ecori  (Thermo Fisher)


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  • 99
    Name:
    EcoRI 10 U µL
    Description:
    5 G ↓A A T T C 3 3 C T T A A ↑G 5 Thermo Scientific EcoRI restriction enzyme recognizes G AATTC sites and cuts best at 37°C in its own unique buffer See Reaction Conditions for Restriction Enzymes for a table of enzyme activity conditions for double digestion and heat inactivation for this and other restriction enzymes Note Also available as a FastDigest enzyme for rapid DNA digestion Thermo Scientific conventional restriction endonucleases are a large collection of high quality restriction enzymes optimized to work in one of the buffers of the Five Buffer System In addition the universal Tango buffer is provided for convenience in double digestions All of the enzymes exhibit 100 activity in the recommended buffer and reaction conditions To ensure consistent performance Thermo Scientific restriction enzyme reaction buffers contain premixed BSA which enhances the stability of many enzymes and binds contaminants that sent in DNA preparations Features• Superior quality stringent quality control and industry leading manufacturing process• Convenient color coded Five Buffer System• Includes universal Tango buffer for double digestions• BSA premixed in reaction buffers• Wide selection of restriction endonuclease specificitiesApplications• Molecular cloning• Restriction site mapping• Genotyping• Southern blotting• Restriction fragment length polymorphism RFLP • SNPNote For methylation sensitivity refer to product specifications
    Catalog Number:
    er0271
    Price:
    None
    Applications:
    Cloning|Restriction Enzyme Cloning
    Category:
    Proteins Enzymes Peptides
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    Structured Review

    Thermo Fisher ecori
    Analysis of DNA fractions obtained by SRD and MND treatment of sperm nuclei. All DNA samples were resolved on 1.8% agarose gels. (Lane 1 ) A 0.4–10-kb DNA ladder. (Lane 2 ) Total (unfractionated) DNA (NF). (Lane 3 ) The soluble DNA released after extraction of sperm nuclei with 0.65 M NaCl followed by digestion with <t>BamHI</t> and <t>EcoRI</t> (SRDS). (Lane 5 ) The corresponding insoluble pellet (SRDI). (Lane 4 ) DNA released from sperm after MNase digestion (MNDS). (Lane 6 ) The corresponding insoluble pellet (MNDI).
    5 G ↓A A T T C 3 3 C T T A A ↑G 5 Thermo Scientific EcoRI restriction enzyme recognizes G AATTC sites and cuts best at 37°C in its own unique buffer See Reaction Conditions for Restriction Enzymes for a table of enzyme activity conditions for double digestion and heat inactivation for this and other restriction enzymes Note Also available as a FastDigest enzyme for rapid DNA digestion Thermo Scientific conventional restriction endonucleases are a large collection of high quality restriction enzymes optimized to work in one of the buffers of the Five Buffer System In addition the universal Tango buffer is provided for convenience in double digestions All of the enzymes exhibit 100 activity in the recommended buffer and reaction conditions To ensure consistent performance Thermo Scientific restriction enzyme reaction buffers contain premixed BSA which enhances the stability of many enzymes and binds contaminants that sent in DNA preparations Features• Superior quality stringent quality control and industry leading manufacturing process• Convenient color coded Five Buffer System• Includes universal Tango buffer for double digestions• BSA premixed in reaction buffers• Wide selection of restriction endonuclease specificitiesApplications• Molecular cloning• Restriction site mapping• Genotyping• Southern blotting• Restriction fragment length polymorphism RFLP • SNPNote For methylation sensitivity refer to product specifications
    https://www.bioz.com/result/ecori/product/Thermo Fisher
    Average 99 stars, based on 1322 article reviews
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    ecori - by Bioz Stars, 2020-07
    99/100 stars

    Images

    1) Product Images from "Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences"

    Article Title: Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences

    Journal: Genome Research

    doi: 10.1101/gr.094953.109

    Analysis of DNA fractions obtained by SRD and MND treatment of sperm nuclei. All DNA samples were resolved on 1.8% agarose gels. (Lane 1 ) A 0.4–10-kb DNA ladder. (Lane 2 ) Total (unfractionated) DNA (NF). (Lane 3 ) The soluble DNA released after extraction of sperm nuclei with 0.65 M NaCl followed by digestion with BamHI and EcoRI (SRDS). (Lane 5 ) The corresponding insoluble pellet (SRDI). (Lane 4 ) DNA released from sperm after MNase digestion (MNDS). (Lane 6 ) The corresponding insoluble pellet (MNDI).
    Figure Legend Snippet: Analysis of DNA fractions obtained by SRD and MND treatment of sperm nuclei. All DNA samples were resolved on 1.8% agarose gels. (Lane 1 ) A 0.4–10-kb DNA ladder. (Lane 2 ) Total (unfractionated) DNA (NF). (Lane 3 ) The soluble DNA released after extraction of sperm nuclei with 0.65 M NaCl followed by digestion with BamHI and EcoRI (SRDS). (Lane 5 ) The corresponding insoluble pellet (SRDI). (Lane 4 ) DNA released from sperm after MNase digestion (MNDS). (Lane 6 ) The corresponding insoluble pellet (MNDI).

    Techniques Used:

    2) Product Images from "Human Mre11/Human Rad50/Nbs1 and DNA Ligase III?/XRCC1 Protein Complexes Act Together in an Alternative Nonhomologous End Joining Pathway *"

    Article Title: Human Mre11/Human Rad50/Nbs1 and DNA Ligase III?/XRCC1 Protein Complexes Act Together in an Alternative Nonhomologous End Joining Pathway *

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M111.274159

    Joining of incompatible DNA ends by MRN and DNA ligase IIIα/XRCC1: microhomology-mediated joining of DNA ends with incompatible 5′ overhangs. A , circular plasmid DNA was digested with either KpnI ( left ) and PstI ( right ) to generate noncomplementary 3′ overhangs or EcoRI ( left ) and BamHI ( right ), to generate noncomplementary 5′ overhangs. Joining of the incompatible DNA ends was detected by the PCR using the indicated primers. B , DNA substrate (0.8 pmol) with noncomplementary 3′ overhangs was incubated with 0.01 pmol of DNA ligase IIIα/XRCC1 alone or in combination with equimolar amounts of hMre11 and MRN as indicated. C , DNA substrate (0.8 pmol) with noncomplementary 5′ overhangs was incubated with 0.01 pmol of DNA ligase IIIα/XRCC1 alone or in combination with equimolar amounts of hMre11 and MRN as indicated. D , DNA substrate (0.8 pmol) with noncomplementary 5′ overhangs was incubated with 0.01 pmol of either DNA ligase IIIα/XRCC1 or DNA ligase IV/XRCC4 in the absence or presence of an equimolar amount of MRN. E , sequences of the junctions generated by the joining of incompatible 5′ ends by DNA ligase IIIα/XRCC1 in combination with either hMre11 or MRN are shown. Bolded residues indicate microhomologies.
    Figure Legend Snippet: Joining of incompatible DNA ends by MRN and DNA ligase IIIα/XRCC1: microhomology-mediated joining of DNA ends with incompatible 5′ overhangs. A , circular plasmid DNA was digested with either KpnI ( left ) and PstI ( right ) to generate noncomplementary 3′ overhangs or EcoRI ( left ) and BamHI ( right ), to generate noncomplementary 5′ overhangs. Joining of the incompatible DNA ends was detected by the PCR using the indicated primers. B , DNA substrate (0.8 pmol) with noncomplementary 3′ overhangs was incubated with 0.01 pmol of DNA ligase IIIα/XRCC1 alone or in combination with equimolar amounts of hMre11 and MRN as indicated. C , DNA substrate (0.8 pmol) with noncomplementary 5′ overhangs was incubated with 0.01 pmol of DNA ligase IIIα/XRCC1 alone or in combination with equimolar amounts of hMre11 and MRN as indicated. D , DNA substrate (0.8 pmol) with noncomplementary 5′ overhangs was incubated with 0.01 pmol of either DNA ligase IIIα/XRCC1 or DNA ligase IV/XRCC4 in the absence or presence of an equimolar amount of MRN. E , sequences of the junctions generated by the joining of incompatible 5′ ends by DNA ligase IIIα/XRCC1 in combination with either hMre11 or MRN are shown. Bolded residues indicate microhomologies.

    Techniques Used: Plasmid Preparation, Polymerase Chain Reaction, Incubation, Generated

    3) Product Images from "Characterization of diverse homoserine lactone synthases in Escherichia coli"

    Article Title: Characterization of diverse homoserine lactone synthases in Escherichia coli

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0202294

    Sender plasmids expressed in Escherichia coli BL21. (A) The modular Sender vector allows facile cloning of any EcoRI , XbaI -flanked synthase open reading frame (ORF) and co-expression with mCherry (mCh) from a single bicistronic mRNA. The vector is represented as SBOL [ 44 ] glyphs (top) and a scaled circular map (bottom). (B) Optical density (OD) readings for E . coli cultures expressing each of the Sender plasmids. (C) mCherry expression is shown as end-point RFP signal normalized to OD 600 after an 8 hour growth period.
    Figure Legend Snippet: Sender plasmids expressed in Escherichia coli BL21. (A) The modular Sender vector allows facile cloning of any EcoRI , XbaI -flanked synthase open reading frame (ORF) and co-expression with mCherry (mCh) from a single bicistronic mRNA. The vector is represented as SBOL [ 44 ] glyphs (top) and a scaled circular map (bottom). (B) Optical density (OD) readings for E . coli cultures expressing each of the Sender plasmids. (C) mCherry expression is shown as end-point RFP signal normalized to OD 600 after an 8 hour growth period.

    Techniques Used: Plasmid Preparation, Clone Assay, Expressing

    4) Product Images from "Iterative Mechanism of Macrodiolide Formation in the Anticancer Compound Conglobatin"

    Article Title: Iterative Mechanism of Macrodiolide Formation in the Anticancer Compound Conglobatin

    Journal: Chemistry & Biology

    doi: 10.1016/j.chembiol.2015.05.010

    One-Step Cloning and Heterologous Expression of the Conglobatin Gene Cluster (A) A 41-kbp XhoI-EcoRI DNA fragment (black) containing the five genes congA–E is generated by XhoI and EcoRI digestion of total genomic DNA. A 5.3-kbp pSET152 fragment was obtained by PCR amplification using as template the pSET152-derived plasmid pIB139. The resulting linear vector fragment had 39- and 41-bp flanking regions, respectively, identical to the termini of the target DNA (see Experimental Procedures ). (B) Gibson assembly leads to specific cloning of the target fragment, to give the bifunctional E. coli - Streptomyces plasmid pYJ24. The deduced open reading frame functions in the fragment are given in Table S1 . (C) Heterologous expression in S. coelicolor M1154 is confirmed by HPLC-MS and comparison with authentic compound produced by S. conglobatus (see also Figure S1 ). The mass extraction of m / z 499–500 is used to display the data. The y axis scale of S. conglobatus is 20 times larger than that of pYJ24/M1154 or M1154.
    Figure Legend Snippet: One-Step Cloning and Heterologous Expression of the Conglobatin Gene Cluster (A) A 41-kbp XhoI-EcoRI DNA fragment (black) containing the five genes congA–E is generated by XhoI and EcoRI digestion of total genomic DNA. A 5.3-kbp pSET152 fragment was obtained by PCR amplification using as template the pSET152-derived plasmid pIB139. The resulting linear vector fragment had 39- and 41-bp flanking regions, respectively, identical to the termini of the target DNA (see Experimental Procedures ). (B) Gibson assembly leads to specific cloning of the target fragment, to give the bifunctional E. coli - Streptomyces plasmid pYJ24. The deduced open reading frame functions in the fragment are given in Table S1 . (C) Heterologous expression in S. coelicolor M1154 is confirmed by HPLC-MS and comparison with authentic compound produced by S. conglobatus (see also Figure S1 ). The mass extraction of m / z 499–500 is used to display the data. The y axis scale of S. conglobatus is 20 times larger than that of pYJ24/M1154 or M1154.

