bp dna  (New England Biolabs)


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    100 bp DNA Ladder
    Description:
    100 bp DNA Ladder 500 gel lanes
    Catalog Number:
    n3231l
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    Category:
    DNA Ladders
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    500 gel lanes
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    New England Biolabs bp dna
    100 bp DNA Ladder
    100 bp DNA Ladder 500 gel lanes
    https://www.bioz.com/result/bp dna/product/New England Biolabs
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bp dna - by Bioz Stars, 2021-03
    95/100 stars

    Images

    1) Product Images from "Leishmania actin binds and nicks kDNA as well as inhibits decatenation activity of type II topoisomerase"

    Article Title: Leishmania actin binds and nicks kDNA as well as inhibits decatenation activity of type II topoisomerase

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkq051

    ( A ) ChIP analysis using anti-rLdACT antibodies showed the in vivo association of LdACT with chromatin and kDNA network. ( a ) and ( b ) are the agarose gels of PCR products after ChIP assay, showing the association of LdACT with nuclear DNA and kDNA, respectively. Lanes are marked on the top with their respective antibodies used in the ChIP assay and arrows indicated the genes amplified after pull down. An irrelevant, non-DNA associating antibody, GRP78, was used as a negative control, whereas, antibodies against DNA polβ, and UMSBP (universal minicircle sequence-binding protein), were used as positive controls for nuclear DNA and kDNA respectively. LdPFN, Leishmania profilin; NM12/17, specific minicircle primers. ( B ) Agarose gel shift assay of supercoiled and linearized pBR322 (400 ng each) in the presence of rLdACT (0.5 2.0 μM), and β- and γ-actins (0.5 2.0 μM) as indicated on the top of the gels. Lane M, shows 1 kb DNA ladder; FI: supercoiled form, FII: relaxed form, FIII: linearized form of DNA. ( C ) Autoradiogram of EMSA on polyacrylamide gel of 32 P end-labelled 30 bp DNA probe in the presence of increasing concentration of rLdACT (0.1–0.6 μM).
    Figure Legend Snippet: ( A ) ChIP analysis using anti-rLdACT antibodies showed the in vivo association of LdACT with chromatin and kDNA network. ( a ) and ( b ) are the agarose gels of PCR products after ChIP assay, showing the association of LdACT with nuclear DNA and kDNA, respectively. Lanes are marked on the top with their respective antibodies used in the ChIP assay and arrows indicated the genes amplified after pull down. An irrelevant, non-DNA associating antibody, GRP78, was used as a negative control, whereas, antibodies against DNA polβ, and UMSBP (universal minicircle sequence-binding protein), were used as positive controls for nuclear DNA and kDNA respectively. LdPFN, Leishmania profilin; NM12/17, specific minicircle primers. ( B ) Agarose gel shift assay of supercoiled and linearized pBR322 (400 ng each) in the presence of rLdACT (0.5 2.0 μM), and β- and γ-actins (0.5 2.0 μM) as indicated on the top of the gels. Lane M, shows 1 kb DNA ladder; FI: supercoiled form, FII: relaxed form, FIII: linearized form of DNA. ( C ) Autoradiogram of EMSA on polyacrylamide gel of 32 P end-labelled 30 bp DNA probe in the presence of increasing concentration of rLdACT (0.1–0.6 μM).

    Techniques Used: Chromatin Immunoprecipitation, In Vivo, Polymerase Chain Reaction, Amplification, Negative Control, Sequencing, Binding Assay, Agarose Gel Electrophoresis, Shift Assay, Concentration Assay

    ( A ) Agarose gel (0.5%), showing the time dependent nicking of kDNA by rLdACT (4.0 μM) which revealed the existence of major nicked DNA and minor concatenated minicircle species. ( B ) Agarose gel, showing rLdACT mediated decatenation of the kDNA network in the presence or absence of anti-rLdACT antibodies. DM, decatenated kDNA marker (Topogen). ( C ) Agarose gel (1.0%), showing rLdACT mediated decatenation of kDNA network with rLdACT in the presence or absence of DNase-1 and its inhibitor EDTA, which completely rules out the possibility of DNA nicking by some contaminating nuclease. ( D ) Agarose gel (1.0%), showing requirement of rLdACT in its polymeric state for its kDNA decatenation activity. ( E ): ( a ), Agarose gel (1.0%), showing requirement of ATP in the rLdACT mediated kDNA decatenation process. ( b ), Graph, showing ATP dependence of rLdACT-mediated kDNA decatenation. ( F ) ( a ), Agarose gel (1.0%), showing rLdACT-mediated decatenation of kDNA in the presence of non-hydrolysable analogs of ATP. ( b ) Graph, showing relative inhibition of rLdACT mediated decatenation of kDNA network in the presence of non-hydrolysable ATP analogs when plotted with the increasing concentration of rLdACT.
    Figure Legend Snippet: ( A ) Agarose gel (0.5%), showing the time dependent nicking of kDNA by rLdACT (4.0 μM) which revealed the existence of major nicked DNA and minor concatenated minicircle species. ( B ) Agarose gel, showing rLdACT mediated decatenation of the kDNA network in the presence or absence of anti-rLdACT antibodies. DM, decatenated kDNA marker (Topogen). ( C ) Agarose gel (1.0%), showing rLdACT mediated decatenation of kDNA network with rLdACT in the presence or absence of DNase-1 and its inhibitor EDTA, which completely rules out the possibility of DNA nicking by some contaminating nuclease. ( D ) Agarose gel (1.0%), showing requirement of rLdACT in its polymeric state for its kDNA decatenation activity. ( E ): ( a ), Agarose gel (1.0%), showing requirement of ATP in the rLdACT mediated kDNA decatenation process. ( b ), Graph, showing ATP dependence of rLdACT-mediated kDNA decatenation. ( F ) ( a ), Agarose gel (1.0%), showing rLdACT-mediated decatenation of kDNA in the presence of non-hydrolysable analogs of ATP. ( b ) Graph, showing relative inhibition of rLdACT mediated decatenation of kDNA network in the presence of non-hydrolysable ATP analogs when plotted with the increasing concentration of rLdACT.

    Techniques Used: Agarose Gel Electrophoresis, Marker, Activity Assay, Inhibition, Concentration Assay

    ( A ) Agarose gel, showing supercoiled pBR322 DNA (400 ng) relaxation separately with rLdACT (0.5 1.0 μM) and E. coli Topo I. Image presented is the negative of original gel image. ( B ) Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT in the presence or absence of anti-rLdACT antibodies, showing specificity of nicking activity associated with rLdACT. ( C ) Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT (0.5 1.0 μM) in the presence or absence of DNase-1 and its inhibitor EDTA which further eliminates the possibility of DNA nicking by contaminating nuclease. ( D ): a and b, Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT in the presence of ATP and its non-hydrolysable ATP analogs as indicated on the top of the gel. ( E ) Graph showing the requirement of ATP in its hydrolysable form during rLdACT mediated relaxation of supercoiled pBR322 DNA. ( F ) Agarose gel, showing requirement of rLdACT (0.5 2.0 μM) in its polymeric state for its scDNA-relaxation activity. ( G ) Graph, representing rLdACT (1.0 μM) mediated relaxation of supercoiled pBR322 DNA in the presence of increasing concentration of NaCl, inset shows the relative % inhibition of rLdACT mediated relaxation of supercoiled pBR322 DNA in presence of 50 mM salts having different ionization constant (Ksp) as indicated on the top of the bars. ( H ) Dynamic light scattering measurements of rLdACT (1.0 μM) showing insignificant effect of 0.2 M NaCl on the polymerized state of rLdACT after complete polymerization.
    Figure Legend Snippet: ( A ) Agarose gel, showing supercoiled pBR322 DNA (400 ng) relaxation separately with rLdACT (0.5 1.0 μM) and E. coli Topo I. Image presented is the negative of original gel image. ( B ) Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT in the presence or absence of anti-rLdACT antibodies, showing specificity of nicking activity associated with rLdACT. ( C ) Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT (0.5 1.0 μM) in the presence or absence of DNase-1 and its inhibitor EDTA which further eliminates the possibility of DNA nicking by contaminating nuclease. ( D ): a and b, Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT in the presence of ATP and its non-hydrolysable ATP analogs as indicated on the top of the gel. ( E ) Graph showing the requirement of ATP in its hydrolysable form during rLdACT mediated relaxation of supercoiled pBR322 DNA. ( F ) Agarose gel, showing requirement of rLdACT (0.5 2.0 μM) in its polymeric state for its scDNA-relaxation activity. ( G ) Graph, representing rLdACT (1.0 μM) mediated relaxation of supercoiled pBR322 DNA in the presence of increasing concentration of NaCl, inset shows the relative % inhibition of rLdACT mediated relaxation of supercoiled pBR322 DNA in presence of 50 mM salts having different ionization constant (Ksp) as indicated on the top of the bars. ( H ) Dynamic light scattering measurements of rLdACT (1.0 μM) showing insignificant effect of 0.2 M NaCl on the polymerized state of rLdACT after complete polymerization.

