in samples derived from MZ-Cstrep-WSN-infected cells were compared to those measured in samples derived from P908-Cstrep-WSN-infected cells, taking into account the sample dilution factor. The MZ/P908 ratios measured in total cell extracts (black bars) and in Strep-tactin eluates (gray bars) are expressed as percentages. The percentage indicated by the asterisk is overestimated due to the fact that the MZ-NP signal was at background levels. The results of one representative experiment out of three are shown.
Figure Legend Snippet: Western blot analysis of P908-Cstrep-WSN- or MZ-Cstrep-WSN-infected cell lysates before and after purification on Strep-tactin beads. (A and B) Analysis of protein complexes eluted from Strep-tactin beads. 293T or DF1 cells were infected at an MOI of 2 with MZ-WSN (MZ), MZ-Cstrep-WSN (MZ-Cstrep), P908-WSN (P908), or P908-Cstrep-WSN (P908-Cstrep) virus and incubated at 37 or 33°C for 6 h. Whole-cell lysates were prepared, and a fraction was incubated with Strep-tactin beads as described in Materials and Methods. Protein complexes were eluted and serially diluted in Laemmli buffer, loaded on a 4 to 12% sodium dodecyl sulfate-polyacrylamide gel, and analyzed by Western blotting as described in Materials and Methods, using either polyclonal antibodies directed against the PB2, PB1, PA, or NP protein or a monoclonal antibody specific for the cellular RNA Pol II, as indicated. (C and D) Analysis of the levels of NP protein before and after purification on Strep-tactin beads. The whole-cell lysates and the Strep-tactin eluates prepared from infected 293T or DF1 cells were serially diluted in whole-cell lysates prepared from uninfected cells and in Laemmli buffer, respectively, loaded on a 4 to 12% sodium dodecyl sulfate-polyacrylamide gel, and analyzed by Western blotting, as described in Materials and Methods, using a polyclonal antibody recognizing the NP protein. The samples are from the same experiment as shown in panels A and B, respectively. The sample dilution factors are indicated using the following notation: 1, undiluted; 1/2, diluted twofold, 1/4, diluted fourfold, and so on. (E to H) Graphic representation of the results of Western blot quantification. After the membranes were scanned using a G-Box (SynGene), the signals corresponding to the PB2, PB1, PA, NP, or RNA Pol II proteins were quantified using the GeneTools software (SynGene). The signals measured in samples derived from MZ-Cstrep-WSN-infected cells were compared to those measured in samples derived from P908-Cstrep-WSN-infected cells, taking into account the sample dilution factor. The MZ/P908 ratios measured in total cell extracts (black bars) and in Strep-tactin eluates (gray bars) are expressed as percentages. The percentage indicated by the asterisk is overestimated due to the fact that the MZ-NP signal was at background levels. The results of one representative experiment out of three are shown.

Techniques Used: Western Blot, Infection, Purification, Incubation, Software, Derivative Assay

11) Product Images from "Regulatory Effect of DNA Topoisomerase I on T3SS Activity, Antibiotic Susceptibility and Quorum- Sensing-Independent Pyocyanin Synthesis in Pseudomonas aeruginosa"

Article Title: Regulatory Effect of DNA Topoisomerase I on T3SS Activity, Antibiotic Susceptibility and Quorum- Sensing-Independent Pyocyanin Synthesis in Pseudomonas aeruginosa

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms20051116

Reduced expression of T3SS effectors in topA -RM. ( A–C ) The expression profiles of T3SS effectors measured using p- lux promoter-reporter system. The values are presented as cps normalized to OD 595 . The values of topA -RM are shown as triangles and those in PAO1 as squares (data shown as averages from triplicate experiments ± standard errors of the means). ( D ) Effect of altered TopA on T3SS effectors protein secretion. A representative gel image is shown on top and the quantitative values (mean and SD) of ExoS and ExoT calculated from the results of three repeats are shown underneath. Proteins in the culture supernatants of various strains grown in T3SS-inducing condition were precipitated by TCA and analyzed by SDS-PAGE, followed by staining with Coomassie blue. The relative quantification of the secreted ExoS protein on the gel was evaluated by the relative density of the bands using the GeneTools software (Syngene, Cambridge, United Kingdom). Two-tailed unpaired t -test was performed using GraphPad software version 5.0 (*, P
Figure Legend Snippet: Reduced expression of T3SS effectors in topA -RM. ( A–C ) The expression profiles of T3SS effectors measured using p- lux promoter-reporter system. The values are presented as cps normalized to OD 595 . The values of topA -RM are shown as triangles and those in PAO1 as squares (data shown as averages from triplicate experiments ± standard errors of the means). ( D ) Effect of altered TopA on T3SS effectors protein secretion. A representative gel image is shown on top and the quantitative values (mean and SD) of ExoS and ExoT calculated from the results of three repeats are shown underneath. Proteins in the culture supernatants of various strains grown in T3SS-inducing condition were precipitated by TCA and analyzed by SDS-PAGE, followed by staining with Coomassie blue. The relative quantification of the secreted ExoS protein on the gel was evaluated by the relative density of the bands using the GeneTools software (Syngene, Cambridge, United Kingdom). Two-tailed unpaired t -test was performed using GraphPad software version 5.0 (*, P