    Techniques Used: Clone Assay, Expressing, Generated, Polymerase Chain Reaction, Amplification, Derivative Assay, Plasmid Preparation, High Performance Liquid Chromatography, Mass Spectrometry, Produced

    5) Product Images from "Glutamate Activates AMPA Receptor Conductance in the Developing Schwann Cells of the Mammalian Peripheral Nerves"

    Article Title: Glutamate Activates AMPA Receptor Conductance in the Developing Schwann Cells of the Mammalian Peripheral Nerves

    Journal: The Journal of Neuroscience

    doi: 10.1523/JNEUROSCI.1168-17.2017

    Detection of AMPAR subunits in the mouse sciatic nerve. A , cDNA for GluA1–GluA4 subunits obtained after the second round of PCR was analyzed with electrophoresis in agarose gel. An example gel is shown. The predicted size of the PCR products was as follows: 632 bp for GluA1, 628 bp for GluA2, 630 bp for GluA3, and 626 bp for GluA4. A1, A2, A3, and A4 represent GluA1, GluA2, GluA3, and GluA4, respectively. M denotes the φX174 DNA/HaeIII molecular weight marker. Band size for the marker is indicated on the left. B , Products of GluA1, GluA2, GluA3, and GluA4 obtained after the second round of PCR were digested with restriction enzymes specific for each subunit : PstI (275 and 357 bp) for GluA1 , SduI (270 and 358 bp) for GluA2, Eco47III (229 and 401 bp) for GluA3, and EcoRI (289 and 337 bp) for GluA4. An example gel is shown. cDNA for each subunits was cut into two fragments of the predicted size. A1, A2, A3, and A4 represent GluA1, GluA2, GluA3, and GluA4, respectively. M denotes the pUC19 DNA/MspI (Hpall) molecular weight marker. Band size for the marker is indicated on the left. Throughout the figure, for positive controls, total RNA was extracted from HEK293 cells transfected with a plasmid encoding GluA1, GluA2, GluA3, or GluA4; this RNA was used as a template. For a negative control, the template was omitted. During RT-PCR, second-round PCR, and digestion, the samples of positive and negative control were always processed in parallel with the samples of RNA extracted from the sciatic nerves.
    Figure Legend Snippet: Detection of AMPAR subunits in the mouse sciatic nerve. A , cDNA for GluA1–GluA4 subunits obtained after the second round of PCR was analyzed with electrophoresis in agarose gel. An example gel is shown. The predicted size of the PCR products was as follows: 632 bp for GluA1, 628 bp for GluA2, 630 bp for GluA3, and 626 bp for GluA4. A1, A2, A3, and A4 represent GluA1, GluA2, GluA3, and GluA4, respectively. M denotes the φX174 DNA/HaeIII molecular weight marker. Band size for the marker is indicated on the left. B , Products of GluA1, GluA2, GluA3, and GluA4 obtained after the second round of PCR were digested with restriction enzymes specific for each subunit : PstI (275 and 357 bp) for GluA1 , SduI (270 and 358 bp) for GluA2, Eco47III (229 and 401 bp) for GluA3, and EcoRI (289 and 337 bp) for GluA4. An example gel is shown. cDNA for each subunits was cut into two fragments of the predicted size. A1, A2, A3, and A4 represent GluA1, GluA2, GluA3, and GluA4, respectively. M denotes the pUC19 DNA/MspI (Hpall) molecular weight marker. Band size for the marker is indicated on the left. Throughout the figure, for positive controls, total RNA was extracted from HEK293 cells transfected with a plasmid encoding GluA1, GluA2, GluA3, or GluA4; this RNA was used as a template. For a negative control, the template was omitted. During RT-PCR, second-round PCR, and digestion, the samples of positive and negative control were always processed in parallel with the samples of RNA extracted from the sciatic nerves.

    Techniques Used: Polymerase Chain Reaction, Electrophoresis, Agarose Gel Electrophoresis, Molecular Weight, Marker, Transfection, Plasmid Preparation, Negative Control, Reverse Transcription Polymerase Chain Reaction

    6) Product Images from "Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex"

    Article Title: Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-11-599

    Isolation of the KS14 plasmid prophage . DNA was isolated using a QIAprep Spin Miniprep plasmid isolation kit (Qiagen) and digested with EcoRI (Invitrogen). Lane 1: 1 Kb Plus DNA ladder (Invitrogen), lane 2: B. cenocepacia C6433, lane 3: B. multivorans ATCC 17616, lane 4: B. cenocepacia CEP511 lane 5: B. cenocepacia K56-2, lane 6: blank, lane 7: 1 Kb Plus DNA ladder, lane 8: KS14-resistant C6433 isolate I, lane 9: KS14-resistant C6433 isolate II, lane 10: KS14-resistant C6433 isolate III, lane 11: KS14-resistant C6433 isolate IV, lane 12: KS14-resistant C6433 isolate V. The size of the markers (in kbp) is shown on the left. A KS14 EcoRI DNA digest and the size of the bands predicted for this digest ( > 1 kbp in size) are shown on the far right.
    Figure Legend Snippet: Isolation of the KS14 plasmid prophage . DNA was isolated using a QIAprep Spin Miniprep plasmid isolation kit (Qiagen) and digested with EcoRI (Invitrogen). Lane 1: 1 Kb Plus DNA ladder (Invitrogen), lane 2: B. cenocepacia C6433, lane 3: B. multivorans ATCC 17616, lane 4: B. cenocepacia CEP511 lane 5: B. cenocepacia K56-2, lane 6: blank, lane 7: 1 Kb Plus DNA ladder, lane 8: KS14-resistant C6433 isolate I, lane 9: KS14-resistant C6433 isolate II, lane 10: KS14-resistant C6433 isolate III, lane 11: KS14-resistant C6433 isolate IV, lane 12: KS14-resistant C6433 isolate V. The size of the markers (in kbp) is shown on the left. A KS14 EcoRI DNA digest and the size of the bands predicted for this digest ( > 1 kbp in size) are shown on the far right.

    Techniques Used: Isolation, Plasmid Preparation

    7) Product Images from "Genome Analysis of Lactobacillus plantarum LL441 and Genetic Characterisation of the Locus for the Lantibiotic Plantaricin C"

    Article Title: Genome Analysis of Lactobacillus plantarum LL441 and Genetic Characterisation of the Locus for the Lantibiotic Plantaricin C

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2018.01916

    Gel electrophoresis of chromosomal and plasmid DNA from L. plantarum LL441 (A) and Southern blot results (B) of the gel in A after transferring of the DNA to a membrane and hybridizing with a digoxigenin-labeled probe (Roche) based on an internal 1-kbp fragment of the lanM gene ( Figure 1 ) amplified by PCR. Order of the samples: 1, undigested chromosomal DNA from LL441; 2, 3, and 4, chromosomal DNA digested with PstI, EcoRI, and HindIII, respectively; 5, undigested plasmid DNA from LL441; 6, 7, and 8, plasmid DNA digested with PstI, EcoRI, and HindIII, respectively. A and B, pre-hybridized molecular weight markers: lambda DNA digested with PstI and lambda DNA digested with HindIII, respectively.
    Figure Legend Snippet: Gel electrophoresis of chromosomal and plasmid DNA from L. plantarum LL441 (A) and Southern blot results (B) of the gel in A after transferring of the DNA to a membrane and hybridizing with a digoxigenin-labeled probe (Roche) based on an internal 1-kbp fragment of the lanM gene ( Figure 1 ) amplified by PCR. Order of the samples: 1, undigested chromosomal DNA from LL441; 2, 3, and 4, chromosomal DNA digested with PstI, EcoRI, and HindIII, respectively; 5, undigested plasmid DNA from LL441; 6, 7, and 8, plasmid DNA digested with PstI, EcoRI, and HindIII, respectively. A and B, pre-hybridized molecular weight markers: lambda DNA digested with PstI and lambda DNA digested with HindIII, respectively.

    Techniques Used: Nucleic Acid Electrophoresis, Plasmid Preparation, Southern Blot, Transferring, Labeling, Amplification, Polymerase Chain Reaction, Molecular Weight, Lambda DNA Preparation

    8) Product Images from "Detection of Molecular Diversity in Bacillus atrophaeus by Amplified Fragment Length Polymorphism Analysis"

    Article Title: Detection of Molecular Diversity in Bacillus atrophaeus by Amplified Fragment Length Polymorphism Analysis

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.70.5.2786-2790.2004

    Digitized AFLP patterns of Bacillus taxa generated using primer sets EcoRI plus C/MseI plus CA (A) and EcoRI plus C/MseI plus CC (B). Across the top of each image is the fragment size scale (in bases). The Bacillus species and strain designations for
    Figure Legend Snippet: Digitized AFLP patterns of Bacillus taxa generated using primer sets EcoRI plus C/MseI plus CA (A) and EcoRI plus C/MseI plus CC (B). Across the top of each image is the fragment size scale (in bases). The Bacillus species and strain designations for

    Techniques Used: Generated

    9) Product Images from "Inhibition of Hepatitis B Virus Replication by MyD88 Involves Accelerated Degradation of Pregenomic RNA and Nuclear Retention of Pre-S/S RNAs ▿"

    Article Title: Inhibition of Hepatitis B Virus Replication by MyD88 Involves Accelerated Degradation of Pregenomic RNA and Nuclear Retention of Pre-S/S RNAs ▿

    Journal: Journal of Virology

    doi: 10.1128/JVI.00236-10

    Mapping of the RNA sequence(s) in HBV pregenomic RNA responsible for HBV RNA decay. (A) Schematic diagram of the truncation and deletion mutants of HBV pregenomic RNA. The numbers indicate the HBV DNA sequence with 1 at the unique EcoRI site in the HBV genome. (B) Huh7 cells were transfected with 0.1 μg of luciferase fusion constructs containing the truncation mutants of HBV DNA and 0.2 μg of pCMV/Myc or pCMV/Myc-MyD88 for 48 h, and the luciferase activity was then assessed. For each transfection, 0.01 μg of pRL-tk was included as an internal control of transfection efficiency. Results represent the means of data from three independent experiments performed in duplicate. *, P
    Figure Legend Snippet: Mapping of the RNA sequence(s) in HBV pregenomic RNA responsible for HBV RNA decay. (A) Schematic diagram of the truncation and deletion mutants of HBV pregenomic RNA. The numbers indicate the HBV DNA sequence with 1 at the unique EcoRI site in the HBV genome. (B) Huh7 cells were transfected with 0.1 μg of luciferase fusion constructs containing the truncation mutants of HBV DNA and 0.2 μg of pCMV/Myc or pCMV/Myc-MyD88 for 48 h, and the luciferase activity was then assessed. For each transfection, 0.01 μg of pRL-tk was included as an internal control of transfection efficiency. Results represent the means of data from three independent experiments performed in duplicate. *, P

    Techniques Used: Sequencing, Transfection, Luciferase, Construct, Activity Assay

    10) Product Images from "Serial analysis of mutation spectra (SAMS): a new approach for the determination of mutation spectra of site-specific DNA damage and their sequence dependence"

    Article Title: Serial analysis of mutation spectra (SAMS): a new approach for the determination of mutation spectra of site-specific DNA damage and their sequence dependence

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkn595

    ( a ) Primer extension opposite an abasic site model in a random flanking sequence library of 16 possible sequences. The abasic site model F and its flanking random sequence are in bold. The EcoRI restriction sites are italicized, the 15-mer primer is underlined. The control template is identical to the F-containing template, except that F was not incorporated. ( b ) Formation of the sequence tags for oligomerization. Polyacrylamide gel electrophoresis of the products of PCR amplification of the bypass products of the abasic site and control sequence followed by restriction digestion with EcoRI. PCR primers are underlined.
    Figure Legend Snippet: ( a ) Primer extension opposite an abasic site model in a random flanking sequence library of 16 possible sequences. The abasic site model F and its flanking random sequence are in bold. The EcoRI restriction sites are italicized, the 15-mer primer is underlined. The control template is identical to the F-containing template, except that F was not incorporated. ( b ) Formation of the sequence tags for oligomerization. Polyacrylamide gel electrophoresis of the products of PCR amplification of the bypass products of the abasic site and control sequence followed by restriction digestion with EcoRI. PCR primers are underlined.