    Techniques Used: Agarose Gel Electrophoresis, Activity Assay, Concentration Assay, Inhibition

    2) Product Images from "Titanium Kirschner Wires Resist Biofilms Better Than Stainless Steel and Hydroxyapatite-coated Wires: An In Vitro Study"

    Article Title: Titanium Kirschner Wires Resist Biofilms Better Than Stainless Steel and Hydroxyapatite-coated Wires: An In Vitro Study

    Journal: Strategies in Trauma and Limb Reconstruction

    doi: 10.5005/jp-journals-10080-1426

    Agarose gel electrophoresis of the nPCR products. (1) 100-bp ladder; (2) OP with S. epidermidis DNA; (3) OP with P. mirabilis DNA; (4) IP with S. epidermidis DNA; (5) IP with P. mirabilis DNA; and (6) Negative control
    Figure Legend Snippet: Agarose gel electrophoresis of the nPCR products. (1) 100-bp ladder; (2) OP with S. epidermidis DNA; (3) OP with P. mirabilis DNA; (4) IP with S. epidermidis DNA; (5) IP with P. mirabilis DNA; and (6) Negative control

    Techniques Used: Agarose Gel Electrophoresis, Negative Control

    Agarose gel electrophoresis of the nPCR products by species. (1) 100-bp ladder; (2) OP S. epidermidis ; (3) OP S. epidermidis ; (4) OP S. epidermidis ; (5) OP S. aureus ; (6) OP S. aureus ; (7) OP P. mirabilis ; (8) OP P. mirabilis ; (9) OP negative control; (10) IP S. epidermidis ; (11) IP S. epidermidis ; (12) IP S. epidermidis ; (13) IP S. aureus ; (14) IP S. aureus ; (15) IP P. mirabilis ; (16) IP P. mirabilis ; and (17) IP negative control
    Figure Legend Snippet: Agarose gel electrophoresis of the nPCR products by species. (1) 100-bp ladder; (2) OP S. epidermidis ; (3) OP S. epidermidis ; (4) OP S. epidermidis ; (5) OP S. aureus ; (6) OP S. aureus ; (7) OP P. mirabilis ; (8) OP P. mirabilis ; (9) OP negative control; (10) IP S. epidermidis ; (11) IP S. epidermidis ; (12) IP S. epidermidis ; (13) IP S. aureus ; (14) IP S. aureus ; (15) IP P. mirabilis ; (16) IP P. mirabilis ; and (17) IP negative control

    Techniques Used: Agarose Gel Electrophoresis, Negative Control

    3) Product Images from "Identification of UDP Glycosyltransferase 3A1 as a UDPN-Acetylglucosaminyltransferase *"

    Article Title: Identification of UDP Glycosyltransferase 3A1 as a UDPN-Acetylglucosaminyltransferase *

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M807961200

    Detection of UGT3A1 transcripts in a human tissue RNA panel. UGT3A1 RNA was amplified by reverse transcription-PCR over 40 cycles and detected by electrophoresis in a 1.5% agarose gel, stained with ethidium bromide. The 100-bp DNA markers are shown
    Figure Legend Snippet: Detection of UGT3A1 transcripts in a human tissue RNA panel. UGT3A1 RNA was amplified by reverse transcription-PCR over 40 cycles and detected by electrophoresis in a 1.5% agarose gel, stained with ethidium bromide. The 100-bp DNA markers are shown

    Techniques Used: Amplification, Polymerase Chain Reaction, Electrophoresis, Agarose Gel Electrophoresis, Staining

    4) Product Images from "Relationship Between Chromatin Structure and Sensitivity to Molecularly Targeted Auger Electron Radiation Therapy"

    Article Title: Relationship Between Chromatin Structure and Sensitivity to Molecularly Targeted Auger Electron Radiation Therapy

    Journal: International journal of radiation oncology, biology, physics

    doi: 10.1016/j.ijrobp.2011.09.051

    Clonogenic survival for (A, B) MDA-MB-468 and (C, D) 231-H2N cells. Cells were incubated with suberoylanilide hydroxamic acid (SAHA) followed by (A, C) IR, (B, D) 111 In-DTPA-hEGF (30 MBq/μg; 100 pM or 0–67 MBq/μg; 12 nM, respectively) or DTPA-hEGF (100 pM or 12 nM). Results are means ± SEM of three experiments or means ± SEM of triplicates in one experiment. Error bars are too small to be seen in (A and D).
    Figure Legend Snippet: Clonogenic survival for (A, B) MDA-MB-468 and (C, D) 231-H2N cells. Cells were incubated with suberoylanilide hydroxamic acid (SAHA) followed by (A, C) IR, (B, D) 111 In-DTPA-hEGF (30 MBq/μg; 100 pM or 0–67 MBq/μg; 12 nM, respectively) or DTPA-hEGF (100 pM or 12 nM). Results are means ± SEM of three experiments or means ± SEM of triplicates in one experiment. Error bars are too small to be seen in (A and D).

    Techniques Used: Multiple Displacement Amplification, Incubation

    5) Product Images from "Identification of Coupling and Repulsion Phase DNA Marker Associated With an Allele of a Gene Conferring Host Plant Resistance to Pigeonpea sterility mosaic virus (PPSMV) in Pigeonpea (Cajanus cajan L. Millsp.)"

    Article Title: Identification of Coupling and Repulsion Phase DNA Marker Associated With an Allele of a Gene Conferring Host Plant Resistance to Pigeonpea sterility mosaic virus (PPSMV) in Pigeonpea (Cajanus cajan L. Millsp.)

    Journal: The Plant Pathology Journal

    doi: 10.5423/PPJ.OA.07.2014.0064

    Segregation of coupling phase RAPD markers IABTPPN7 983 and repulsion phase RAPD marker IABTPPN7 414 across F 2 plant DNA of the cross Gullyal white × BSMR 736 linked to PSMD. P1=PSMD susceptible parent Gullyal white, P2=PSMD resistant parent BSMR 736, Lane M=100 bp DNA ladder.
    Figure Legend Snippet: Segregation of coupling phase RAPD markers IABTPPN7 983 and repulsion phase RAPD marker IABTPPN7 414 across F 2 plant DNA of the cross Gullyal white × BSMR 736 linked to PSMD. P1=PSMD susceptible parent Gullyal white, P2=PSMD resistant parent BSMR 736, Lane M=100 bp DNA ladder.