Techniques Used: Expressing, SDS Page, Staining, Software, Two Tailed Test

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Methylation:

Article Title: GADD45? inhibition of DNMT1 dependent DNA methylation during homology directed DNA repair
Article Snippet: .. The methylation was quantified using a GeneTools software (SynGene, Cambridge, UK). .. In vitro DNA methylation assays DNA methylation activity assays were performed as described ( ) with slight modifications.

Generated:

Article Title: Phosphorylation of Ser78 of Hsp27 correlated with HER-2/neu status and lymph node positivity in breast cancer
Article Snippet: .. The horseradish peroxidase-conjugated goat anti-mouse IgG (1:10,000, Upstate Biotechnology Inc., Lake Placid, NY) or goat anti-rabbit IgG (1:10,000, ZyMED Laboratories Inc., San Francisco, CA) secondary antibody was then applied and the chemiluminescent signals generated using the SuperSignal® West Pico Chemiluminescent Substrate (Pierce) were captured with the MULTI GENIUS Bio Imaging System (Syngene, Frederick, MD) and the signal intensities analyzed using the GeneTools software (Syngene). ..

Activity Assay:

Article Title: Effect of Metal Chelators on γ-Secretase Indicates That Calcium and Magnesium Ions Facilitate Cleavage of Alzheimer Amyloid Precursor Substrate
Article Snippet: .. Data were analysed using GeneTools software (Syngene). γ -Secretase activity was expressed as the ratio of AICD signal to the sum of C100 plus AICD signals after subtracting blank values. ..

Imaging:

Article Title: Phosphorylation of Ser78 of Hsp27 correlated with HER-2/neu status and lymph node positivity in breast cancer
Article Snippet: .. The horseradish peroxidase-conjugated goat anti-mouse IgG (1:10,000, Upstate Biotechnology Inc., Lake Placid, NY) or goat anti-rabbit IgG (1:10,000, ZyMED Laboratories Inc., San Francisco, CA) secondary antibody was then applied and the chemiluminescent signals generated using the SuperSignal® West Pico Chemiluminescent Substrate (Pierce) were captured with the MULTI GENIUS Bio Imaging System (Syngene, Frederick, MD) and the signal intensities analyzed using the GeneTools software (Syngene). ..

Expressing:

Article Title: Effect of GA3 Treatment on Seed Development and Seed-Related Gene Expression in Grape
Article Snippet: .. The results of all semi-quantitative RT-PCR assays were quantified using GeneTools software (Syngene, Frederick, MD, USA) and log-transformed values of relative expression levels following GA3 treatment compared to untreated controls were used for hierarchical cluster analysis with the MultiExperiment Viewer (MeV version 4.8.1, http://www.tm4.org/). .. Statistical analysis Data were analyzed using student’s t-tests carried out using SPSS software (SPSS 17.0® , Chicago, IL, USA).

Reverse Transcription Polymerase Chain Reaction:

Article Title: Effect of GA3 Treatment on Seed Development and Seed-Related Gene Expression in Grape
Article Snippet: .. The results of all semi-quantitative RT-PCR assays were quantified using GeneTools software (Syngene, Frederick, MD, USA) and log-transformed values of relative expression levels following GA3 treatment compared to untreated controls were used for hierarchical cluster analysis with the MultiExperiment Viewer (MeV version 4.8.1, http://www.tm4.org/). .. Statistical analysis Data were analyzed using student’s t-tests carried out using SPSS software (SPSS 17.0® , Chicago, IL, USA).