    Techniques Used: Sequencing, Polyacrylamide Gel Electrophoresis, Polymerase Chain Reaction, Amplification

    11) Product Images from "Regulation of p53 during senescence in normal human keratinocytes"

    Article Title: Regulation of p53 during senescence in normal human keratinocytes

    Journal: Aging Cell

    doi: 10.1111/acel.12364

    The loss of p53 enhances mutational frequency in normal human keratinocytes (NHKs). (A) NHKs infected with retrovirus expressing empty vector (EV) or p53shRNA (p53sh) were selected using puromycin (1 μg mL −1 ) and maintained. p53 expression was observed using Western blotting. (B) In vitro end joining assay was performed by incubating the lysates from these cells with ECoRI-or ECoRV- linearized pCR2.1-TOPO plasmid. The resultant reaction was subjected to PCR amplification with M13 primers to examine ligation efficiency. (C) Amplified PCR products from the ECoRI linearized and ligated pCR2.1-TOPO plasmid were subcloned and introduced into TOP10 cells. Subsequently, the single colony from a bacto-agar plate was subjected to PCR and sequencing analysis to examine errors in DNA. * p
    Figure Legend Snippet: The loss of p53 enhances mutational frequency in normal human keratinocytes (NHKs). (A) NHKs infected with retrovirus expressing empty vector (EV) or p53shRNA (p53sh) were selected using puromycin (1 μg mL −1 ) and maintained. p53 expression was observed using Western blotting. (B) In vitro end joining assay was performed by incubating the lysates from these cells with ECoRI-or ECoRV- linearized pCR2.1-TOPO plasmid. The resultant reaction was subjected to PCR amplification with M13 primers to examine ligation efficiency. (C) Amplified PCR products from the ECoRI linearized and ligated pCR2.1-TOPO plasmid were subcloned and introduced into TOP10 cells. Subsequently, the single colony from a bacto-agar plate was subjected to PCR and sequencing analysis to examine errors in DNA. * p

    Techniques Used: Infection, Expressing, Plasmid Preparation, Western Blot, In Vitro, Polymerase Chain Reaction, Amplification, Ligation, Sequencing

    12) Product Images from "Mutation of the histidin residue of the DRH motif in vasopressin V2 receptor expression and function"

    Article Title: Mutation of the histidin residue of the DRH motif in vasopressin V2 receptor expression and function

    Journal: DARU : Journal of Faculty of Pharmacy, Tehran University of Medical Sciences

    doi:

    Digestion of pcDNA3 plasmid containing wild type V2R by XbaI-EcoRI enzymes. Products of digestion were electrophoresed on 0.7% agarose gel. The band of V2R (1200 bp) was digested out of the pcDNA3 plasmid. M: molecular weight marker, 250 bp unit.
    Figure Legend Snippet: Digestion of pcDNA3 plasmid containing wild type V2R by XbaI-EcoRI enzymes. Products of digestion were electrophoresed on 0.7% agarose gel. The band of V2R (1200 bp) was digested out of the pcDNA3 plasmid. M: molecular weight marker, 250 bp unit.

    Techniques Used: Plasmid Preparation, Agarose Gel Electrophoresis, Molecular Weight, Marker

    13) Product Images from "RNA silencing of South African cassava mosaic virus in transgenic cassava expressing AC1/AC4 hp- RNA induces tolerance"

    Article Title: RNA silencing of South African cassava mosaic virus in transgenic cassava expressing AC1/AC4 hp- RNA induces tolerance

    Journal: Biotechnology Reports

    doi: 10.1016/j.btre.2019.e00383

    Southern hybridisation of total DNA from transgenic cassava cv.60444 transformed with SACMV AC1AC4 construct, digested with restriction enzymes EcoRI and HindIII, and hybridized with DNA probe specific to Hyg gene. Lane M: DIG-labelled molecular weight parker (ThermoFisher Scientific), lane 1-16: independent transgenic cassava lines. Purified binary vector pC1305.1-AC1/AC4 and wild-type untransformed cv.60444 were included as positive (+) and negative (-) controls respectively.
    Figure Legend Snippet: Southern hybridisation of total DNA from transgenic cassava cv.60444 transformed with SACMV AC1AC4 construct, digested with restriction enzymes EcoRI and HindIII, and hybridized with DNA probe specific to Hyg gene. Lane M: DIG-labelled molecular weight parker (ThermoFisher Scientific), lane 1-16: independent transgenic cassava lines. Purified binary vector pC1305.1-AC1/AC4 and wild-type untransformed cv.60444 were included as positive (+) and negative (-) controls respectively.

    Techniques Used: Hybridization, Transgenic Assay, Transformation Assay, Construct, Molecular Weight, Purification, Plasmid Preparation

    14) Product Images from "Roles of the Phosphorylation of Herpes Simplex Virus 1 UL51 at a Specific Site in Viral Replication and Pathogenicity"

    Article Title: Roles of the Phosphorylation of Herpes Simplex Virus 1 UL51 at a Specific Site in Viral Replication and Pathogenicity

    Journal: Journal of Virology

    doi: 10.1128/JVI.01035-18

    Strategy to construct a self-excisable HSV-1(F) BAC clone. (A) Lines 1 and 2, schematic diagrams of E. coli plasmid pYEbac102 and pYEbac102Cre, respectively, contained in GS1783; line 3, schematic diagrams of recombinant virus YK312 (ΔBAC). (B) Schematic diagram of the genome structures of wild-type HSV-1(F) and relevant domains of the recombinant viruses. Line 1, sequence arrangement of the HSV-1(F) genome. Line 2, location of the EcoRV-HindIII fragment used as a labeled probe in panel C. Line 3, an enlarged portion of the EcoRI J and D fragments of HSV-1(F). Lines 4 and 6, double-headed arrow represents the fragment region. Lines 5 and 7, summary of DNA fragments from recombinant viruses with or without the BAC sequence and the poly(A) signals. (C) Southern blot analysis of EcoRI-digested DNA isolated from YK312 (ΔBAC)- or YK304 (BAC)-infected cells using the EcoRV-HindIII fragment of pRB442 as a probe. The letters on the right refer to the designations of the DNA fragments generated by restriction endonuclease EcoRI cleavage.
    Figure Legend Snippet: Strategy to construct a self-excisable HSV-1(F) BAC clone. (A) Lines 1 and 2, schematic diagrams of E. coli plasmid pYEbac102 and pYEbac102Cre, respectively, contained in GS1783; line 3, schematic diagrams of recombinant virus YK312 (ΔBAC). (B) Schematic diagram of the genome structures of wild-type HSV-1(F) and relevant domains of the recombinant viruses. Line 1, sequence arrangement of the HSV-1(F) genome. Line 2, location of the EcoRV-HindIII fragment used as a labeled probe in panel C. Line 3, an enlarged portion of the EcoRI J and D fragments of HSV-1(F). Lines 4 and 6, double-headed arrow represents the fragment region. Lines 5 and 7, summary of DNA fragments from recombinant viruses with or without the BAC sequence and the poly(A) signals. (C) Southern blot analysis of EcoRI-digested DNA isolated from YK312 (ΔBAC)- or YK304 (BAC)-infected cells using the EcoRV-HindIII fragment of pRB442 as a probe. The letters on the right refer to the designations of the DNA fragments generated by restriction endonuclease EcoRI cleavage.

    Techniques Used: Construct, BAC Assay, Plasmid Preparation, Recombinant, Sequencing, Labeling, Southern Blot, Isolation, Infection, Generated

    15) Product Images from "Bacteriophage application for biocontrolling Shigella flexneri in contaminated foods"

    Article Title: Bacteriophage application for biocontrolling Shigella flexneri in contaminated foods

    Journal: Journal of Food Science and Technology

    doi: 10.1007/s13197-017-2964-2

    Phage vB_SflS-ISF001 genomic DNA size. Lane M: X-large DNA marker (SinaClon, Iran); lane 1: Untreated genomic DNA; lane 2: EcoRI; lane 3: EcoRV; lane 4: HindIII; lane 5: BamHI
    Figure Legend Snippet: Phage vB_SflS-ISF001 genomic DNA size. Lane M: X-large DNA marker (SinaClon, Iran); lane 1: Untreated genomic DNA; lane 2: EcoRI; lane 3: EcoRV; lane 4: HindIII; lane 5: BamHI

    Techniques Used: Marker

    16) Product Images from "The combined effect of Pdx1 overexpression and Shh manipulation on the function of insulin‐producing cells derived from adipose‐tissue stem cells"

    Article Title: The combined effect of Pdx1 overexpression and Shh manipulation on the function of insulin‐producing cells derived from adipose‐tissue stem cells

    Journal: FEBS Open Bio

    doi: 10.1002/2211-5463.12378

    (A) Characterization of Pdx1‐ pCDNA 3.1(+) vector. Lane 1: the recombinant plasmid before digestion. Lane 2: the 850‐bp Pdx1 gene separated from the recombinant Pdx1‐ pCDNA 3.1(+) digested using EcoRI and Hind III enzymes. Lane 3: 900‐bp PCR product of recombinant Pdx1‐ pCDNA 3.1(+) vector. Lane 4: 1‐kb DNA ladder. (B) Western blot analysis results. The CHO cells transfected with Pdx1‐ pCDNA 3.1(+) (lane 1) showed a significantly higher expression of Pdx1 compared with the CHO cells transfected with pCDNA 3.1(+) alone (Lane 2).
    Figure Legend Snippet: (A) Characterization of Pdx1‐ pCDNA 3.1(+) vector. Lane 1: the recombinant plasmid before digestion. Lane 2: the 850‐bp Pdx1 gene separated from the recombinant Pdx1‐ pCDNA 3.1(+) digested using EcoRI and Hind III enzymes. Lane 3: 900‐bp PCR product of recombinant Pdx1‐ pCDNA 3.1(+) vector. Lane 4: 1‐kb DNA ladder. (B) Western blot analysis results. The CHO cells transfected with Pdx1‐ pCDNA 3.1(+) (lane 1) showed a significantly higher expression of Pdx1 compared with the CHO cells transfected with pCDNA 3.1(+) alone (Lane 2).