    Techniques Used: Marker

    Screening of the seven resistant and seven susceptible F 2 plant DNA of the cross Gullyal white × BSMR 736 with a coupling phase RAPD markers IABTPPN7 983 and repulsion phase RAPD marker IABTPPN7 414 , linked to PSMD. SP=PSMD susceptible parent Gullyal white, RP=PSMD resistant parent BSMR 736, Lane M=100 bp DNA ladder.
    Figure Legend Snippet: Screening of the seven resistant and seven susceptible F 2 plant DNA of the cross Gullyal white × BSMR 736 with a coupling phase RAPD markers IABTPPN7 983 and repulsion phase RAPD marker IABTPPN7 414 , linked to PSMD. SP=PSMD susceptible parent Gullyal white, RP=PSMD resistant parent BSMR 736, Lane M=100 bp DNA ladder.

    Techniques Used: Marker

    Amplification pattern of coupling phase RAPD markers IABTPPN7 983 and repulsion phase RAPD marker IABTPPN7 414 in parents and resistant and susceptible bulks. M, 100 bp ladder DNA; RP, Resistant parent - BSMR 736; RB, resistant bulk; SP, susceptible parent - Gullyal white; SB, susceptible bulk.
    Figure Legend Snippet: Amplification pattern of coupling phase RAPD markers IABTPPN7 983 and repulsion phase RAPD marker IABTPPN7 414 in parents and resistant and susceptible bulks. M, 100 bp ladder DNA; RP, Resistant parent - BSMR 736; RB, resistant bulk; SP, susceptible parent - Gullyal white; SB, susceptible bulk.

    Techniques Used: Amplification, Marker

    6) Product Images from "ADH1B, ALDH2, GSTM1 and GSTT1 Gene Polymorphic Frequencies among Alcoholics and Controls in the Arcadian Population of Central India"

    Article Title: ADH1B, ALDH2, GSTM1 and GSTT1 Gene Polymorphic Frequencies among Alcoholics and Controls in the Arcadian Population of Central India

    Journal: Asian Pacific Journal of Cancer Prevention : APJCP

    doi: 10.22034/APJCP.2018.19.3.725

    For ADH1B Genotyping–Lane L, 100bp DNA Ladder; Lane 1–7, Undigested 155bp bands for ADH1B.
    Figure Legend Snippet: For ADH1B Genotyping–Lane L, 100bp DNA Ladder; Lane 1–7, Undigested 155bp bands for ADH1B.

    Techniques Used:

    For ALDH2 Genotyping–Lane L, 100bp DNA Ladder; Lane 1–2, Digested fragments of 90bp and 18bp bands; Lane 3–6, One uncut (119bp) with two digested fragments (90bp and 18bp); Lane 7, Undigested band (119bp).
    Figure Legend Snippet: For ALDH2 Genotyping–Lane L, 100bp DNA Ladder; Lane 1–2, Digested fragments of 90bp and 18bp bands; Lane 3–6, One uncut (119bp) with two digested fragments (90bp and 18bp); Lane 7, Undigested band (119bp).

    Techniques Used:

    GSTM1 Genotyping; Lane L, 100bp DNA Ladder; Lane 1, Null allele for GSTM1; Lane 2–6, Positive allele for GSTM1 (215bp).
    Figure Legend Snippet: GSTM1 Genotyping; Lane L, 100bp DNA Ladder; Lane 1, Null allele for GSTM1; Lane 2–6, Positive allele for GSTM1 (215bp).

    Techniques Used:

    7) Product Images from "A selectable, plasmid-based system to generate CRISPR/Cas9 gene edited and knock-in mosquito cell lines"

    Article Title: A selectable, plasmid-based system to generate CRISPR/Cas9 gene edited and knock-in mosquito cell lines

    Journal: Scientific Reports

    doi: 10.1038/s41598-020-80436-5

    CRISPR/Cas9-mediated editing and knock-in of AGO1 in Aag2 cells. ( a ) Three sgRNAs (sg) were designed near the AGO1 translation start site in Aag2 cells. PCRs were designed for surveyor assay (green arrows 1 and 2) and to assess integration (green arrows 1 + and 3). ( b ) Homology-directed repair (HDR) donor template design. The PUb promoter drives expression of red fluorescent protein (RFP); the PUb-RFP cassette is flanked by two loxP sites, followed by a 3xFLAG-tag. Aag2 AGO1 sgRNAs transfections were performed as in Fig. 3 b with the HDR donor template added. Workflows to obtain edited or integrated clones are shown. ( c ) Editing efficiency was assessed by surveyor assay. Expected size of wild-type (WT) amplicon = ~ 410 base pairs (bp; black arrow); expected size of digested fragments based on sgRNA cleavage sites = ~ 180 bp + ~ 230 bp (red arrow); m = marker. ( d ) Single cell clones were sequenced to determine the percentage of edited clones. Immunoblot of AGO1 (top) showed clones with WT and reduced AGO1 protein levels (salmon arrows); A, B, C denote clones. 3xFLAG-tagged Aag2 AGO1 short and long isoforms were detected by both the anti-AGO1 antibody and the anti-FLAG antibody (bottom). ( e ) RFP-positive Aag2 clones from ( b ) were screened for HDR-mediated integration of the donor template. Expected size of amplicons from WT clones = ~ 1500 bp (black arrow); expected size of amplicons from clones containing the integrated HDR donor template = ~ 3700 bp (dark red arrow). B2 and C10 clones were knock-in at the AGO1 locus . ( f ) The PUb-RFP cassette was excised from Aag2 AGO1 knock-in clones (B2 and C10) by transfection of PUb-driven Cre-T2A-pAc and puro selection. WT and un-transfected B2 cells are shown; expected WT and integrated HDR donor template amplicon sizes as in ( e ); expected size of Cre excised amplicon = ~ 1500 bp (black arrow). Puro treatment increases the proportion of Cre excision (B2 + Cre + puro). ( g ) B2 and C10 Cre excised cell lines were sorted for RFP negative clones to obtain homozygous knock-in 3xFLAG- AGO1 Aag2 cell lines. Expected amplicon sizes as in ( e – f ). All full-length immunoblots in Supplementary Fig. 4 ; all full-length DNA gels in Supplementary Fig. 5 .
    Figure Legend Snippet: CRISPR/Cas9-mediated editing and knock-in of AGO1 in Aag2 cells. ( a ) Three sgRNAs (sg) were designed near the AGO1 translation start site in Aag2 cells. PCRs were designed for surveyor assay (green arrows 1 and 2) and to assess integration (green arrows 1 + and 3). ( b ) Homology-directed repair (HDR) donor template design. The PUb promoter drives expression of red fluorescent protein (RFP); the PUb-RFP cassette is flanked by two loxP sites, followed by a 3xFLAG-tag. Aag2 AGO1 sgRNAs transfections were performed as in Fig. 3 b with the HDR donor template added. Workflows to obtain edited or integrated clones are shown. ( c ) Editing efficiency was assessed by surveyor assay. Expected size of wild-type (WT) amplicon = ~ 410 base pairs (bp; black arrow); expected size of digested fragments based on sgRNA cleavage sites = ~ 180 bp + ~ 230 bp (red arrow); m = marker. ( d ) Single cell clones were sequenced to determine the percentage of edited clones. Immunoblot of AGO1 (top) showed clones with WT and reduced AGO1 protein levels (salmon arrows); A, B, C denote clones. 3xFLAG-tagged Aag2 AGO1 short and long isoforms were detected by both the anti-AGO1 antibody and the anti-FLAG antibody (bottom). ( e ) RFP-positive Aag2 clones from ( b ) were screened for HDR-mediated integration of the donor template. Expected size of amplicons from WT clones = ~ 1500 bp (black arrow); expected size of amplicons from clones containing the integrated HDR donor template = ~ 3700 bp (dark red arrow). B2 and C10 clones were knock-in at the AGO1 locus . ( f ) The PUb-RFP cassette was excised from Aag2 AGO1 knock-in clones (B2 and C10) by transfection of PUb-driven Cre-T2A-pAc and puro selection. WT and un-transfected B2 cells are shown; expected WT and integrated HDR donor template amplicon sizes as in ( e ); expected size of Cre excised amplicon = ~ 1500 bp (black arrow). Puro treatment increases the proportion of Cre excision (B2 + Cre + puro). ( g ) B2 and C10 Cre excised cell lines were sorted for RFP negative clones to obtain homozygous knock-in 3xFLAG- AGO1 Aag2 cell lines. Expected amplicon sizes as in ( e – f ). All full-length immunoblots in Supplementary Fig. 4 ; all full-length DNA gels in Supplementary Fig. 5 .