Software:

Article Title: Avian Influenza A Virus Polymerase Association with Nucleoprotein, but Not Polymerase Assembly, Is Impaired in Human Cells during the Course of Infection ▿
Article Snippet: .. After the membranes were scanned using a G-Box (SynGene), the signals corresponding to the PB2, PB1, PA, NP, or RNA Pol II proteins were quantified using the GeneTools software (SynGene). .. Semiconfluent 293T cells on coverslips were infected with the PB2-wt or PB2-HA recombinant viruses at an MOI of 2.

Article Title: Bixin protects against particle-induced long-term lung injury in an NRF2-dependent manner protects against particle-induced long-term lung injury in an NRF2-dependent manner †Electronic supplementary information (ESI) available: S1 – The relative changes of body weight (A) and the relative changes of lung weight of the mice with the indicated treatments (B). See DOI: 10.1039/c7tx00304h
Article Snippet: .. The relative intensities of the immunoblot bands were quantified using the Syngene gel documentation system and GeneTools software from Syngene (Frederick, MD). .. Total RNA was extracted from THP-1 cells and mice lung tissues using TRIzol reagent from CWBIO (Beijing, China).

Article Title: GADD45? inhibition of DNMT1 dependent DNA methylation during homology directed DNA repair
Article Snippet: .. The methylation was quantified using a GeneTools software (SynGene, Cambridge, UK). .. In vitro DNA methylation assays DNA methylation activity assays were performed as described ( ) with slight modifications.

Article Title: Effect of GA3 Treatment on Seed Development and Seed-Related Gene Expression in Grape
Article Snippet: .. The results of all semi-quantitative RT-PCR assays were quantified using GeneTools software (Syngene, Frederick, MD, USA) and log-transformed values of relative expression levels following GA3 treatment compared to untreated controls were used for hierarchical cluster analysis with the MultiExperiment Viewer (MeV version 4.8.1, http://www.tm4.org/). .. Statistical analysis Data were analyzed using student’s t-tests carried out using SPSS software (SPSS 17.0® , Chicago, IL, USA).

Article Title: Involvement of the Carboxyl-Terminal Region of the Yeast Peroxisomal Half ABC Transporter Pxa2p in Its Interaction with Pxa1p and in Transporter Function
Article Snippet: .. Signals were quantitated by using GeneTools software (SynGene, Frederick, MD) when required. .. Ni-NTA affinity chromatography Cell extracts were prepared by sonication from yeast strain BJ2168 co-expressing Pxa2_NBD-CT-His/Pxa1_NBD-HA, Pxa2_NBD-CT1+2 -His/Pxa1_NBD-HA, Pxa2_NBD-CT1 -His/Pxa1_NBD-HA, or Pxa2_NBD-His/Pxa1_NBD-HA.

Article Title: Effect of Metal Chelators on γ-Secretase Indicates That Calcium and Magnesium Ions Facilitate Cleavage of Alzheimer Amyloid Precursor Substrate
Article Snippet: .. Data were analysed using GeneTools software (Syngene). γ -Secretase activity was expressed as the ratio of AICD signal to the sum of C100 plus AICD signals after subtracting blank values. ..

Article Title: Secretion of Fc-amidated peptide fusion proteins by Chinese hamster ovary cells
Article Snippet: .. GeneTools software [Syngene, Frederick, MD] was used for quantification; exposure times were selected to avoid saturation. ..

Article Title: Phosphorylation of Ser78 of Hsp27 correlated with HER-2/neu status and lymph node positivity in breast cancer
Article Snippet: .. The horseradish peroxidase-conjugated goat anti-mouse IgG (1:10,000, Upstate Biotechnology Inc., Lake Placid, NY) or goat anti-rabbit IgG (1:10,000, ZyMED Laboratories Inc., San Francisco, CA) secondary antibody was then applied and the chemiluminescent signals generated using the SuperSignal® West Pico Chemiluminescent Substrate (Pierce) were captured with the MULTI GENIUS Bio Imaging System (Syngene, Frederick, MD) and the signal intensities analyzed using the GeneTools software (Syngene). ..