    Techniques Used: Plasmid Preparation, Recombinant, Polymerase Chain Reaction, Western Blot, Transfection, Expressing

    17) Product Images from "Borrelia burgdorferi Requires Glycerol for Maximum Fitness During The Tick Phase of the Enzootic Cycle"

    Article Title: Borrelia burgdorferi Requires Glycerol for Maximum Fitness During The Tick Phase of the Enzootic Cycle

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1002102

    Confirmation of glpD disruption. A ) Southern blot analysis confirms the disruption of glpD . Whole genomic DNA from B31-A3 and glpD disruption mutants CP176, CP177, CP257 were digested with BamHI and blotted on a nylon membrane. Digoxygenein-11-dUTP labeled bb0243 probe was utilized to visualize glpD . Migration positions of DNA molecular size markers are indicated on the left. B ) glpD disruption occurred via by a double crossover insertion of flgB - aadA . Whole genomic DNA from B31-A3 and glpD disruption mutants CP176, CP177, CP257 were digested with BamHI or EcoRI, which would be specific for the proximal or distal bb0243 flanking chromosomal regions, respectively, and blotted to a nylon membrane. Blots were developed with a digoxygenein-11-dUTP-labeled aadA probe. A schematic diagram indicates the sizes of the fragments expected to contain flgB - aadA . Migration positions of DNA molecular size markers are indicated on the left of each panel.
    Figure Legend Snippet: Confirmation of glpD disruption. A ) Southern blot analysis confirms the disruption of glpD . Whole genomic DNA from B31-A3 and glpD disruption mutants CP176, CP177, CP257 were digested with BamHI and blotted on a nylon membrane. Digoxygenein-11-dUTP labeled bb0243 probe was utilized to visualize glpD . Migration positions of DNA molecular size markers are indicated on the left. B ) glpD disruption occurred via by a double crossover insertion of flgB - aadA . Whole genomic DNA from B31-A3 and glpD disruption mutants CP176, CP177, CP257 were digested with BamHI or EcoRI, which would be specific for the proximal or distal bb0243 flanking chromosomal regions, respectively, and blotted to a nylon membrane. Blots were developed with a digoxygenein-11-dUTP-labeled aadA probe. A schematic diagram indicates the sizes of the fragments expected to contain flgB - aadA . Migration positions of DNA molecular size markers are indicated on the left of each panel.

    Techniques Used: Southern Blot, Labeling, Migration

    18) Product Images from "A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication"

    Article Title: A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0185310

    PCR-RFLP analysis of pairs of BUSCO orthologs. A: Schematic display of the method. Specific primers were developed that distinguish between the two very similar paralogs. As second distinctive feature only one of the two PCR fragments contains an EcoRI or DraI restriction site. B: Gel image of a PCR-RFPL analysis of the paralogous sequences DR002900 and DR003069 with six different isolates. Ladder: 1 KB plus (Thermo Fisher, Waltham, USA).
    Figure Legend Snippet: PCR-RFLP analysis of pairs of BUSCO orthologs. A: Schematic display of the method. Specific primers were developed that distinguish between the two very similar paralogs. As second distinctive feature only one of the two PCR fragments contains an EcoRI or DraI restriction site. B: Gel image of a PCR-RFPL analysis of the paralogous sequences DR002900 and DR003069 with six different isolates. Ladder: 1 KB plus (Thermo Fisher, Waltham, USA).

    Techniques Used: Polymerase Chain Reaction

    19) Product Images from "Shifts in targeting of class switch recombination sites in mice that lack ? switch region tandem repeats or Msh2"

    Article Title: Shifts in targeting of class switch recombination sites in mice that lack ? switch region tandem repeats or Msh2

    Journal: The Journal of Experimental Medicine

    doi: 10.1084/jem.20042491

    CSR within sequences upstream of the S μ TR are reduced in Msh2 − / − mice. (a) Twofold dilutions of genomic DNAs were assayed by Sμ/Sγ1 EcoRI DC-PCR and EcoRI–BsrGI DC-PCR. Samples were normalized using nAChR DC-PCR. (b) CSR sites in wild-type or Msh2 −/− mice measured relative to total wild-type CSR (set to 100%). Mean values and SEM of at least four independent experiments are presented. (c) CSR events in Msh2 −/− mice measured by EcoRI, HindIII, and XbaI real-time DC-PCR and compared with wild-type mice. Mean values and SEM are from six independent experiments with two Msh2 −/− mice and seven independent experiments with four wild-type mice.
    Figure Legend Snippet: CSR within sequences upstream of the S μ TR are reduced in Msh2 − / − mice. (a) Twofold dilutions of genomic DNAs were assayed by Sμ/Sγ1 EcoRI DC-PCR and EcoRI–BsrGI DC-PCR. Samples were normalized using nAChR DC-PCR. (b) CSR sites in wild-type or Msh2 −/− mice measured relative to total wild-type CSR (set to 100%). Mean values and SEM of at least four independent experiments are presented. (c) CSR events in Msh2 −/− mice measured by EcoRI, HindIII, and XbaI real-time DC-PCR and compared with wild-type mice. Mean values and SEM are from six independent experiments with two Msh2 −/− mice and seven independent experiments with four wild-type mice.

    Techniques Used: Mouse Assay, Polymerase Chain Reaction

    S μ TR − / − and wild-type mice have similar numbers of upstream CSR events. (a) DC-PCR measures CSR events upstream of the SμTR region. A BsrGI site distinguished CSR junctions located upstream and downstream of the site. Only CSR sites in sequences upstream of BsrGI generate PCR signals. Total CSR events are measured by EcoRI DC-PCR (E, EcoRI; BGI, BsrGI). PCR primers are indicated by arrowheads. (b) Twofold dilutions of genomic DNAs were assayed by Sμ/Sγ1 EcoRI DC-PCR and EcoRI–BsrGI DC-PCR. Samples were normalized using nAChR DC-PCR reactions. (c) CSR events in wild-type or SμTR −/− mice as percentages of total wild-type CSR events (set to 100%). Mean values and SEM are from six independent experiments with two mice per group.
    Figure Legend Snippet: S μ TR − / − and wild-type mice have similar numbers of upstream CSR events. (a) DC-PCR measures CSR events upstream of the SμTR region. A BsrGI site distinguished CSR junctions located upstream and downstream of the site. Only CSR sites in sequences upstream of BsrGI generate PCR signals. Total CSR events are measured by EcoRI DC-PCR (E, EcoRI; BGI, BsrGI). PCR primers are indicated by arrowheads. (b) Twofold dilutions of genomic DNAs were assayed by Sμ/Sγ1 EcoRI DC-PCR and EcoRI–BsrGI DC-PCR. Samples were normalized using nAChR DC-PCR reactions. (c) CSR events in wild-type or SμTR −/− mice as percentages of total wild-type CSR events (set to 100%). Mean values and SEM are from six independent experiments with two mice per group.

    Techniques Used: Mouse Assay, Polymerase Chain Reaction

    S μ TR − / − mice have increased levels of CSR events targeted to downstream sequences. (a) DC-PCR measuring CSR junction sites downstream of the SμTR region. HindIII and XbaI sites downstream of the SμTR region were used in DC-PCR assays to measure CSR junctions in sequences downstream of each site. Total CSR sites were determined by EcoRI DC-PCR (E, EcoRI; H1 and H2, HindIII; X, XbaI). Primer pairs used for the different DC-PCR assays are indicated by small arrows of different types. (b) Wild-type and SμTR −/− CSR events measured by EcoRI, HindIII, and XbaI real-time DC-PCR. Copy numbers for CSR events were derived from pSμ/Sγ3 standard curves. Rag-1 PCR normalized CSR events relative to Rag-1 copy number. Mean values and SEM are from seven independent experiments with four mice per group. (c) Percentage of SμTR −/− switch events downstream of the H2 relative to events downstream of H1 (set to 100%). Mean values and SEM are from three independent experiments per group.
    Figure Legend Snippet: S μ TR − / − mice have increased levels of CSR events targeted to downstream sequences. (a) DC-PCR measuring CSR junction sites downstream of the SμTR region. HindIII and XbaI sites downstream of the SμTR region were used in DC-PCR assays to measure CSR junctions in sequences downstream of each site. Total CSR sites were determined by EcoRI DC-PCR (E, EcoRI; H1 and H2, HindIII; X, XbaI). Primer pairs used for the different DC-PCR assays are indicated by small arrows of different types. (b) Wild-type and SμTR −/− CSR events measured by EcoRI, HindIII, and XbaI real-time DC-PCR. Copy numbers for CSR events were derived from pSμ/Sγ3 standard curves. Rag-1 PCR normalized CSR events relative to Rag-1 copy number. Mean values and SEM are from seven independent experiments with four mice per group. (c) Percentage of SμTR −/− switch events downstream of the H2 relative to events downstream of H1 (set to 100%). Mean values and SEM are from three independent experiments per group.

    Techniques Used: Mouse Assay, Polymerase Chain Reaction, Derivative Assay

    20) Product Images from "Construction of a Novel DNA Vaccine Candidate encoding LmSTI1-PpSP42 Fusion Protein from Leishmania major and Phlebotomus papatasi Against Cutaneous Leishmaniasi"

    Article Title: Construction of a Novel DNA Vaccine Candidate encoding LmSTI1-PpSP42 Fusion Protein from Leishmania major and Phlebotomus papatasi Against Cutaneous Leishmaniasi

    Journal: Reports of Biochemistry & Molecular Biology

    doi:

    A: Schematic diagram of pCLmSTI1Pp42 construct composed of pcDNA3.1(+) eukaryotic expression vector and in-frame L. major LMSTI1 and Ph. Papatasi SP42 genes. B: pCLmSTI1 double-digested with KpnI and EcoRI (expected digested fragments: ∼5400 bp and ∼1600 bp). C: pCLmSTI1Pp42 double-digested with KpnI and XhoI (expected digested fragments: ∼5400 bp and ∼2500 bp).
    Figure Legend Snippet: A: Schematic diagram of pCLmSTI1Pp42 construct composed of pcDNA3.1(+) eukaryotic expression vector and in-frame L. major LMSTI1 and Ph. Papatasi SP42 genes. B: pCLmSTI1 double-digested with KpnI and EcoRI (expected digested fragments: ∼5400 bp and ∼1600 bp). C: pCLmSTI1Pp42 double-digested with KpnI and XhoI (expected digested fragments: ∼5400 bp and ∼2500 bp).

    Techniques Used: Construct, Expressing, Plasmid Preparation

    21) Product Images from "Overexpression of Ubiquitin and Amino Acid Permease Genes in Association with Antimony Resistance in Leishmania tropica Field Isolates"

    Article Title: Overexpression of Ubiquitin and Amino Acid Permease Genes in Association with Antimony Resistance in Leishmania tropica Field Isolates

    Journal: The Korean Journal of Parasitology

    doi: 10.3347/kjp.2013.51.4.413

    Expression patterns of TDFs extracted from cDNA-AFLP PAGE. Sensitive amplification of cDNA-AFLP on a PAGE from 3 different primer combinations of S3 MboI /S2 EcoRI , S3 MboI /S1 EcoRI , and S4 MboI /S4 MboI . Arrows point to differentially expressed TDFs which were isolated with code numbers of 1, 2, and 3 (associated genes which derived from these TDFs mentioned in Table 2 ). M, 50 bp molecular weight marker; S, sensitve; R, resistant.
    Figure Legend Snippet: Expression patterns of TDFs extracted from cDNA-AFLP PAGE. Sensitive amplification of cDNA-AFLP on a PAGE from 3 different primer combinations of S3 MboI /S2 EcoRI , S3 MboI /S1 EcoRI , and S4 MboI /S4 MboI . Arrows point to differentially expressed TDFs which were isolated with code numbers of 1, 2, and 3 (associated genes which derived from these TDFs mentioned in Table 2 ). M, 50 bp molecular weight marker; S, sensitve; R, resistant.