    Techniques Used: CRISPR, Knock-In, Expressing, Transfection, Clone Assay, Amplification, Marker, Selection, Western Blot

    8) Product Images from "Simple and Reliable Multiplex PCR Assay for Surveillance Isolates of Vancomycin-Resistant Enterococci"

    Article Title: Simple and Reliable Multiplex PCR Assay for Surveillance Isolates of Vancomycin-Resistant Enterococci

    Journal: Journal of Clinical Microbiology

    doi:

    Agarose gel electrophoresis of amplified vanA , vanB , vanC1 , vanC2 , E. faecalis -specific, E. faecium -specific, and rrs genes by the optimized multiplex PCR assay containing seven primer sets. Lanes: M, 100-bp DNA ladder (New England Biolabs); 1, an E. faecalis vanA isolate; 2, an E. faecalis vanB isolate; 3, an E. faecium vanA isolate; 4, an E. faecium vanB isolate; 5, an E. gallinarum vanC1 isolate; 6, an E. casseliflavus vanC2 isolate; 7, a Pediococcus isolate; 8, a Leuconostoc isolate.
    Figure Legend Snippet: Agarose gel electrophoresis of amplified vanA , vanB , vanC1 , vanC2 , E. faecalis -specific, E. faecium -specific, and rrs genes by the optimized multiplex PCR assay containing seven primer sets. Lanes: M, 100-bp DNA ladder (New England Biolabs); 1, an E. faecalis vanA isolate; 2, an E. faecalis vanB isolate; 3, an E. faecium vanA isolate; 4, an E. faecium vanB isolate; 5, an E. gallinarum vanC1 isolate; 6, an E. casseliflavus vanC2 isolate; 7, a Pediococcus isolate; 8, a Leuconostoc isolate.

    Techniques Used: Agarose Gel Electrophoresis, Amplification, Multiplex Assay, Polymerase Chain Reaction

    9) Product Images from "A Stop-Gain Mutation within MLPH Is Responsible for the Lilac Dilution Observed in Jacob Sheep"

    Article Title: A Stop-Gain Mutation within MLPH Is Responsible for the Lilac Dilution Observed in Jacob Sheep

    Journal: Genes

    doi: 10.3390/genes11060618

    Gel image of the RFLP gel electrophoresis validation of the NC_019458.2:g.3451931C > A mutation. Lane 1 represents the 100-bp reference ladder, with the 1000, 500, and 100 bp bands labeled. Lanes 2 through 4 represent the three genotypes at this variant. The normal allele (C) results in four expected fragments of 121, 57, 38, and 29 bp while the dilute allele (A) results in only three expected fragments of 178, 38, and 29 bp. The 178- and 121-bp fragments were the primary ones used for genotyping, as the smaller bands were more difficult to identify. The bands of approximately 150 bp and 200 bp are likely to be the result of an incomplete digestion of the last EarI recognition site within the PCR product.
    Figure Legend Snippet: Gel image of the RFLP gel electrophoresis validation of the NC_019458.2:g.3451931C > A mutation. Lane 1 represents the 100-bp reference ladder, with the 1000, 500, and 100 bp bands labeled. Lanes 2 through 4 represent the three genotypes at this variant. The normal allele (C) results in four expected fragments of 121, 57, 38, and 29 bp while the dilute allele (A) results in only three expected fragments of 178, 38, and 29 bp. The 178- and 121-bp fragments were the primary ones used for genotyping, as the smaller bands were more difficult to identify. The bands of approximately 150 bp and 200 bp are likely to be the result of an incomplete digestion of the last EarI recognition site within the PCR product.

    Techniques Used: Nucleic Acid Electrophoresis, Mutagenesis, Labeling, Variant Assay, Polymerase Chain Reaction

    10) Product Images from "RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes"

    Article Title: RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

    Journal: Methods (San Diego, Calif.)

    doi: 10.1016/j.ymeth.2013.09.013

    Biochemical analysis of proteins and RNAs from the RIPiT procedure A. Western blots showing tetracycline (Tet)-mediated induction of eIF4AIII protein with the FLAG tag at its N- or C-terminus (top and bottom panels, respectively). The Tet concentration used for induction is indicated at the top of each lane; protein identities are indicated to the right. B. Levels of proteins detected by western blots in different fractions during EJC RIPiT. The table on the top indicates the different fractions from the RIPiT procedure and the antibodies used for 1 st and 2 nd IPs. The stably expressed FLAG-tag fusion protein used in each sample is indicated directly above lane. Proteins detected by western blot are indicated to the right. C. Size distribution of EJC footprints upon RNase I titration. An autoradiogram of 26% denaturing PAGE with 5′ [ 32 P]-labeled RNA fragments from base-hydrolysis of poly U 30 oligonucleotide (lane 1) or FLAG-Magoh:eIF4AIII RIPiT (lanes 2–5). RNase I concentrations used are indicated at top of each lane; nucleotide (nt) lengths are to the left. D. Quantification of desired size RNA footprints in RIPiT elution. An autoradiogram of 20% denaturing PAGE with 5′ [ 32 P]-labeled 100 bp NEB DNA ladder (lane 1), low molecular weight ssDNA ladder (lane 2), footprints of RIPiTs indicated on top (lanes 3 and 4) and a 21 nt ssRNA oligo of known specific activity (lane 5). The signal from red rectangles is quantified in comparison to that of the 21 nt oligo to estimate the amount of RIPiT footprints in the indicated size range.
    Figure Legend Snippet: Biochemical analysis of proteins and RNAs from the RIPiT procedure A. Western blots showing tetracycline (Tet)-mediated induction of eIF4AIII protein with the FLAG tag at its N- or C-terminus (top and bottom panels, respectively). The Tet concentration used for induction is indicated at the top of each lane; protein identities are indicated to the right. B. Levels of proteins detected by western blots in different fractions during EJC RIPiT. The table on the top indicates the different fractions from the RIPiT procedure and the antibodies used for 1 st and 2 nd IPs. The stably expressed FLAG-tag fusion protein used in each sample is indicated directly above lane. Proteins detected by western blot are indicated to the right. C. Size distribution of EJC footprints upon RNase I titration. An autoradiogram of 26% denaturing PAGE with 5′ [ 32 P]-labeled RNA fragments from base-hydrolysis of poly U 30 oligonucleotide (lane 1) or FLAG-Magoh:eIF4AIII RIPiT (lanes 2–5). RNase I concentrations used are indicated at top of each lane; nucleotide (nt) lengths are to the left. D. Quantification of desired size RNA footprints in RIPiT elution. An autoradiogram of 20% denaturing PAGE with 5′ [ 32 P]-labeled 100 bp NEB DNA ladder (lane 1), low molecular weight ssDNA ladder (lane 2), footprints of RIPiTs indicated on top (lanes 3 and 4) and a 21 nt ssRNA oligo of known specific activity (lane 5). The signal from red rectangles is quantified in comparison to that of the 21 nt oligo to estimate the amount of RIPiT footprints in the indicated size range.