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  • 91
    Syngene genetools analysis software
    Phosphorylation of cellular eIF2α in FHM cells. Subconfluent monolayers of FHM cells were transfected with either pcDNA, pcDNA:25R or pcDNA:57R for 20 – 24 hours and then treated with indicated concentration of poly I:C. At 6 hpt of polyI:C, (A.) total proteins were harvested and separated by SDS-PAGE electrophoresis followed by Western blot analysis using the indicated antibodies. Bands were visualized by chemiluminescence. (B.) Quantification of eIF2α phosphorylation. Phosphorylated eIF2α was quantified using the <t>GeneTools</t> (Syngene) analysis software. The relative intensity of each phosphorylated eIF2α was normalized to levels observed in mock treated cells. Data presented are averages and standard error from multiple independent experiments. Statistical analysis was performed using ANOVA and statistically significant differences are indicated (*; P value
    Genetools Analysis Software, supplied by Syngene, used in various techniques. Bioz Stars score: 91/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Characterization of γ -secretase in vitro assay with guinea pig brain enzyme. ~1 μ g of purified recombinant C100-3XFLAG was incubated with 2.75 μ g of CHAPSO solubilised membranes of guinea pig brain in 20 mM HEPES buffer, pH 7.3, plus 3 mM CaCl 2 , 3 mM MgCl 2 and 150 mM KCl. The reactions were stopped by adding Laemmli buffer, boiled, and separated on Tris-Tricine gels. M2 (anti-FLAG) antibody and WO2 (anti-A β 1–16) were used for western blot detection. (a) Production of an AICD fragment in the assay is inhibited by the γ -secretase inhibitors, L-685,458 and DAPT. (b) Both AICD and A β are produced in the reaction and inhibited by L-685,458. AICD signal increases in a time dependent manner over 20 h. A β signal is increased at 4 h compared to 2 h, but decreased at 20 h, possibly due to degradation. (Inc, incubation at 37°C). (c) Positive effect of phospholipids on AICD production in the γ -secretase assay. PC, phosphatidylcholine; PE, phosphatidylethanolamine. (d) Positive effect of ATP on the γ -secretase assay. ATP was added 1.25 mM concentration. (e) Quantitation of three separate experiments using <t>GeneTools</t> Syngene software shows ~1.6 fold enhancement of γ -secretase activity in the presence of 1.25 mM ATP. The error bars represent SEM.
    Genetools Software, supplied by Syngene, used in various techniques. Bioz Stars score: 92/100, based on 757 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Filamin B knockdown inhibits the replication of HBV. ( A ) Huh7 and HepG2 cells were transfected with siNC, filamin B-targeting siFLNB-1, siFLNB-2 or siFLNB-3 separately. Western blot analysis of filamin B was used to confirm the silencing efficiency. ( B ) Levels of HBV total RNAs and pgRNA in Huh7 cells were determined by real-time PCR. ( C ) Levels of HBV total RNAs and pgRNA in HepG2 cells were determined by real-time PCR. ( D ) Levels of HBeAg and HBsAg in culture medium supernatant of Huh7 cells were detected with ELISA. ( E ) Levels of HBeAg and HBsAg in culture medium supernatant of HepG2 cells were detected with ELISA. ( F ) HBV DNA was extracted at 96 h post transfection, and then subjected to Southern blotting. Western blot showed that filamin B was successfully knocked down. Co-transfection with pHBV1.3 and siNC was used as a loading control. Ratios were quantified by gray analysis with <t>GeneTools</t> from Syngene software (GeneGnome5). rcDNA, relaxed circular DNA; dsDNA, double stranded DNA; ssDNA, single stranded DNA. All results are shown as mean ± SD. (* P
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    Phosphorylation of cellular eIF2α in FHM cells. Subconfluent monolayers of FHM cells were transfected with either pcDNA, pcDNA:25R or pcDNA:57R for 20 – 24 hours and then treated with indicated concentration of poly I:C. At 6 hpt of polyI:C, (A.) total proteins were harvested and separated by SDS-PAGE electrophoresis followed by Western blot analysis using the indicated antibodies. Bands were visualized by chemiluminescence. (B.) Quantification of eIF2α phosphorylation. Phosphorylated eIF2α was quantified using the GeneTools (Syngene) analysis software. The relative intensity of each phosphorylated eIF2α was normalized to levels observed in mock treated cells. Data presented are averages and standard error from multiple independent experiments. Statistical analysis was performed using ANOVA and statistically significant differences are indicated (*; P value

    Journal: Virology

    Article Title: The Ambystoma tigrinum virus (ATV) RNase III gene can modulate host PKR activation and interferon production

    doi: 10.1016/j.virol.2017.08.013

    Figure Lengend Snippet: Phosphorylation of cellular eIF2α in FHM cells. Subconfluent monolayers of FHM cells were transfected with either pcDNA, pcDNA:25R or pcDNA:57R for 20 – 24 hours and then treated with indicated concentration of poly I:C. At 6 hpt of polyI:C, (A.) total proteins were harvested and separated by SDS-PAGE electrophoresis followed by Western blot analysis using the indicated antibodies. Bands were visualized by chemiluminescence. (B.) Quantification of eIF2α phosphorylation. Phosphorylated eIF2α was quantified using the GeneTools (Syngene) analysis software. The relative intensity of each phosphorylated eIF2α was normalized to levels observed in mock treated cells. Data presented are averages and standard error from multiple independent experiments. Statistical analysis was performed using ANOVA and statistically significant differences are indicated (*; P value

    Article Snippet: The relative intensity of proteins was quantified using the GeneTools analysis software (Syngene).