    Techniques Used: Expressing, cDNA-AFLP Assay, Polyacrylamide Gel Electrophoresis, Amplification, Isolation, Derivative Assay, Molecular Weight, Marker

    22) Product Images from "The structural characterization of a prophage-encoded extracellular DNase from Streptococcus pyogenes"

    Article Title: The structural characterization of a prophage-encoded extracellular DNase from Streptococcus pyogenes

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr789

    Observation of the pUC19 plasmid DNA states during cleavage by Spd1. Aliquots were taken from the reaction mixture at the indicated time points, and digested products were analysed by electrophoresis in 1% agarose gel, staining with SYBR® Safe (Invitrogen). Control lanes 1: Hyperladder I (Bioline); Lane 2: Untreated pUC19; Lane 3: EcoRI linearized pUC19; Lane 4: Reaction mixture prior to the addition of Spd1. The digestion of plasmid DNA proceeds via single-strand nick mediated relaxation of supercoiled DNA, this can be seen 30 s to 1 min into the reaction; within the same time frame a linear form can also be seen emerging.
    Figure Legend Snippet: Observation of the pUC19 plasmid DNA states during cleavage by Spd1. Aliquots were taken from the reaction mixture at the indicated time points, and digested products were analysed by electrophoresis in 1% agarose gel, staining with SYBR® Safe (Invitrogen). Control lanes 1: Hyperladder I (Bioline); Lane 2: Untreated pUC19; Lane 3: EcoRI linearized pUC19; Lane 4: Reaction mixture prior to the addition of Spd1. The digestion of plasmid DNA proceeds via single-strand nick mediated relaxation of supercoiled DNA, this can be seen 30 s to 1 min into the reaction; within the same time frame a linear form can also be seen emerging.

    Techniques Used: Plasmid Preparation, Electrophoresis, Agarose Gel Electrophoresis, Staining

    23) Product Images from "Protective Effects of Bacteriophages against Aeromonas hydrophila Causing Motile Aeromonas Septicemia (MAS) in Striped Catfish"

    Article Title: Protective Effects of Bacteriophages against Aeromonas hydrophila Causing Motile Aeromonas Septicemia (MAS) in Striped Catfish

    Journal: Antibiotics

    doi: 10.3390/antibiotics7010016

    Restriction enzyme-digested fragments of the genomic DNA of A. hydrophila -phage 2. Footnote: Lane M: 1kb Plus Opti-DNA Marker (ABM, Canada); Lane L1: genomic DNA of Φ2; Lanes L2–L8: genomic DNA of Φ2 digested with EcoRV; EcoRI; Ncol; SalI; MspI; XmnI; KpnI, restriction enzymes respectively.
    Figure Legend Snippet: Restriction enzyme-digested fragments of the genomic DNA of A. hydrophila -phage 2. Footnote: Lane M: 1kb Plus Opti-DNA Marker (ABM, Canada); Lane L1: genomic DNA of Φ2; Lanes L2–L8: genomic DNA of Φ2 digested with EcoRV; EcoRI; Ncol; SalI; MspI; XmnI; KpnI, restriction enzymes respectively.

    Techniques Used: Marker

    24) Product Images from "Molecular and antigenic characterization of bovine herpesvirus type 1 (BoHV-1) strains from cattle with diverse clinical cases in Turkey"

    Article Title: Molecular and antigenic characterization of bovine herpesvirus type 1 (BoHV-1) strains from cattle with diverse clinical cases in Turkey

    Journal: Tropical Animal Health and Production

    doi: 10.1007/s11250-019-02042-6

    REA of BoHV-1 isolates and reference strain by BamHI (A), HindIII (B), and EcoRI (C). Lane (1):DNA ladder (100 bp plus and 1kbp plus, ThermoScientific), Lane (2): KY748023 (KYS-73675-Milk), Lane (3): KY748022 (TGM-IZ41-Milk), Lane (4): KY748020 (ANK-SKR-Lng), Lane (5): KY748021 (Halk-THYM-Thm), Lane (6): Cooper strain. REA pattern differences indicated by *; KY748022 (Lane3) and KY748021 (Lane 5) were BoHV-1.2a while the other viruses in the test were BoHV-1.1 strains
    Figure Legend Snippet: REA of BoHV-1 isolates and reference strain by BamHI (A), HindIII (B), and EcoRI (C). Lane (1):DNA ladder (100 bp plus and 1kbp plus, ThermoScientific), Lane (2): KY748023 (KYS-73675-Milk), Lane (3): KY748022 (TGM-IZ41-Milk), Lane (4): KY748020 (ANK-SKR-Lng), Lane (5): KY748021 (Halk-THYM-Thm), Lane (6): Cooper strain. REA pattern differences indicated by *; KY748022 (Lane3) and KY748021 (Lane 5) were BoHV-1.2a while the other viruses in the test were BoHV-1.1 strains

    Techniques Used:

    25) Product Images from "Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages"

    Article Title: Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-13-223

    RFLP analysis of KL1 and AH2 genomic DNA. 5 μg of genomic DNA were digested overnight with EcoRI and separated on a 0.8% agarose gel. The DNA in the ambient gel (left) was not heated, while the DNA in the 80°C gel (right) was incubated 20 min at 80°C and chilled on ice prior to loading. Arrows indicate bands containing cos site DNA. L: 1 Kb Plus DNA Ladder (Invitrogen).
    Figure Legend Snippet: RFLP analysis of KL1 and AH2 genomic DNA. 5 μg of genomic DNA were digested overnight with EcoRI and separated on a 0.8% agarose gel. The DNA in the ambient gel (left) was not heated, while the DNA in the 80°C gel (right) was incubated 20 min at 80°C and chilled on ice prior to loading. Arrows indicate bands containing cos site DNA. L: 1 Kb Plus DNA Ladder (Invitrogen).

    Techniques Used: Agarose Gel Electrophoresis, Incubation

    26) Product Images from "Emergence of Serratia marcescens, Klebsiella pneumoniae, and Escherichia coli Isolates Possessing the Plasmid-Mediated Carbapenem-Hydrolyzing β-Lactamase KPC-2 in Intensive Care Units of a Chinese Hospital "

    Article Title: Emergence of Serratia marcescens, Klebsiella pneumoniae, and Escherichia coli Isolates Possessing the Plasmid-Mediated Carbapenem-Hydrolyzing β-Lactamase KPC-2 in Intensive Care Units of a Chinese Hospital

    Journal: Antimicrobial Agents and Chemotherapy

    doi: 10.1128/AAC.01539-07

    Restriction patterns of plasmid DNA from E. coli transconjugants of E. coli , partial K. pneumoniae and S. marcescens isolates, and partial original S. marcescens isolates. Lane 1, E. coli transconjugant of E. coli E1; lanes 2 to 4, E. coli transconjugants of K. pneumoniae K1, K8, and K10; lanes 5 to 7, E. coli transconjugants of S. marcescens S1, S10, and S20; lanes 8 and 9, original S. marcescens S1 and S10; lane 10, E. coli EC600 as a negative control; M, 1-kb DNA ladder (MBI Fermentas). Plasmid DNA was digested with EcoRI, HindIII, and BcuI endonucleases.
    Figure Legend Snippet: Restriction patterns of plasmid DNA from E. coli transconjugants of E. coli , partial K. pneumoniae and S. marcescens isolates, and partial original S. marcescens isolates. Lane 1, E. coli transconjugant of E. coli E1; lanes 2 to 4, E. coli transconjugants of K. pneumoniae K1, K8, and K10; lanes 5 to 7, E. coli transconjugants of S. marcescens S1, S10, and S20; lanes 8 and 9, original S. marcescens S1 and S10; lane 10, E. coli EC600 as a negative control; M, 1-kb DNA ladder (MBI Fermentas). Plasmid DNA was digested with EcoRI, HindIII, and BcuI endonucleases.

    Techniques Used: Plasmid Preparation, Negative Control

    27) Product Images from "Two Inducible Prophages of an Antarctic Pseudomonas sp. ANT_H14 Use the Same Capsid for Packaging Their Genomes – Characterization of a Novel Phage Helper-Satellite System"

    Article Title: Two Inducible Prophages of an Antarctic Pseudomonas sp. ANT_H14 Use the Same Capsid for Packaging Their Genomes – Characterization of a Novel Phage Helper-Satellite System

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0158889

    Restriction patterns of DNA extracted from purified virions cleaved with the selected REases. Panel A: HindIII (H), Eco32I (E32), SalI (S) and EcoRI (EI). ND, undigested DNA. M, GeneRuler 100- to 10,000-bp size marker. λ/H, λ DNA cleaved with HindIII. ~14 kb restriction fragment of EcoR32I digested virion DNA is marked with a triangle. Panel B: Arrows indicate restriction fragments assigned to ФAH14a (left) and ФAH14b (right) genomic DNA, obtained by SalI digestion.
    Figure Legend Snippet: Restriction patterns of DNA extracted from purified virions cleaved with the selected REases. Panel A: HindIII (H), Eco32I (E32), SalI (S) and EcoRI (EI). ND, undigested DNA. M, GeneRuler 100- to 10,000-bp size marker. λ/H, λ DNA cleaved with HindIII. ~14 kb restriction fragment of EcoR32I digested virion DNA is marked with a triangle. Panel B: Arrows indicate restriction fragments assigned to ФAH14a (left) and ФAH14b (right) genomic DNA, obtained by SalI digestion.

    Techniques Used: Purification, Marker

    28) Product Images from "Replication, Gene Expression and Particle Production by a Consensus Merkel Cell Polyomavirus (MCPyV) Genome"

    Article Title: Replication, Gene Expression and Particle Production by a Consensus Merkel Cell Polyomavirus (MCPyV) Genome

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0029112

    R17a replication in PFSK-1 cells. 2 µg low molecular weight DNA from PFSK-1 cells transfected with MCVSyn or R17a viral DNA was EcoRI and DpnI digested and separated on an agarose gel, followed by EtBr staining (left panel). The DNA was transferred via southern blotting and probed with a radioactively labelled LT-Ag PCR fragment (right panel). The blot was exposed for 24 h.
    Figure Legend Snippet: R17a replication in PFSK-1 cells. 2 µg low molecular weight DNA from PFSK-1 cells transfected with MCVSyn or R17a viral DNA was EcoRI and DpnI digested and separated on an agarose gel, followed by EtBr staining (left panel). The DNA was transferred via southern blotting and probed with a radioactively labelled LT-Ag PCR fragment (right panel). The blot was exposed for 24 h.

    Techniques Used: Molecular Weight, Transfection, Agarose Gel Electrophoresis, Staining, Southern Blot, Polymerase Chain Reaction

    SV40 replication and gene expression in CV-1 cells transfected with SV40 DNA. (A) 100 ng of intramolecular religated SV40 viral DNA was transfected in CV-1 cells and cells were lysed 12 h, 24 h, 36 h, 2d and 7d post transfection. Protein lysates were subsequently analyzed for SV40 LT-Ag (Pab419 antibody) and VP1 expression (α-VP1 polyclonal rabbit serum) by SDS-page and Western Blotting. Staining of actin was used to ensure that equal protein amounts were loaded per lane. (B) Low molecular weight DNA was isolated from SV40 DNA transfected CV-1 cells at the indicated time points by HIRT extraction, 1 µg DNA was DpnI and EcoRI digested; DNA was separated on an agarose gel and stained with EtBr (left panel), followed by southern blotting and detection of viral DNA using a 32 PdCTP-labeled SV40 LT-Ag PCR fragment as a probe. The blot was exposed for 30 min. Numbers below the lanes correspond to the quantification of newly replicated DNA using a Fuji phosphoimager FLA7000 and MultiGauge software.
    Figure Legend Snippet: SV40 replication and gene expression in CV-1 cells transfected with SV40 DNA. (A) 100 ng of intramolecular religated SV40 viral DNA was transfected in CV-1 cells and cells were lysed 12 h, 24 h, 36 h, 2d and 7d post transfection. Protein lysates were subsequently analyzed for SV40 LT-Ag (Pab419 antibody) and VP1 expression (α-VP1 polyclonal rabbit serum) by SDS-page and Western Blotting. Staining of actin was used to ensure that equal protein amounts were loaded per lane. (B) Low molecular weight DNA was isolated from SV40 DNA transfected CV-1 cells at the indicated time points by HIRT extraction, 1 µg DNA was DpnI and EcoRI digested; DNA was separated on an agarose gel and stained with EtBr (left panel), followed by southern blotting and detection of viral DNA using a 32 PdCTP-labeled SV40 LT-Ag PCR fragment as a probe. The blot was exposed for 30 min. Numbers below the lanes correspond to the quantification of newly replicated DNA using a Fuji phosphoimager FLA7000 and MultiGauge software.