    Techniques Used: Western Blot, FLAG-tag, Concentration Assay, Stable Transfection, Titration, Polyacrylamide Gel Electrophoresis, Labeling, Molecular Weight, Activity Assay

    11) Product Images from "The latency-associated nuclear antigen of Kaposi sarcoma-associated herpesvirus induces B cell hyperplasia and lymphoma"

    Article Title: The latency-associated nuclear antigen of Kaposi sarcoma-associated herpesvirus induces B cell hyperplasia and lymphoma

    Journal: Journal of Clinical Investigation

    doi: 10.1172/JCI26190

    PCR analysis of VDJ H and DJ H rearrangements in tumors of LANA transgenic mice. Total spleen genomic DNAs were used in the PCR reactions analyzing tumors. ( A – C ) PCR analysis of total spleen genomic DNAs from 4 LANA transgenic mice with tumors, 2 C57BL/6 mice older than 300 days (WT), and 2 different murine B cell lines resolved on a 1.5% Tris-acetate-EDTA–agarose gel, used as controls for the clonality. WT lanes demonstrate VDJ H 1, VDJ H 2, VDJ H 3, and VDJ H 4 rearrangements ( A and B ) using V H 7183 ( A ) or V H J558 primers ( B ) and DJ H 1, DJ H 2, DJ H 3, and DJ H 4 rearrangements ( C ) using Dq52 primers. The primers were designed to amplify all rearrangement products between J H 4 and V H 7183, V H J558, or Dq52; 4 different bands would be expected by the combination of each primer set. M, 100-bp DNA Ladder (New England Biolabs Inc.) ( D ) DNA samples used for the Ig rearrangement PCRs were quantified using real-time quantitative PCR to demonstrate equal total DNA concentrations.
    Figure Legend Snippet: PCR analysis of VDJ H and DJ H rearrangements in tumors of LANA transgenic mice. Total spleen genomic DNAs were used in the PCR reactions analyzing tumors. ( A – C ) PCR analysis of total spleen genomic DNAs from 4 LANA transgenic mice with tumors, 2 C57BL/6 mice older than 300 days (WT), and 2 different murine B cell lines resolved on a 1.5% Tris-acetate-EDTA–agarose gel, used as controls for the clonality. WT lanes demonstrate VDJ H 1, VDJ H 2, VDJ H 3, and VDJ H 4 rearrangements ( A and B ) using V H 7183 ( A ) or V H J558 primers ( B ) and DJ H 1, DJ H 2, DJ H 3, and DJ H 4 rearrangements ( C ) using Dq52 primers. The primers were designed to amplify all rearrangement products between J H 4 and V H 7183, V H J558, or Dq52; 4 different bands would be expected by the combination of each primer set. M, 100-bp DNA Ladder (New England Biolabs Inc.) ( D ) DNA samples used for the Ig rearrangement PCRs were quantified using real-time quantitative PCR to demonstrate equal total DNA concentrations.

    Techniques Used: Polymerase Chain Reaction, Transgenic Assay, Mouse Assay, Agarose Gel Electrophoresis, Real-time Polymerase Chain Reaction

    12) Product Images from "Nitrogen regulation of protein-protein interactions and transcript levels of GlnK PII regulator and AmtB ammonium transporter homologs in Archaea"

    Article Title: Nitrogen regulation of protein-protein interactions and transcript levels of GlnK PII regulator and AmtB ammonium transporter homologs in Archaea

    Journal: MicrobiologyOpen

    doi: 10.1002/mbo3.120

    RT-PCR analysis of amtB-glnK transcription in ΔglnK and flag:amtB mutant strains. (A) RT-PCR analysis of amtB-glnK transcription in ΔglnK strains. First panel: nitrate RNA samples amplified with amtB1 primers; second panel: ammonium RNA samples amplified with amtB1 primers; third panel: nitrate RNA samples amplified with amtB2 primers; fourth panel: ammonium RNA samples amplified with amtB2 primers. Lanes correspond to the following PCR products: (1) PCR negative control (water instead of template cDNA), (2) RT negative control (cDNA obtained from RT reactions without template RNA), (3) PCR positive control (genomic DNA amplification), (M) Quick-Load 100 bp DNA Ladder from New England Biolabs , (4 and 5) HM26 RNA sample and corresponding negative control (cDNA obtained from RT reaction with RNA but without retrotranscriptase), (6 and 7) HM26-K1 RNA sample and corresponding negative control, (8 and 9) HM26-K2 RNA sample and corresponding negative control, (10 and 11) HM26-K1K2 RNA sample and corresponding negative control. (B) RT-PCR analysis of the amtB transcription in flag:amtB strains. The four Flag-tagged strains and HM26 as control were grown in complex medium (OD 600 of 1) and nitrogen starved for 48 h prior to RNA isolation. Lanes correspond to (1) negative control for the PCR reaction performed in the absence of cDNA, (2) positive control with genomic DNA as PCR template, (M) Quick-Load 100 bp DNA Ladder from New England Biolabs , (3 and 4) HM26 RT-PCR reaction and negative control in the absence of retrotranscriptase to check for DNA contamination, respectively, the same for (5 and 6) HM26-F1, (7 and 8) HM26-F2, (9 and 10) HM26-F3, (11 and 12) HM26-F4. (A) and (B) RT of the RNA samples was performed with random hexamers and PCR amplification of cDNA with amtB1 and amtB2 specific primers (RT-Amt1For/RT-Amt1Rev and RT-Amt2For/RT-Amt2Rev, respectively). PCR amplification products of the cDNA separated by 1.8% (w/v) agarose gel electrophoresis and stained with ethidium bromide are presented.
    Figure Legend Snippet: RT-PCR analysis of amtB-glnK transcription in ΔglnK and flag:amtB mutant strains. (A) RT-PCR analysis of amtB-glnK transcription in ΔglnK strains. First panel: nitrate RNA samples amplified with amtB1 primers; second panel: ammonium RNA samples amplified with amtB1 primers; third panel: nitrate RNA samples amplified with amtB2 primers; fourth panel: ammonium RNA samples amplified with amtB2 primers. Lanes correspond to the following PCR products: (1) PCR negative control (water instead of template cDNA), (2) RT negative control (cDNA obtained from RT reactions without template RNA), (3) PCR positive control (genomic DNA amplification), (M) Quick-Load 100 bp DNA Ladder from New England Biolabs , (4 and 5) HM26 RNA sample and corresponding negative control (cDNA obtained from RT reaction with RNA but without retrotranscriptase), (6 and 7) HM26-K1 RNA sample and corresponding negative control, (8 and 9) HM26-K2 RNA sample and corresponding negative control, (10 and 11) HM26-K1K2 RNA sample and corresponding negative control. (B) RT-PCR analysis of the amtB transcription in flag:amtB strains. The four Flag-tagged strains and HM26 as control were grown in complex medium (OD 600 of 1) and nitrogen starved for 48 h prior to RNA isolation. Lanes correspond to (1) negative control for the PCR reaction performed in the absence of cDNA, (2) positive control with genomic DNA as PCR template, (M) Quick-Load 100 bp DNA Ladder from New England Biolabs , (3 and 4) HM26 RT-PCR reaction and negative control in the absence of retrotranscriptase to check for DNA contamination, respectively, the same for (5 and 6) HM26-F1, (7 and 8) HM26-F2, (9 and 10) HM26-F3, (11 and 12) HM26-F4. (A) and (B) RT of the RNA samples was performed with random hexamers and PCR amplification of cDNA with amtB1 and amtB2 specific primers (RT-Amt1For/RT-Amt1Rev and RT-Amt2For/RT-Amt2Rev, respectively). PCR amplification products of the cDNA separated by 1.8% (w/v) agarose gel electrophoresis and stained with ethidium bromide are presented.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Mutagenesis, Amplification, Polymerase Chain Reaction, Negative Control, Positive Control, Isolation, Agarose Gel Electrophoresis, Staining