    Techniques: Transfection, Concentration Assay, SDS Page, Electrophoresis, Western Blot, Software

    Regulation of the PKR pathway in HeLa cells. Subconfluent monolayers of HeLa cells were transfected with either pcDNA, pcDNA:25R or pcDNA:57R for 20 – 24 hours and then treated with 500 ng of poly I:C. At 6 hpt of polyI:C, (A.) total proteins were harvested, separated by SDS-PAGE electrophoresis followed by Western blot analysis using the indicated antibodies. Bands were visualized by chemiluminescence. (B.) Quantification of PKR phosphorylation. The experiment was repeated multiple times and the quantity of PKR phosphorylation was determined using the GeneTools (Syngene) analysis software. The relative intensity of each phosphorylated PKR was normalized to levels observed in mock treated cells. Data presented are averages and standard error from multiple independent experiments. Statistical analysis was performed using ANOVA and statistically significant differences are indicated (*; P value

    Journal: Virology

    Article Title: The Ambystoma tigrinum virus (ATV) RNase III gene can modulate host PKR activation and interferon production

    doi: 10.1016/j.virol.2017.08.013

    Figure Lengend Snippet: Regulation of the PKR pathway in HeLa cells. Subconfluent monolayers of HeLa cells were transfected with either pcDNA, pcDNA:25R or pcDNA:57R for 20 – 24 hours and then treated with 500 ng of poly I:C. At 6 hpt of polyI:C, (A.) total proteins were harvested, separated by SDS-PAGE electrophoresis followed by Western blot analysis using the indicated antibodies. Bands were visualized by chemiluminescence. (B.) Quantification of PKR phosphorylation. The experiment was repeated multiple times and the quantity of PKR phosphorylation was determined using the GeneTools (Syngene) analysis software. The relative intensity of each phosphorylated PKR was normalized to levels observed in mock treated cells. Data presented are averages and standard error from multiple independent experiments. Statistical analysis was performed using ANOVA and statistically significant differences are indicated (*; P value

    Article Snippet: The relative intensity of proteins was quantified using the GeneTools analysis software (Syngene).

    Techniques: Transfection, SDS Page, Electrophoresis, Western Blot, Software

    Characterization of γ -secretase in vitro assay with guinea pig brain enzyme. ~1 μ g of purified recombinant C100-3XFLAG was incubated with 2.75 μ g of CHAPSO solubilised membranes of guinea pig brain in 20 mM HEPES buffer, pH 7.3, plus 3 mM CaCl 2 , 3 mM MgCl 2 and 150 mM KCl. The reactions were stopped by adding Laemmli buffer, boiled, and separated on Tris-Tricine gels. M2 (anti-FLAG) antibody and WO2 (anti-A β 1–16) were used for western blot detection. (a) Production of an AICD fragment in the assay is inhibited by the γ -secretase inhibitors, L-685,458 and DAPT. (b) Both AICD and A β are produced in the reaction and inhibited by L-685,458. AICD signal increases in a time dependent manner over 20 h. A β signal is increased at 4 h compared to 2 h, but decreased at 20 h, possibly due to degradation. (Inc, incubation at 37°C). (c) Positive effect of phospholipids on AICD production in the γ -secretase assay. PC, phosphatidylcholine; PE, phosphatidylethanolamine. (d) Positive effect of ATP on the γ -secretase assay. ATP was added 1.25 mM concentration. (e) Quantitation of three separate experiments using GeneTools Syngene software shows ~1.6 fold enhancement of γ -secretase activity in the presence of 1.25 mM ATP. The error bars represent SEM.