    Techniques Used: Expressing, Transfection, SDS Page, Western Blot, Staining, Molecular Weight, Isolation, Agarose Gel Electrophoresis, Southern Blot, Labeling, Polymerase Chain Reaction, Software

    MCVSyn replication assays in H1299, PFSK-1 and 293 cells. 5 µg low molecular weight DNA isolated from cell cultures at the indicated time points post-transfection with MCVSyn DNA was digested with DpnI and EcoRI, separated on an agarose gel and stained with EtBr (left panels), then transferred via southern blot and probed with a radioactively labelled LT-Ag PCR fragment [13] . The blot was exposed for 24 h and scanned using a Fuji phosphoimager FLA7000; MultiGauge software was used for quantification.
    Figure Legend Snippet: MCVSyn replication assays in H1299, PFSK-1 and 293 cells. 5 µg low molecular weight DNA isolated from cell cultures at the indicated time points post-transfection with MCVSyn DNA was digested with DpnI and EcoRI, separated on an agarose gel and stained with EtBr (left panels), then transferred via southern blot and probed with a radioactively labelled LT-Ag PCR fragment [13] . The blot was exposed for 24 h and scanned using a Fuji phosphoimager FLA7000; MultiGauge software was used for quantification.

    Techniques Used: Molecular Weight, Isolation, Transfection, Agarose Gel Electrophoresis, Staining, Southern Blot, Polymerase Chain Reaction, Software

    29) Product Images from "Phase-locked mutants of Mycoplasma agalactiae: defining the molecular switch of high-frequency Vpma antigenic variation"

    Article Title: Phase-locked mutants of Mycoplasma agalactiae: defining the molecular switch of high-frequency Vpma antigenic variation

    Journal: Molecular Microbiology

    doi: 10.1111/j.1365-2958.2007.06103.x

    Arrangement of the ORFs, terminator structures and inversions in the vpma loci of M. agalactiae type strain PG2 clonal variant 55-5, PLMY and PLMU. Grey arrows represent the vpma genes, whereby a dark grey arrow denotes the vpma gene which is transcribed in the respective clonal variant or PLM. The black arrows indicate the location of the unique promoter (P) in each vpma locus. Putative recombination sites are indicated by white rectangles (RS) and denote sequences from −1 to −72 relative to the start codons of the corresponding vpma genes. White arrows indicate ORFs other than vpma genes, like the intact xer1 recombinase ( xer1 ) and a tRNA (tRNA LYS ) gene in 55-5, whereas the discontinued white rectangles represent the promoter proximal regions of the disrupted xer1 genes ( xer ′) in the PLMs and a partial ORF (ORF′) in 55-5. A small grey rectangle indicates sequences derived from the integrated plasmid pR3. Non-translated repeats of the vpmaY genes are indicated with a dotted-lined white arrow. Terminator structures are indicated with symbolized hairpins, whereby Rho-independent terminator structures, for which experimental evidence is given, are drawn with a black-filled loop and are white-filled otherwise. Sequence-identical blocks between PLMs and 55-5 are designated A to E and are indicated with INV when inverted compared with 55-5. B, BamHI; E, EcoRI; H, HindIII; P, PstI; X, XbaI.
    Figure Legend Snippet: Arrangement of the ORFs, terminator structures and inversions in the vpma loci of M. agalactiae type strain PG2 clonal variant 55-5, PLMY and PLMU. Grey arrows represent the vpma genes, whereby a dark grey arrow denotes the vpma gene which is transcribed in the respective clonal variant or PLM. The black arrows indicate the location of the unique promoter (P) in each vpma locus. Putative recombination sites are indicated by white rectangles (RS) and denote sequences from −1 to −72 relative to the start codons of the corresponding vpma genes. White arrows indicate ORFs other than vpma genes, like the intact xer1 recombinase ( xer1 ) and a tRNA (tRNA LYS ) gene in 55-5, whereas the discontinued white rectangles represent the promoter proximal regions of the disrupted xer1 genes ( xer ′) in the PLMs and a partial ORF (ORF′) in 55-5. A small grey rectangle indicates sequences derived from the integrated plasmid pR3. Non-translated repeats of the vpmaY genes are indicated with a dotted-lined white arrow. Terminator structures are indicated with symbolized hairpins, whereby Rho-independent terminator structures, for which experimental evidence is given, are drawn with a black-filled loop and are white-filled otherwise. Sequence-identical blocks between PLMs and 55-5 are designated A to E and are indicated with INV when inverted compared with 55-5. B, BamHI; E, EcoRI; H, HindIII; P, PstI; X, XbaI.

    Techniques Used: Variant Assay, Derivative Assay, Plasmid Preparation, Sequencing

    30) Product Images from "Evaluation of Protective Immune Response Induced by a DNA Vaccine Encoding GRA8 against Acute Toxoplasmosis in a Murine Model"

    Article Title: Evaluation of Protective Immune Response Induced by a DNA Vaccine Encoding GRA8 against Acute Toxoplasmosis in a Murine Model

    Journal: The Korean Journal of Parasitology

    doi: 10.3347/kjp.2018.56.4.325

    T. gondii GRA8 was expressed successfully in ARPE-19 cells. (A) The coding sequence of the T. gondii GRA8 gene was amplified by PCR (814 bp) from the cDNA of T. gondii strain GFP-RH. (B) The PCR products were digested with the appropriate restriction enzymes and cloned into the XhoI and EcoRI sites of the pDsRed2-N1 expression vector, which contains the DsRed open reading frame. The constructed recombinant plasmid was named pDsRed2-GRA8. (C) ARPE-19 cells transfected with pDsRed2-GRA8 showed specific expression of GRA8 mRNA. (D) pDsRed2-GRA8 and the pDsRed2-N1 empty vector both expressed the DsRed2 protein, which localized to the cytoplasm of the transfected cells.
    Figure Legend Snippet: T. gondii GRA8 was expressed successfully in ARPE-19 cells. (A) The coding sequence of the T. gondii GRA8 gene was amplified by PCR (814 bp) from the cDNA of T. gondii strain GFP-RH. (B) The PCR products were digested with the appropriate restriction enzymes and cloned into the XhoI and EcoRI sites of the pDsRed2-N1 expression vector, which contains the DsRed open reading frame. The constructed recombinant plasmid was named pDsRed2-GRA8. (C) ARPE-19 cells transfected with pDsRed2-GRA8 showed specific expression of GRA8 mRNA. (D) pDsRed2-GRA8 and the pDsRed2-N1 empty vector both expressed the DsRed2 protein, which localized to the cytoplasm of the transfected cells.

    Techniques Used: Sequencing, Amplification, Polymerase Chain Reaction, Clone Assay, Expressing, Plasmid Preparation, Construct, Recombinant, Transfection

    31) Product Images from "A Type II Protein Secretory Pathway Required for Levansucrase Secretion by Gluconacetobacter diazotrophicus"

    Article Title: A Type II Protein Secretory Pathway Required for Levansucrase Secretion by Gluconacetobacter diazotrophicus

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.186.15.5031-5039.2004

    Localization of the region of the library cosmid p21R1 complementing LsdA secretion in mutant M31. lsd genes are represented by arrows. lsdA and lsdB encode levansucrase and levanase, respectively. lsdX , -G , and - O are the first genes of the type II secretion operon. The ability of each plasmid to restore LsdA secretion is indicated in parentheses. Plasmid pALS118 encodes a mutated LsdG (C126G). Restriction sites: E, EcoRI; B, BamHI; Bg, BglII.
    Figure Legend Snippet: Localization of the region of the library cosmid p21R1 complementing LsdA secretion in mutant M31. lsd genes are represented by arrows. lsdA and lsdB encode levansucrase and levanase, respectively. lsdX , -G , and - O are the first genes of the type II secretion operon. The ability of each plasmid to restore LsdA secretion is indicated in parentheses. Plasmid pALS118 encodes a mutated LsdG (C126G). Restriction sites: E, EcoRI; B, BamHI; Bg, BglII.

    Techniques Used: Mutagenesis, Plasmid Preparation

    32) Product Images from "Introducing cloned genes into cultured neurons providing novel in vitro models for neuropathology and neurotoxicity studies"

    Article Title: Introducing cloned genes into cultured neurons providing novel in vitro models for neuropathology and neurotoxicity studies

    Journal: Neuromethods

    doi: 10.1007/978-1-61779-077-5_9

    Insert-vector ligation and strategies to avoid recircularization. A) Ligation reaction of an EcoRI cleaved DNA fragment (red) in an EcoRI cleaved vector (black) without further treatment. Self-circularization of vector is highly favored. B) Second cleavage of vector and insert with XhoI make incompatible both ends of the vector, avoiding self-circularization. C) Vector dephosphorylation with alkaline phosphatase eliminates 5’phosphate groups at the ends of the vector, necessary for recircularization. Note that in B) , as well as in C) , the only possible ligation reaction is between vector and insert.
    Figure Legend Snippet: Insert-vector ligation and strategies to avoid recircularization. A) Ligation reaction of an EcoRI cleaved DNA fragment (red) in an EcoRI cleaved vector (black) without further treatment. Self-circularization of vector is highly favored. B) Second cleavage of vector and insert with XhoI make incompatible both ends of the vector, avoiding self-circularization. C) Vector dephosphorylation with alkaline phosphatase eliminates 5’phosphate groups at the ends of the vector, necessary for recircularization. Note that in B) , as well as in C) , the only possible ligation reaction is between vector and insert.

    Techniques Used: Plasmid Preparation, Ligation, De-Phosphorylation Assay

    33) Product Images from "Innate Immune Responses in Peptidoglycan Recognition Protein L-Deficient Mice"

    Article Title: Innate Immune Responses in Peptidoglycan Recognition Protein L-Deficient Mice

    Journal: Molecular and Cellular Biology

    doi: 10.1128/MCB.24.18.7949-7957.2004

    Generation of PGRP-L-deficient mouse. (A) The PGRP-L gene locus is depicted as a single line, with exons represented as filled boxes. Relevant restriction enzyme sites are shown. B, BamHI; H3, HindIII; RI, EcoRI. The organization of the targeting construct and the arrangement of the recombined PGRP-L allele are also shown. The dotted box indicates the GFP cassette that was engineered in-frame with the PGRP-L ATG start codon. The drug selection neomycin cassette (Neo) is depicted as a striped box, with two flanking loxP sites depicted as filled triangles. (B) Genotyping with Southern blot analysis. Tail DNA was subjected to agarose gel electrophoresis. The presence of the mutant allele (7.5 kb) and the wild-type allele (9.6 kb) was determined by Southern blotting, using a probe upstream of the homologous recombined sequence. (C) RT-PCR assay to determine PGRP-L expression. Liver RNA from wild-type, heterozygous, and homozygous gene-targeted mice was extracted and reverse transcribed into cDNA. PGRP-L expression was determined by PCR. The expression of hypoxanthine phosphoribosyltransferase was used as a control. (D) Serum from wild-type, heterozygous, and homozygous gene-targeted mice was immunoprecipitated using rat anti-PGRP-L antibodies. The immunoprecipitates were blotted with rabbit anti-PGRP-L antibodies.
    Figure Legend Snippet: Generation of PGRP-L-deficient mouse. (A) The PGRP-L gene locus is depicted as a single line, with exons represented as filled boxes. Relevant restriction enzyme sites are shown. B, BamHI; H3, HindIII; RI, EcoRI. The organization of the targeting construct and the arrangement of the recombined PGRP-L allele are also shown. The dotted box indicates the GFP cassette that was engineered in-frame with the PGRP-L ATG start codon. The drug selection neomycin cassette (Neo) is depicted as a striped box, with two flanking loxP sites depicted as filled triangles. (B) Genotyping with Southern blot analysis. Tail DNA was subjected to agarose gel electrophoresis. The presence of the mutant allele (7.5 kb) and the wild-type allele (9.6 kb) was determined by Southern blotting, using a probe upstream of the homologous recombined sequence. (C) RT-PCR assay to determine PGRP-L expression. Liver RNA from wild-type, heterozygous, and homozygous gene-targeted mice was extracted and reverse transcribed into cDNA. PGRP-L expression was determined by PCR. The expression of hypoxanthine phosphoribosyltransferase was used as a control. (D) Serum from wild-type, heterozygous, and homozygous gene-targeted mice was immunoprecipitated using rat anti-PGRP-L antibodies. The immunoprecipitates were blotted with rabbit anti-PGRP-L antibodies.