    13) Product Images from "Isothermal amplification of long DNA segments by quadruplex priming amplification"

    Article Title: Isothermal amplification of long DNA segments by quadruplex priming amplification

    Journal: Analytical methods : advancing methods and applications

    doi: 10.1039/C8AY00843D

    Rate dependence of linear QPA on the length of AT-rich segment. (A) Targets and primer sequences; targets 1, 2 and 3 contain 34-nt, 20-nt and 5-nt AT-rich segments, respectively. (B) Typical dGTP-QPA (black) and dNTP-QPA profiles (colored) obtained using 0.5 μM primer, 10 nM target 2, 100 μM dGTP or 800 μM dNTP, 0.08 U/uL Bst 2.0 polymerase in 10 mM KCl, 40 mM CsCl, 2 mM MgCl 2 and 10 mM Tris-HCl, pH 8.7 at 62 °C. Dashed line corresponds to no-template control (NTC). (C) Temperature dependence of the rate of linear QPA using target 1 (blue), target 2 (red) and target 3 (black).
    Figure Legend Snippet: Rate dependence of linear QPA on the length of AT-rich segment. (A) Targets and primer sequences; targets 1, 2 and 3 contain 34-nt, 20-nt and 5-nt AT-rich segments, respectively. (B) Typical dGTP-QPA (black) and dNTP-QPA profiles (colored) obtained using 0.5 μM primer, 10 nM target 2, 100 μM dGTP or 800 μM dNTP, 0.08 U/uL Bst 2.0 polymerase in 10 mM KCl, 40 mM CsCl, 2 mM MgCl 2 and 10 mM Tris-HCl, pH 8.7 at 62 °C. Dashed line corresponds to no-template control (NTC). (C) Temperature dependence of the rate of linear QPA using target 1 (blue), target 2 (red) and target 3 (black).

    Techniques Used:

    14) Product Images from "Chromatin Tandem Affinity Purification Sequencing (ChTAP-Seq)"

    Article Title: Chromatin Tandem Affinity Purification Sequencing (ChTAP-Seq)

    Journal: Nature protocols

    doi: 10.1038/nprot.2013.088

    Chromatin Tandem Affinity Purification The protein of interest is expressed as a C-terminal, TAP-tagged fusion protein at near-physiological levels. Cells stably expressing the fusion protein are subjected to a process by which proteins attached to chromatin are cross-linked to DNA by formaldehyde (using a 1%(vol/vol) formaldehyde solution in 1X PBS). After cell lysis and chromatin shearing, the DNA-bound protein complex of interest is purified using anti FLAG antibody conjugated to agarose beads. Following three sequential washes, the complex is eluted from the beads by either 3XFLAG peptide competition or proteolytic cleavage with tobacco etch virus (TEV) protease. The eluted material is used for a second step of purification using nickel affinity gel. Further contaminants are removed by three washes and chromatin is eluted from the beads with imidazole. The protein–DNA complex is dissociated by reverse cross-linking and DNA is purified by phenol/chloroform extraction.
    Figure Legend Snippet: Chromatin Tandem Affinity Purification The protein of interest is expressed as a C-terminal, TAP-tagged fusion protein at near-physiological levels. Cells stably expressing the fusion protein are subjected to a process by which proteins attached to chromatin are cross-linked to DNA by formaldehyde (using a 1%(vol/vol) formaldehyde solution in 1X PBS). After cell lysis and chromatin shearing, the DNA-bound protein complex of interest is purified using anti FLAG antibody conjugated to agarose beads. Following three sequential washes, the complex is eluted from the beads by either 3XFLAG peptide competition or proteolytic cleavage with tobacco etch virus (TEV) protease. The eluted material is used for a second step of purification using nickel affinity gel. Further contaminants are removed by three washes and chromatin is eluted from the beads with imidazole. The protein–DNA complex is dissociated by reverse cross-linking and DNA is purified by phenol/chloroform extraction.

    Techniques Used: Affinity Purification, Stable Transfection, Expressing, Lysis, Purification

    15) Product Images from "Diagnostic Microbiologic Methods in the GEMS-1 Case/Control Study"

    Article Title: Diagnostic Microbiologic Methods in the GEMS-1 Case/Control Study

    Journal: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America

    doi: 10.1093/cid/cis754

    Gels showing the results of a multiplex polymerase chain reaction (PCR) assay for enteropathogenic Escherichia coli (EPEC), Shiga toxin–producing E. coli , and enterohemorrhagic E. coli (EHEC). Individual isolates from 34 specimens were subjected to a multiplex PCR as described in the text. Each specimen, separated by yellow vertical lines, consists of 3 individual isolates. The yellow values indicate the cycle threshold obtained for each specimen in the real-time PCR used in the initial screening for eae . The amplicons produced by the positive controls, EPEC E2348/69 ( eae and bfpA ) and EHEC EH48 ( stx1 , stx2 , and ehxA ) are also shown. 100 bp DNA ladder was used as a molecular size marker. Abbreviation: NTC, no template control.
    Figure Legend Snippet: Gels showing the results of a multiplex polymerase chain reaction (PCR) assay for enteropathogenic Escherichia coli (EPEC), Shiga toxin–producing E. coli , and enterohemorrhagic E. coli (EHEC). Individual isolates from 34 specimens were subjected to a multiplex PCR as described in the text. Each specimen, separated by yellow vertical lines, consists of 3 individual isolates. The yellow values indicate the cycle threshold obtained for each specimen in the real-time PCR used in the initial screening for eae . The amplicons produced by the positive controls, EPEC E2348/69 ( eae and bfpA ) and EHEC EH48 ( stx1 , stx2 , and ehxA ) are also shown. 100 bp DNA ladder was used as a molecular size marker. Abbreviation: NTC, no template control.

    Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Produced, Marker

    Appearance of diarrheagenic Escherichia coli amplicons separated by agarose gel electrophoresis. Lane 1, enteropathogenic E. coli ; lane 2, enteroaggregative E. coli ; 3, enterotoxigenic E. coli ; lanes 4 and 5, negative control strains; lane 6, 100 bp DNA ladder (New England Biolabs).
    Figure Legend Snippet: Appearance of diarrheagenic Escherichia coli amplicons separated by agarose gel electrophoresis. Lane 1, enteropathogenic E. coli ; lane 2, enteroaggregative E. coli ; 3, enterotoxigenic E. coli ; lanes 4 and 5, negative control strains; lane 6, 100 bp DNA ladder (New England Biolabs).

    Techniques Used: Agarose Gel Electrophoresis, Negative Control

    Appearance of enteric viral amplicons separated by agarose gel electrophoresis. Lane M, 100 bp DNA ladder (New England Biolabs); lane 1, Norovirus GI (330 bp); lane 2, Norovirus GII positive (387 bp); lane 3, sapovirus (434 bp); lane 4, astrovirus (719 bp).
    Figure Legend Snippet: Appearance of enteric viral amplicons separated by agarose gel electrophoresis. Lane M, 100 bp DNA ladder (New England Biolabs); lane 1, Norovirus GI (330 bp); lane 2, Norovirus GII positive (387 bp); lane 3, sapovirus (434 bp); lane 4, astrovirus (719 bp).