    Journal: International Journal of Alzheimer's Disease

    Article Title: Effect of Metal Chelators on γ-Secretase Indicates That Calcium and Magnesium Ions Facilitate Cleavage of Alzheimer Amyloid Precursor Substrate

    doi: 10.4061/2011/950932

    Figure Lengend Snippet: Characterization of γ -secretase in vitro assay with guinea pig brain enzyme. ~1 μ g of purified recombinant C100-3XFLAG was incubated with 2.75 μ g of CHAPSO solubilised membranes of guinea pig brain in 20 mM HEPES buffer, pH 7.3, plus 3 mM CaCl 2 , 3 mM MgCl 2 and 150 mM KCl. The reactions were stopped by adding Laemmli buffer, boiled, and separated on Tris-Tricine gels. M2 (anti-FLAG) antibody and WO2 (anti-A β 1–16) were used for western blot detection. (a) Production of an AICD fragment in the assay is inhibited by the γ -secretase inhibitors, L-685,458 and DAPT. (b) Both AICD and A β are produced in the reaction and inhibited by L-685,458. AICD signal increases in a time dependent manner over 20 h. A β signal is increased at 4 h compared to 2 h, but decreased at 20 h, possibly due to degradation. (Inc, incubation at 37°C). (c) Positive effect of phospholipids on AICD production in the γ -secretase assay. PC, phosphatidylcholine; PE, phosphatidylethanolamine. (d) Positive effect of ATP on the γ -secretase assay. ATP was added 1.25 mM concentration. (e) Quantitation of three separate experiments using GeneTools Syngene software shows ~1.6 fold enhancement of γ -secretase activity in the presence of 1.25 mM ATP. The error bars represent SEM.

    Article Snippet: Data were analysed using GeneTools software (Syngene). γ -Secretase activity was expressed as the ratio of AICD signal to the sum of C100 plus AICD signals after subtracting blank values.

    Techniques: In Vitro, Purification, Recombinant, Incubation, Western Blot, Produced, Concentration Assay, Quantitation Assay, Software, Activity Assay

    Effect of metalloprotease inhibitors, and metal chelators on γ -secretase. Chelators and inhibitors were added as DMSO solutions (final DMSO concentration 2.5%) to the guinea pig brain γ -secretase/C100-3XFLAG reactions. (a) Representative western blot of γ -secretase assay in the presence of various inhibitors. Phpm, phosphoramidon; Ilmst, ilomastat; Pht, phenanthroline; CQ, clioquinol; γ -inh, L-685,458, used at 10 nM (lane 6) and 100 nM (lane 7). (b) Effect of metalloprotease inhibitors on the γ -secretase assay. Activity is expressed as the % of substrate converted into AICD, as determined from band density analysis with GeneTools software. The error bars represent SEM. Inhibitor concentrations were selected as follows: thiorphan, 250 nM; phosphoramidon, 25 μ M; ilomastat, 250 nM; phenanthroline, 5 mM; clioquinol, 100 μ M.

    Journal: International Journal of Alzheimer's Disease

    Article Title: Effect of Metal Chelators on γ-Secretase Indicates That Calcium and Magnesium Ions Facilitate Cleavage of Alzheimer Amyloid Precursor Substrate

    doi: 10.4061/2011/950932

    Figure Lengend Snippet: Effect of metalloprotease inhibitors, and metal chelators on γ -secretase. Chelators and inhibitors were added as DMSO solutions (final DMSO concentration 2.5%) to the guinea pig brain γ -secretase/C100-3XFLAG reactions. (a) Representative western blot of γ -secretase assay in the presence of various inhibitors. Phpm, phosphoramidon; Ilmst, ilomastat; Pht, phenanthroline; CQ, clioquinol; γ -inh, L-685,458, used at 10 nM (lane 6) and 100 nM (lane 7). (b) Effect of metalloprotease inhibitors on the γ -secretase assay. Activity is expressed as the % of substrate converted into AICD, as determined from band density analysis with GeneTools software. The error bars represent SEM. Inhibitor concentrations were selected as follows: thiorphan, 250 nM; phosphoramidon, 25 μ M; ilomastat, 250 nM; phenanthroline, 5 mM; clioquinol, 100 μ M.

    Article Snippet: Data were analysed using GeneTools software (Syngene). γ -Secretase activity was expressed as the ratio of AICD signal to the sum of C100 plus AICD signals after subtracting blank values.

    Techniques: Concentration Assay, Western Blot, Activity Assay, Software

    Hierarchical clustering of antioxidant gene expression in the flowers of three grape cultivars following GA 3 treatment. Results of semi-quantitative RT-PCR assays were quantified using GeneTools software, and log-transformed values of the relative expression levels of genes encoding antioxidant enzymes following GA 3 treatment compared to untreated controls were used for hierarchical cluster analysis. The color scale represents relative expression levels with red denoting up-regulation and green denoting down-regulation. Sampling times are indicated at the top of the figure; F represents floral tissue; K represents the ‘Kyoho’ cultivar; R represents the ‘Red Globe’ cultivar; T represents the ‘Thompson seedless’ cultivar.