    Techniques Used: Construct, Selection, Southern Blot, Agarose Gel Electrophoresis, Mutagenesis, Sequencing, Reverse Transcription Polymerase Chain Reaction, Expressing, Mouse Assay, Polymerase Chain Reaction, Immunoprecipitation

    34) Product Images from "empty pericarp2 Encodes a Negative Regulator of the Heat Shock Response and Is Required for Maize Embryogenesis"

    Article Title: empty pericarp2 Encodes a Negative Regulator of the Heat Shock Response and Is Required for Maize Embryogenesis

    Journal: The Plant Cell

    doi: 10.1105/tpc.006726

    DNA Gel Blot Analyses of Clones Linked to emp2. (A) A Mu1 transposon-tagged EcoRI fragment (arrow) is linked to the emp2-R mutation. (B) Nonmutant siblings (lanes 2 to 8) of the original isolate harboring the emp2-R mutation segregate for nonmutant inbred-sized (either inbred q66 or q67) restriction fragments of clones linked to the emp2-R mutation (probe 1, as described in Methods). The Mu1 transposon-tagged, 3-kb emp2-R –linked EcoRI fragment is absent from nonmutant sibling DNA, indicating that the emp2-R –linked allele did not preexist in the genetic background that gave rise to the emp2-R mutation.
    Figure Legend Snippet: DNA Gel Blot Analyses of Clones Linked to emp2. (A) A Mu1 transposon-tagged EcoRI fragment (arrow) is linked to the emp2-R mutation. (B) Nonmutant siblings (lanes 2 to 8) of the original isolate harboring the emp2-R mutation segregate for nonmutant inbred-sized (either inbred q66 or q67) restriction fragments of clones linked to the emp2-R mutation (probe 1, as described in Methods). The Mu1 transposon-tagged, 3-kb emp2-R –linked EcoRI fragment is absent from nonmutant sibling DNA, indicating that the emp2-R –linked allele did not preexist in the genetic background that gave rise to the emp2-R mutation.

    Techniques Used: Western Blot, Clone Assay, Mutagenesis

    35) Product Images from "Silencing of SPC2 Expression Using an Engineered δ Ribozyme in the Mouse βTC-3 Endocrine Cell Line *"

    Article Title: Silencing of SPC2 Expression Using an Engineered δ Ribozyme in the Mouse βTC-3 Endocrine Cell Line *

    Journal: The Journal of biological chemistry

    doi: 10.1074/jbc.M310632200

    Expression of tRNA Val - δ Rz chimeric constructions A , vector used for cultured cells studies. We attenuated the CMV promoter of pcDNA3.1/hygro by the cleavage of MfeI before the promoter sequence. MfeI and EcoRI are two compatible sites that have been used for the cloning. The δ Rz has been first cloned in the pPUR-KE vector. Then the tRNA Val - δ Rz cassette has been subcloned from pPUR-KE to pcDNA3.1/hygro without CMV promoter to obtain ptRNA Val - δ Rz-SPC2-X (where X indicates the position of the cleavage site). The hygromycin gene resistance allowed selection of positive clones upon transfection. B , drawing of the chimeric tRNA Val - δ Rz RNA produced from the ptRNA Val - δ Rz-SPC2 hybridized with the SPC2 mRNA substrate. The tRNA Val portion drives the δ Rz to the cytoplasm, and the poly(U) ensures the transcription termination. C , analysis of the expression levels of the chimeric tRNA Val - δ Rz and U6 RNA. Primer extension of the chimeric constructions tRNA Val - δ Rz ( δ Rz line) on total RNA of four cell lines established with either ptRNA Val - δ Rz-SPC2–154 (154-1 and 154-2) or -394 (394-1 and 394-9). Untransfected β TC-3 and cell line established with the vector ptRNA Val -KE ( β TC-3 and KE, respectively) served as controls. Primer extension of the endogenous U6 RNA (U6 line) served as internal control.
    Figure Legend Snippet: Expression of tRNA Val - δ Rz chimeric constructions A , vector used for cultured cells studies. We attenuated the CMV promoter of pcDNA3.1/hygro by the cleavage of MfeI before the promoter sequence. MfeI and EcoRI are two compatible sites that have been used for the cloning. The δ Rz has been first cloned in the pPUR-KE vector. Then the tRNA Val - δ Rz cassette has been subcloned from pPUR-KE to pcDNA3.1/hygro without CMV promoter to obtain ptRNA Val - δ Rz-SPC2-X (where X indicates the position of the cleavage site). The hygromycin gene resistance allowed selection of positive clones upon transfection. B , drawing of the chimeric tRNA Val - δ Rz RNA produced from the ptRNA Val - δ Rz-SPC2 hybridized with the SPC2 mRNA substrate. The tRNA Val portion drives the δ Rz to the cytoplasm, and the poly(U) ensures the transcription termination. C , analysis of the expression levels of the chimeric tRNA Val - δ Rz and U6 RNA. Primer extension of the chimeric constructions tRNA Val - δ Rz ( δ Rz line) on total RNA of four cell lines established with either ptRNA Val - δ Rz-SPC2–154 (154-1 and 154-2) or -394 (394-1 and 394-9). Untransfected β TC-3 and cell line established with the vector ptRNA Val -KE ( β TC-3 and KE, respectively) served as controls. Primer extension of the endogenous U6 RNA (U6 line) served as internal control.

    Techniques Used: Expressing, Plasmid Preparation, Cell Culture, Sequencing, Clone Assay, Selection, Transfection, Produced

    36) Product Images from "Identification of a Naegleria fowleri Membrane Protein Reactive with Anti-Human CD59 Antibody"

    Article Title: Identification of a Naegleria fowleri Membrane Protein Reactive with Anti-Human CD59 Antibody

    Journal:

    doi: 10.1128/IAI.74.2.1189-1195.2006

    Southern blot analysis of pathogenic and nonpathogenic Naegleria genomic DNAs (10 μg) hybridized with human CD59 cDNA. Genomic DNA was digested overnight with restriction enzyme EcoRI (A), BamHI (B), or HindIII (C); separated by gel electrophoresis;
    Figure Legend Snippet: Southern blot analysis of pathogenic and nonpathogenic Naegleria genomic DNAs (10 μg) hybridized with human CD59 cDNA. Genomic DNA was digested overnight with restriction enzyme EcoRI (A), BamHI (B), or HindIII (C); separated by gel electrophoresis;

    Techniques Used: Southern Blot, Nucleic Acid Electrophoresis

    37) Product Images from "Novel Roles for Selected Genes in Meiotic DNA Processing"

    Article Title: Novel Roles for Selected Genes in Meiotic DNA Processing

    Journal: PLoS Genetics

    doi: 10.1371/journal.pgen.0030222

    Assessment of def1 Δ in Meiosis and Mitosis (A) Immunocytology of nuclear spreads of SK1 wild-type and def1Δ strains after 8 h of sporulation. The meiosis-specific subunit of cohesin, Rec8, was tagged with multiple Haemagglutinin (HA) epitopes. Using antibodies for HA and Zip1 allowed analysis of sister chormatid cohesion and synaptonemal complex formation, respectively. It can be seen in the wild-type example that all 16 chromosomes have long cohesin axes and close to full chromosome synapsis except for the rDNA region on Chromosome XII. Whereas from the first panel for def1Δ it can be seen that axes are aligned but synapsis is minimal. The second and third panels for def1Δ again show aligned axes, but homologues are only partially synapsed. However, as shown in the final panel, synapsis was observed in some meiotic nuclei of the def1Δ strain. Polycomplexes (PCs) of Zip1 were observed in 20% of the nuclei counted for def1Δ at this time point whereas less than 1% PCs were observed for the wild type. (B) Time course of the meiotic nuclei counted using immunocytology for both wild type and def1Δ during meiosis. The def1Δ mutant synapsis phenotype represented in (A) was counted as “aligned” axes in the Rec8 analysis graph. At least 200 nuclei were counted per time point. (C) Ectopic URA3 - ARG4 interval on Chromosome III described in Figure 3 . XhoI and EcoRI restriction sites are indicated by “X” and “E,” respectively. To detect NCOs, COs, and DSBs, DNA is digested with XhoI and EcoRI then probed with HIS4 sequences (hisU; [ 44 ]). For graphs (D–F), wild-type and def1Δ are represented by blue squares and pink diamonds, respectively. The corresponding XhoI and EcoRI double digest Southern blots, the XhoI single digest Southern blots, together with the molecular analyses, are presented in Figure S5 . (D) Molecular analysis for DSB (DSB2) signal/total lane signal from Southern blots of DNA extracted from synchronized meiotic cultures. (E) Molecular analysis for NCO (NCO1) signal/total lane signal from Southern blots of DNA extracted from synchronized meiotic cultures. (F) Molecular analysis for CO (CO1') signal/total lane signal from Southern blots of DNA extracted from synchronized meiotic cultures. (G) Southern blot of DNA isolated from wild-type and def1Δ SK1 strains containing the ectopic URA3 - ARG4 interval on Chromosome III. DNA was digested with XhoI and EcoRI then probed to detect NCOs, COs, and DSBs; mw represents the 1-kb molecular weight marker (Fermentas).
    Figure Legend Snippet: Assessment of def1 Δ in Meiosis and Mitosis (A) Immunocytology of nuclear spreads of SK1 wild-type and def1Δ strains after 8 h of sporulation. The meiosis-specific subunit of cohesin, Rec8, was tagged with multiple Haemagglutinin (HA) epitopes. Using antibodies for HA and Zip1 allowed analysis of sister chormatid cohesion and synaptonemal complex formation, respectively. It can be seen in the wild-type example that all 16 chromosomes have long cohesin axes and close to full chromosome synapsis except for the rDNA region on Chromosome XII. Whereas from the first panel for def1Δ it can be seen that axes are aligned but synapsis is minimal. The second and third panels for def1Δ again show aligned axes, but homologues are only partially synapsed. However, as shown in the final panel, synapsis was observed in some meiotic nuclei of the def1Δ strain. Polycomplexes (PCs) of Zip1 were observed in 20% of the nuclei counted for def1Δ at this time point whereas less than 1% PCs were observed for the wild type. (B) Time course of the meiotic nuclei counted using immunocytology for both wild type and def1Δ during meiosis. The def1Δ mutant synapsis phenotype represented in (A) was counted as “aligned” axes in the Rec8 analysis graph. At least 200 nuclei were counted per time point. (C) Ectopic URA3 - ARG4 interval on Chromosome III described in Figure 3 . XhoI and EcoRI restriction sites are indicated by “X” and “E,” respectively. To detect NCOs, COs, and DSBs, DNA is digested with XhoI and EcoRI then probed with HIS4 sequences (hisU; [ 44 ]). For graphs (D–F), wild-type and def1Δ are represented by blue squares and pink diamonds, respectively. The corresponding XhoI and EcoRI double digest Southern blots, the XhoI single digest Southern blots, together with the molecular analyses, are presented in Figure S5 . (D) Molecular analysis for DSB (DSB2) signal/total lane signal from Southern blots of DNA extracted from synchronized meiotic cultures. (E) Molecular analysis for NCO (NCO1) signal/total lane signal from Southern blots of DNA extracted from synchronized meiotic cultures. (F) Molecular analysis for CO (CO1') signal/total lane signal from Southern blots of DNA extracted from synchronized meiotic cultures. (G) Southern blot of DNA isolated from wild-type and def1Δ SK1 strains containing the ectopic URA3 - ARG4 interval on Chromosome III. DNA was digested with XhoI and EcoRI then probed to detect NCOs, COs, and DSBs; mw represents the 1-kb molecular weight marker (Fermentas).