    Techniques Used: Agarose Gel Electrophoresis

    16) Product Images from "RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes"

    Article Title: RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

    Journal: Methods (San Diego, Calif.)

    doi: 10.1016/j.ymeth.2013.09.013

    Biochemical analysis of proteins and RNAs from the RIPiT procedure A. Western blots showing tetracycline (Tet)-mediated induction of eIF4AIII protein with the FLAG tag at its N- or C-terminus (top and bottom panels, respectively). The Tet concentration used for induction is indicated at the top of each lane; protein identities are indicated to the right. B. Levels of proteins detected by western blots in different fractions during EJC RIPiT. The table on the top indicates the different fractions from the RIPiT procedure and the antibodies used for 1 st and 2 nd IPs. The stably expressed FLAG-tag fusion protein used in each sample is indicated directly above lane. Proteins detected by western blot are indicated to the right. C. Size distribution of EJC footprints upon RNase I titration. An autoradiogram of 26% denaturing PAGE with 5′ [ 32 P]-labeled RNA fragments from base-hydrolysis of poly U 30 oligonucleotide (lane 1) or FLAG-Magoh:eIF4AIII RIPiT (lanes 2–5). RNase I concentrations used are indicated at top of each lane; nucleotide (nt) lengths are to the left. D. Quantification of desired size RNA footprints in RIPiT elution. An autoradiogram of 20% denaturing PAGE with 5′ [ 32 P]-labeled 100 bp NEB DNA ladder (lane 1), low molecular weight ssDNA ladder (lane 2), footprints of RIPiTs indicated on top (lanes 3 and 4) and a 21 nt ssRNA oligo of known specific activity (lane 5). The signal from red rectangles is quantified in comparison to that of the 21 nt oligo to estimate the amount of RIPiT footprints in the indicated size range.
    Figure Legend Snippet: Biochemical analysis of proteins and RNAs from the RIPiT procedure A. Western blots showing tetracycline (Tet)-mediated induction of eIF4AIII protein with the FLAG tag at its N- or C-terminus (top and bottom panels, respectively). The Tet concentration used for induction is indicated at the top of each lane; protein identities are indicated to the right. B. Levels of proteins detected by western blots in different fractions during EJC RIPiT. The table on the top indicates the different fractions from the RIPiT procedure and the antibodies used for 1 st and 2 nd IPs. The stably expressed FLAG-tag fusion protein used in each sample is indicated directly above lane. Proteins detected by western blot are indicated to the right. C. Size distribution of EJC footprints upon RNase I titration. An autoradiogram of 26% denaturing PAGE with 5′ [ 32 P]-labeled RNA fragments from base-hydrolysis of poly U 30 oligonucleotide (lane 1) or FLAG-Magoh:eIF4AIII RIPiT (lanes 2–5). RNase I concentrations used are indicated at top of each lane; nucleotide (nt) lengths are to the left. D. Quantification of desired size RNA footprints in RIPiT elution. An autoradiogram of 20% denaturing PAGE with 5′ [ 32 P]-labeled 100 bp NEB DNA ladder (lane 1), low molecular weight ssDNA ladder (lane 2), footprints of RIPiTs indicated on top (lanes 3 and 4) and a 21 nt ssRNA oligo of known specific activity (lane 5). The signal from red rectangles is quantified in comparison to that of the 21 nt oligo to estimate the amount of RIPiT footprints in the indicated size range.

    Techniques Used: Western Blot, FLAG-tag, Concentration Assay, Stable Transfection, Titration, Polyacrylamide Gel Electrophoresis, Labeling, Molecular Weight, Activity Assay

    17) Product Images from "RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes"

    Article Title: RIPiT-Seq: A high-throughput approach for footprinting RNA:protein complexes

    Journal: Methods (San Diego, Calif.)

    doi: 10.1016/j.ymeth.2013.09.013

    Biochemical analysis of proteins and RNAs from the RIPiT procedure A. Western blots showing tetracycline (Tet)-mediated induction of eIF4AIII protein with the FLAG tag at its N- or C-terminus (top and bottom panels, respectively). The Tet concentration used for induction is indicated at the top of each lane; protein identities are indicated to the right. B. Levels of proteins detected by western blots in different fractions during EJC RIPiT. The table on the top indicates the different fractions from the RIPiT procedure and the antibodies used for 1 st and 2 nd IPs. The stably expressed FLAG-tag fusion protein used in each sample is indicated directly above lane. Proteins detected by western blot are indicated to the right. C. Size distribution of EJC footprints upon RNase I titration. An autoradiogram of 26% denaturing PAGE with 5′ [ 32 P]-labeled RNA fragments from base-hydrolysis of poly U 30 oligonucleotide (lane 1) or FLAG-Magoh:eIF4AIII RIPiT (lanes 2–5). RNase I concentrations used are indicated at top of each lane; nucleotide (nt) lengths are to the left. D. Quantification of desired size RNA footprints in RIPiT elution. An autoradiogram of 20% denaturing PAGE with 5′ [ 32 P]-labeled 100 bp NEB DNA ladder (lane 1), low molecular weight ssDNA ladder (lane 2), footprints of RIPiTs indicated on top (lanes 3 and 4) and a 21 nt ssRNA oligo of known specific activity (lane 5). The signal from red rectangles is quantified in comparison to that of the 21 nt oligo to estimate the amount of RIPiT footprints in the indicated size range.
    Figure Legend Snippet: Biochemical analysis of proteins and RNAs from the RIPiT procedure A. Western blots showing tetracycline (Tet)-mediated induction of eIF4AIII protein with the FLAG tag at its N- or C-terminus (top and bottom panels, respectively). The Tet concentration used for induction is indicated at the top of each lane; protein identities are indicated to the right. B. Levels of proteins detected by western blots in different fractions during EJC RIPiT. The table on the top indicates the different fractions from the RIPiT procedure and the antibodies used for 1 st and 2 nd IPs. The stably expressed FLAG-tag fusion protein used in each sample is indicated directly above lane. Proteins detected by western blot are indicated to the right. C. Size distribution of EJC footprints upon RNase I titration. An autoradiogram of 26% denaturing PAGE with 5′ [ 32 P]-labeled RNA fragments from base-hydrolysis of poly U 30 oligonucleotide (lane 1) or FLAG-Magoh:eIF4AIII RIPiT (lanes 2–5). RNase I concentrations used are indicated at top of each lane; nucleotide (nt) lengths are to the left. D. Quantification of desired size RNA footprints in RIPiT elution. An autoradiogram of 20% denaturing PAGE with 5′ [ 32 P]-labeled 100 bp NEB DNA ladder (lane 1), low molecular weight ssDNA ladder (lane 2), footprints of RIPiTs indicated on top (lanes 3 and 4) and a 21 nt ssRNA oligo of known specific activity (lane 5). The signal from red rectangles is quantified in comparison to that of the 21 nt oligo to estimate the amount of RIPiT footprints in the indicated size range.

    Techniques Used: Western Blot, FLAG-tag, Concentration Assay, Stable Transfection, Titration, Polyacrylamide Gel Electrophoresis, Labeling, Molecular Weight, Activity Assay

    18) Product Images from "Role of the FeoB Protein and Siderophore in Promoting Virulence of Xanthomonas oryzae pv. oryzae on Rice ▿"

    Article Title: Role of the FeoB Protein and Siderophore in Promoting Virulence of Xanthomonas oryzae pv. oryzae on Rice ▿