    Journal: PLoS ONE

    Article Title: Effect of GA3 Treatment on Seed Development and Seed-Related Gene Expression in Grape

    doi: 10.1371/journal.pone.0080044

    Figure Lengend Snippet: Hierarchical clustering of antioxidant gene expression in the flowers of three grape cultivars following GA 3 treatment. Results of semi-quantitative RT-PCR assays were quantified using GeneTools software, and log-transformed values of the relative expression levels of genes encoding antioxidant enzymes following GA 3 treatment compared to untreated controls were used for hierarchical cluster analysis. The color scale represents relative expression levels with red denoting up-regulation and green denoting down-regulation. Sampling times are indicated at the top of the figure; F represents floral tissue; K represents the ‘Kyoho’ cultivar; R represents the ‘Red Globe’ cultivar; T represents the ‘Thompson seedless’ cultivar.

    Article Snippet: The results of all semi-quantitative RT-PCR assays were quantified using GeneTools software (Syngene, Frederick, MD, USA) and log-transformed values of relative expression levels following GA3 treatment compared to untreated controls were used for hierarchical cluster analysis with the MultiExperiment Viewer (MeV version 4.8.1, http://www.tm4.org/).

    Techniques: Expressing, Quantitative RT-PCR, Software, Transformation Assay, Sampling

    Hierarchical clustering of genes related to seed development in three grape cultivars following GA 3 treatment. Results of semi-quantitative RT-PCR assays were quantified using GeneTools software, and log-transformed values of the relative expression levels of genes involved in seed development following GA 3 treatments compared to untreated controls were used for hierarchical cluster analysis. The color scale represents relative expression levels with red denoting up-regulation and green denoting down-regulation. Sampling times are indicated at the top of the figure; F represents floral tissue; K represents the ‘Kyoho’ cultivar; S represents seed tissue; R represents the ‘Red Globe’ cultivar; T represents the ‘Thompson seedless’ cultivar.

    Journal: PLoS ONE

    Article Title: Effect of GA3 Treatment on Seed Development and Seed-Related Gene Expression in Grape

    doi: 10.1371/journal.pone.0080044

    Figure Lengend Snippet: Hierarchical clustering of genes related to seed development in three grape cultivars following GA 3 treatment. Results of semi-quantitative RT-PCR assays were quantified using GeneTools software, and log-transformed values of the relative expression levels of genes involved in seed development following GA 3 treatments compared to untreated controls were used for hierarchical cluster analysis. The color scale represents relative expression levels with red denoting up-regulation and green denoting down-regulation. Sampling times are indicated at the top of the figure; F represents floral tissue; K represents the ‘Kyoho’ cultivar; S represents seed tissue; R represents the ‘Red Globe’ cultivar; T represents the ‘Thompson seedless’ cultivar.

    Article Snippet: The results of all semi-quantitative RT-PCR assays were quantified using GeneTools software (Syngene, Frederick, MD, USA) and log-transformed values of relative expression levels following GA3 treatment compared to untreated controls were used for hierarchical cluster analysis with the MultiExperiment Viewer (MeV version 4.8.1, http://www.tm4.org/).

    Techniques: Quantitative RT-PCR, Software, Transformation Assay, Expressing, Sampling

    Filamin B knockdown inhibits the replication of HBV. ( A ) Huh7 and HepG2 cells were transfected with siNC, filamin B-targeting siFLNB-1, siFLNB-2 or siFLNB-3 separately. Western blot analysis of filamin B was used to confirm the silencing efficiency. ( B ) Levels of HBV total RNAs and pgRNA in Huh7 cells were determined by real-time PCR. ( C ) Levels of HBV total RNAs and pgRNA in HepG2 cells were determined by real-time PCR. ( D ) Levels of HBeAg and HBsAg in culture medium supernatant of Huh7 cells were detected with ELISA. ( E ) Levels of HBeAg and HBsAg in culture medium supernatant of HepG2 cells were detected with ELISA. ( F ) HBV DNA was extracted at 96 h post transfection, and then subjected to Southern blotting. Western blot showed that filamin B was successfully knocked down. Co-transfection with pHBV1.3 and siNC was used as a loading control. Ratios were quantified by gray analysis with GeneTools from Syngene software (GeneGnome5). rcDNA, relaxed circular DNA; dsDNA, double stranded DNA; ssDNA, single stranded DNA. All results are shown as mean ± SD. (* P