    Techniques Used: Mutagenesis, Southern Blot, Isolation, Molecular Weight, Marker

    38) Product Images from "Characterization of diverse homoserine lactone synthases in Escherichia coli"

    Article Title: Characterization of diverse homoserine lactone synthases in Escherichia coli

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0202294

    Sender plasmids expressed in Escherichia coli BL21. (A) The modular Sender vector allows facile cloning of any EcoRI , XbaI ] glyphs (top) and a scaled circular map (bottom). (B) Optical density (OD) readings for E . coli cultures expressing each of the Sender plasmids. (C) mCherry expression is shown as end-point RFP signal normalized to OD 600 after an 8 hour growth period.
    Figure Legend Snippet: Sender plasmids expressed in Escherichia coli BL21. (A) The modular Sender vector allows facile cloning of any EcoRI , XbaI ] glyphs (top) and a scaled circular map (bottom). (B) Optical density (OD) readings for E . coli cultures expressing each of the Sender plasmids. (C) mCherry expression is shown as end-point RFP signal normalized to OD 600 after an 8 hour growth period.

    Techniques Used: Plasmid Preparation, Clone Assay, Expressing

    39) Product Images from "Evaluation of Protective Immune Response Induced by a DNA Vaccine Encoding GRA8 against Acute Toxoplasmosis in a Murine Model"

    Article Title: Evaluation of Protective Immune Response Induced by a DNA Vaccine Encoding GRA8 against Acute Toxoplasmosis in a Murine Model

    Journal: The Korean Journal of Parasitology

    doi: 10.3347/kjp.2018.56.4.325

    T. gondii GRA8 was expressed successfully in ARPE-19 cells. (A) The coding sequence of the T. gondii GRA8 gene was amplified by PCR (814 bp) from the cDNA of T. gondii strain GFP-RH. (B) The PCR products were digested with the appropriate restriction enzymes and cloned into the XhoI and EcoRI sites of the pDsRed2-N1 expression vector, which contains the DsRed open reading frame. The constructed recombinant plasmid was named pDsRed2-GRA8. (C) ARPE-19 cells transfected with pDsRed2-GRA8 showed specific expression of GRA8 mRNA. (D) pDsRed2-GRA8 and the pDsRed2-N1 empty vector both expressed the DsRed2 protein, which localized to the cytoplasm of the transfected cells.
    Figure Legend Snippet: T. gondii GRA8 was expressed successfully in ARPE-19 cells. (A) The coding sequence of the T. gondii GRA8 gene was amplified by PCR (814 bp) from the cDNA of T. gondii strain GFP-RH. (B) The PCR products were digested with the appropriate restriction enzymes and cloned into the XhoI and EcoRI sites of the pDsRed2-N1 expression vector, which contains the DsRed open reading frame. The constructed recombinant plasmid was named pDsRed2-GRA8. (C) ARPE-19 cells transfected with pDsRed2-GRA8 showed specific expression of GRA8 mRNA. (D) pDsRed2-GRA8 and the pDsRed2-N1 empty vector both expressed the DsRed2 protein, which localized to the cytoplasm of the transfected cells.

    Techniques Used: Sequencing, Amplification, Polymerase Chain Reaction, Clone Assay, Expressing, Plasmid Preparation, Construct, Recombinant, Transfection

    40) Product Images from "Construction of a Novel DNA Vaccine Candidate encoding LmSTI1-PpSP42 Fusion Protein from Leishmania major and Phlebotomus papatasi Against Cutaneous Leishmaniasi"

    Article Title: Construction of a Novel DNA Vaccine Candidate encoding LmSTI1-PpSP42 Fusion Protein from Leishmania major and Phlebotomus papatasi Against Cutaneous Leishmaniasi

    Journal: Reports of Biochemistry & Molecular Biology

    doi:

    A: Schematic diagram of pCLmSTI1Pp42 construct composed of pcDNA3.1(+) eukaryotic expression vector and in-frame L. major LMSTI1 and Ph. Papatasi SP42 genes. B: pCLmSTI1 double-digested with KpnI and EcoRI (expected digested fragments: ∼5400 bp and ∼1600 bp). C: pCLmSTI1Pp42 double-digested with KpnI and XhoI (expected digested fragments: ∼5400 bp and ∼2500 bp).
    Figure Legend Snippet: A: Schematic diagram of pCLmSTI1Pp42 construct composed of pcDNA3.1(+) eukaryotic expression vector and in-frame L. major LMSTI1 and Ph. Papatasi SP42 genes. B: pCLmSTI1 double-digested with KpnI and EcoRI (expected digested fragments: ∼5400 bp and ∼1600 bp). C: pCLmSTI1Pp42 double-digested with KpnI and XhoI (expected digested fragments: ∼5400 bp and ∼2500 bp).

    Techniques Used: Construct, Expressing, Plasmid Preparation

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    Article Title: Regulation of p53 during senescence in normal human keratinocytes
    Article Snippet: .. To access the accuracy of the end joining activity, we cloned the PCR products from the ECoRI-linearized and ligated pCR2.1-TOPO plasmid into pcDNA3.1/V5-His TOPO plasmid (Invitrogen). .. The resulting ligated products were introduced into TOP10 cells (Invitrogen), and the single colony PCR was performed using the M13 primers (100 clones per samples).

    Article Title: Characterization of diverse homoserine lactone synthases in Escherichia coli
    Article Snippet: .. The Modular Sender Vector and each HSL synthase oligo were cut with EcoRI and XbaI (Thermo Fisher Scientific) and ligated using T4 ligase (New England Biolabs). ..

    Article Title: Proteomics and Transcriptomics of BJAB Cells Expressing the Epstein-Barr Virus Noncoding RNAs EBER1 and EBER2
    Article Snippet: .. pCEP4 vector constructs To introduce more than one copy of the EcoRI-J fragment into the pCEP4 plasmid (Invitrogen), we took advantage of the BglII and HindIII restriction sites up- and downstream, respectively, of the CMV promoter and of a BamHI one downstream the HindIII site as described in . .. To make stable cell lines, we transfected BJAB cells with each of these plasmids by electroporating at 230 V with 10 μg of pCEP4 empty or containing the EcoRI-J fragment, plus a similar amount of a GFP-expressing plasmid (pGFP-MAX) to trace the transfection efficiency as described above before [ ].

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  • 94
    Thermo Fisher ecori
    Sender plasmids expressed in Escherichia coli BL21. (A) The modular Sender vector allows facile cloning of any <t>EcoRI</t> , XbaI -flanked <t>synthase</t> open reading frame (ORF) and co-expression with mCherry (mCh) from a single bicistronic mRNA. The vector is represented as SBOL [ 44 ] glyphs (top) and a scaled circular map (bottom). (B) Optical density (OD) readings for E . coli cultures expressing each of the Sender plasmids. (C) mCherry expression is shown as end-point RFP signal normalized to OD 600 after an 8 hour growth period.
    Ecori, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 1364 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Sender plasmids expressed in Escherichia coli BL21. (A) The modular Sender vector allows facile cloning of any EcoRI , XbaI -flanked synthase open reading frame (ORF) and co-expression with mCherry (mCh) from a single bicistronic mRNA. The vector is represented as SBOL [ 44 ] glyphs (top) and a scaled circular map (bottom). (B) Optical density (OD) readings for E . coli cultures expressing each of the Sender plasmids. (C) mCherry expression is shown as end-point RFP signal normalized to OD 600 after an 8 hour growth period.

    Journal: PLoS ONE

    Article Title: Characterization of diverse homoserine lactone synthases in Escherichia coli

    doi: 10.1371/journal.pone.0202294

    Figure Lengend Snippet: Sender plasmids expressed in Escherichia coli BL21. (A) The modular Sender vector allows facile cloning of any EcoRI , XbaI -flanked synthase open reading frame (ORF) and co-expression with mCherry (mCh) from a single bicistronic mRNA. The vector is represented as SBOL [ 44 ] glyphs (top) and a scaled circular map (bottom). (B) Optical density (OD) readings for E . coli cultures expressing each of the Sender plasmids. (C) mCherry expression is shown as end-point RFP signal normalized to OD 600 after an 8 hour growth period.

    Article Snippet: The Modular Sender Vector and each HSL synthase oligo were cut with EcoRI and XbaI (Thermo Fisher Scientific) and ligated using T4 ligase (New England Biolabs).

    Techniques: Plasmid Preparation, Clone Assay, Expressing

    Electrophoretic product of PvAMA-1 gene treated with EcoR I, PvuII, and HindIII, enzymes using RFLP-PCR technique including Columns 1,2 3 treated with EcoRI. Column 4 main bound of Pv AMA-1. Column 5 size marker with 1000bp. Columns 6, 7 and 8 treated with PvuII. Columns 9 10 treated with HindIII

    Journal: Iranian Journal of Parasitology

    Article Title: Allelic Variations of Plasmodium vivax Apical Membrane Antigen-1 (Pv AMA-1) in Malarious Areas of Southeastern Iran Using PCR-RFLP Technique

    doi:

    Figure Lengend Snippet: Electrophoretic product of PvAMA-1 gene treated with EcoR I, PvuII, and HindIII, enzymes using RFLP-PCR technique including Columns 1,2 3 treated with EcoRI. Column 4 main bound of Pv AMA-1. Column 5 size marker with 1000bp. Columns 6, 7 and 8 treated with PvuII. Columns 9 10 treated with HindIII

    Article Snippet: RFLP In order to determine the presence of different alleles of Pv AMA-1 gene in the region, PCR–RFLP technique was done to digest the gene using three restriction enzymes EcoR-1, Pvu-II and Hind3 (Thermo cat No #ER0271, #ER0631 and ferments cat No #ER0501 respectively) according to the manufacturer’s recommendations.

    Techniques: Polymerase Chain Reaction, Marker

    Southern blot analysis of the four STS markers- CtR-431, CtR-594., CtR-496, and AFLP-376. Restriction enzymes used are EcoRI, HinDIII and XbaI . M, molecular weight marker; R resistant genotype Punjab Lal; S susceptible genotype Arka Lohit. Hybridization

    Journal: 3 Biotech

    Article Title: Sequence-tagged site-based diagnostic markers linked to a novel anthracnose resistance gene RCt1 in chili pepper (Capsicum annuum L.)

    doi: 10.1007/s13205-018-1552-0

    Figure Lengend Snippet: Southern blot analysis of the four STS markers- CtR-431, CtR-594., CtR-496, and AFLP-376. Restriction enzymes used are EcoRI, HinDIII and XbaI . M, molecular weight marker; R resistant genotype Punjab Lal; S susceptible genotype Arka Lohit. Hybridization

    Article Snippet: Three different restriction endonucleases- EcoRI, HinDIII and XbaI (Thermo Fischer Scientific, USA) were used to digest the genomic DNA from the resistant line ‘Punjab Lal’ and the susceptible line ‘Arka Lohit’.

    Techniques: Southern Blot, Molecular Weight, Marker, Hybridization