    Journal: Virologica Sinica

    Article Title: Mechanisms and Effects on HBV Replication of the Interaction between HBV Core Protein and Cellular Filamin B

    doi: 10.1007/s12250-018-0023-4

    Figure Lengend Snippet: Filamin B knockdown inhibits the replication of HBV. ( A ) Huh7 and HepG2 cells were transfected with siNC, filamin B-targeting siFLNB-1, siFLNB-2 or siFLNB-3 separately. Western blot analysis of filamin B was used to confirm the silencing efficiency. ( B ) Levels of HBV total RNAs and pgRNA in Huh7 cells were determined by real-time PCR. ( C ) Levels of HBV total RNAs and pgRNA in HepG2 cells were determined by real-time PCR. ( D ) Levels of HBeAg and HBsAg in culture medium supernatant of Huh7 cells were detected with ELISA. ( E ) Levels of HBeAg and HBsAg in culture medium supernatant of HepG2 cells were detected with ELISA. ( F ) HBV DNA was extracted at 96 h post transfection, and then subjected to Southern blotting. Western blot showed that filamin B was successfully knocked down. Co-transfection with pHBV1.3 and siNC was used as a loading control. Ratios were quantified by gray analysis with GeneTools from Syngene software (GeneGnome5). rcDNA, relaxed circular DNA; dsDNA, double stranded DNA; ssDNA, single stranded DNA. All results are shown as mean ± SD. (* P

    Article Snippet: Ratios were quantified by gray analysis using GeneTools from Syngene software (GeneGnome5).

    Techniques: Transfection, Western Blot, Real-time Polymerase Chain Reaction, Enzyme-linked Immunosorbent Assay, Southern Blot, Cotransfection, Software

    Interaction of filamin B and core protein promotes HBV replication. ( A ) Levels of HBV total RNAs and pgRNA in Huh7 cells were determined by real-time PCR. ( B ) HBV total RNAs and pgRNA levels in HepG2 cells were determined by real-time PCR. ( C ) Levels of HBeAg and HBsAg in culture medium supernatant of Huh7 cells were detected with ELISA. ( D ) Levels of HBeAg and HBsAg in culture medium supernatant of HepG2 cells were detected with ELISA. ( E ) HBV DNA was extracted at 96 h post-transfection and subjected to Southern blotting. Western blot showed that all proteins were overexpressed. Co-transfection with pHBV1.3, GFP and pXJ40-HA was used as a loading control. Ratios were quantified by gray analysis with GeneTools from Syngene software (GeneGnome5). HBV DNA marker bands are shown for relaxed circular DNA (rcDNA), double stranded DNA (dsDNA), and single stranded DNA (ssDNA). All results are shown as mean ± SD. (* P

    Journal: Virologica Sinica

    Article Title: Mechanisms and Effects on HBV Replication of the Interaction between HBV Core Protein and Cellular Filamin B

    doi: 10.1007/s12250-018-0023-4

    Figure Lengend Snippet: Interaction of filamin B and core protein promotes HBV replication. ( A ) Levels of HBV total RNAs and pgRNA in Huh7 cells were determined by real-time PCR. ( B ) HBV total RNAs and pgRNA levels in HepG2 cells were determined by real-time PCR. ( C ) Levels of HBeAg and HBsAg in culture medium supernatant of Huh7 cells were detected with ELISA. ( D ) Levels of HBeAg and HBsAg in culture medium supernatant of HepG2 cells were detected with ELISA. ( E ) HBV DNA was extracted at 96 h post-transfection and subjected to Southern blotting. Western blot showed that all proteins were overexpressed. Co-transfection with pHBV1.3, GFP and pXJ40-HA was used as a loading control. Ratios were quantified by gray analysis with GeneTools from Syngene software (GeneGnome5). HBV DNA marker bands are shown for relaxed circular DNA (rcDNA), double stranded DNA (dsDNA), and single stranded DNA (ssDNA). All results are shown as mean ± SD. (* P

    Article Snippet: Ratios were quantified by gray analysis using GeneTools from Syngene software (GeneGnome5).

    Techniques: Real-time Polymerase Chain Reaction, Enzyme-linked Immunosorbent Assay, Transfection, Southern Blot, Western Blot, Cotransfection, Software, Marker