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.01558-09

    Operon mapping and expression analysis of xss gene cluster of X. oryzae pv. oryzae. (A) Solid arrows represent the xssABCDE , xsuA , and mhpE ORFs. The long arrow represents the mRNA transcript. The small arrows denote the positions and directions of primers used in RT-PCR. MF1 primer was used in cDNA first-strand synthesis, and MF1 as well as other primers were used in subsequent PCRs. Lengths of expected PCR products are also shown for every primer pair. (B) Lanes contain RT-PCR products amplified from total RNA isolated from X. oryzae pv. oryzae cultures grown under iron-supplemented (+Fe; 100 μM FeSO 4 ) and iron-limiting (-Fe; 100 μM DP, an iron chelator) conditions as described in Materials and Methods. The primer pairs MF1/MR2, MF3/MR4, and MF5/MR6 yielded the expected DNA fragments of 790 bp, 722 bp, and 680 bp, respectively, exclusively from mRNA templates under iron-limiting conditions. No amplification was observed from mRNA templates expressed under iron-supplemented conditions. Lanes −RT and +RT, without and with reverse transcriptase, respectively; lane M, 100-bp DNA molecular marker. (C) Transcriptional analysis of xssE gene involved in siderophore biosynthesis carried out with GUS reporter strain BXO2229 ( xssE2 :: gusA ). BXO2229 was grown under either iron-supplemented (different concentrations of FeSO 4 ; Fe) or iron-limited (different concentrations of [DP]) conditions or with no supplementation (NS). β-Glucuronidase activity is represented as the nanomoles of methyl-umbelliferone produced/minute/10 8 CFU of bacteria. Data represent mean ± standard deviation of values from three independent experiments.
    Figure Legend Snippet: Operon mapping and expression analysis of xss gene cluster of X. oryzae pv. oryzae. (A) Solid arrows represent the xssABCDE , xsuA , and mhpE ORFs. The long arrow represents the mRNA transcript. The small arrows denote the positions and directions of primers used in RT-PCR. MF1 primer was used in cDNA first-strand synthesis, and MF1 as well as other primers were used in subsequent PCRs. Lengths of expected PCR products are also shown for every primer pair. (B) Lanes contain RT-PCR products amplified from total RNA isolated from X. oryzae pv. oryzae cultures grown under iron-supplemented (+Fe; 100 μM FeSO 4 ) and iron-limiting (-Fe; 100 μM DP, an iron chelator) conditions as described in Materials and Methods. The primer pairs MF1/MR2, MF3/MR4, and MF5/MR6 yielded the expected DNA fragments of 790 bp, 722 bp, and 680 bp, respectively, exclusively from mRNA templates under iron-limiting conditions. No amplification was observed from mRNA templates expressed under iron-supplemented conditions. Lanes −RT and +RT, without and with reverse transcriptase, respectively; lane M, 100-bp DNA molecular marker. (C) Transcriptional analysis of xssE gene involved in siderophore biosynthesis carried out with GUS reporter strain BXO2229 ( xssE2 :: gusA ). BXO2229 was grown under either iron-supplemented (different concentrations of FeSO 4 ; Fe) or iron-limited (different concentrations of [DP]) conditions or with no supplementation (NS). β-Glucuronidase activity is represented as the nanomoles of methyl-umbelliferone produced/minute/10 8 CFU of bacteria. Data represent mean ± standard deviation of values from three independent experiments.

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Amplification, Isolation, Marker, Activity Assay, Produced, Standard Deviation

    Operon mapping and expression analysis of X. oryzae pv. oryzae feo operon. (A) Solid arrows represent the feoA , feoB , and feoC ORFs. The long arrow represents the feoABC mRNA. The small arrows denote the positions and directions of primers used in RT-PCR. FeoCR primer was used in cDNA first-strand synthesis while FeoCR as well as other primers were used in subsequent PCRs. Lengths of expected PCR products are also shown for every primer pair. (B) RT-PCR analysis indicates that feoABC genes are cotranscribed as a single mRNA. The FeoBF2/FeoCR and the FeoAF/FeoBR1 primer pairs yield the expected 748-bp and 800-bp fragments, respectively. (C) The feoB transcript is present under iron-supplemented (100 μM FeSO 4 ; +Fe) and iron-limited (100 μM DP, an iron chelator; −Fe) growth conditions. The expected 510-bp fragment is amplified by the FeoBF/FeoBR primer pair under both conditions. Lanes: −RT, without reverse transcriptase; +RT, with reverse transcriptase; M, 100-bp DNA molecular markers. (D) Expression of feo :: gusA transcriptional fusion. The feo :: gusA strain (BXO2230; FeoB + ) was grown under either iron-supplemented (different concentrations of FeSO 4 ; Fe), or iron-limited (different concentrations of DP) conditions or with no supplementation (NS). β-Glucuronidase activity is represented as nanomoles of methyl-umbelliferone (MU) produced/minute/10 8 CFU of bacteria. Data represent means ± standard deviations of values from three independent experiments.
    Figure Legend Snippet: Operon mapping and expression analysis of X. oryzae pv. oryzae feo operon. (A) Solid arrows represent the feoA , feoB , and feoC ORFs. The long arrow represents the feoABC mRNA. The small arrows denote the positions and directions of primers used in RT-PCR. FeoCR primer was used in cDNA first-strand synthesis while FeoCR as well as other primers were used in subsequent PCRs. Lengths of expected PCR products are also shown for every primer pair. (B) RT-PCR analysis indicates that feoABC genes are cotranscribed as a single mRNA. The FeoBF2/FeoCR and the FeoAF/FeoBR1 primer pairs yield the expected 748-bp and 800-bp fragments, respectively. (C) The feoB transcript is present under iron-supplemented (100 μM FeSO 4 ; +Fe) and iron-limited (100 μM DP, an iron chelator; −Fe) growth conditions. The expected 510-bp fragment is amplified by the FeoBF/FeoBR primer pair under both conditions. Lanes: −RT, without reverse transcriptase; +RT, with reverse transcriptase; M, 100-bp DNA molecular markers. (D) Expression of feo :: gusA transcriptional fusion. The feo :: gusA strain (BXO2230; FeoB + ) was grown under either iron-supplemented (different concentrations of FeSO 4 ; Fe), or iron-limited (different concentrations of DP) conditions or with no supplementation (NS). β-Glucuronidase activity is represented as nanomoles of methyl-umbelliferone (MU) produced/minute/10 8 CFU of bacteria. Data represent means ± standard deviations of values from three independent experiments.

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Amplification, Activity Assay, Produced

    19) Product Images from "Expression and function of umami receptors T1R1/T1R3 in gastric smooth muscle"

    Article Title: Expression and function of umami receptors T1R1/T1R3 in gastric smooth muscle

    Journal: Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society

    doi: 10.1111/nmo.13737

    Expression of T1R1 and T1R3 in isolated gastric muscle cells. A, Total RNA isolated from cultured gastric SMCs was reverse transcribed, and cDNA amplified with specific primers for T1R1 and T1R3 as indicated in methods. Sizes are indicated for 100 bp DNA ladder. GAPDH was used as control. B, Lysates prepared from isolated gastric SMCs were homogenized and protein in the supernatant was separated by SDS-PAGE followed by Western blot analysis using antibodies specific for T1R1 and T1R3. Protein bands were visualized by chemiluminescence. Arrows indicate bands at T1R1 (94 kDa) and T1R3 (93 kDa), respectively. C, T1R1 and T1R3 were detected on cultured gastric SMCs using a specific antibody (sc-50308, 1:100 and sc-50352, 1:100) and Alexa Fluor 488 (1:300) (right panel; green). Cell nuclei were stained with DAPI (blue). In the absence of the primary antibody for T1R1 or T1R3 (left panels), there was no detectable staining for the secondary antibody. Scale bar equals 25 μm
    Figure Legend Snippet: Expression of T1R1 and T1R3 in isolated gastric muscle cells. A, Total RNA isolated from cultured gastric SMCs was reverse transcribed, and cDNA amplified with specific primers for T1R1 and T1R3 as indicated in methods. Sizes are indicated for 100 bp DNA ladder. GAPDH was used as control. B, Lysates prepared from isolated gastric SMCs were homogenized and protein in the supernatant was separated by SDS-PAGE followed by Western blot analysis using antibodies specific for T1R1 and T1R3. Protein bands were visualized by chemiluminescence. Arrows indicate bands at T1R1 (94 kDa) and T1R3 (93 kDa), respectively. C, T1R1 and T1R3 were detected on cultured gastric SMCs using a specific antibody (sc-50308, 1:100 and sc-50352, 1:100) and Alexa Fluor 488 (1:300) (right panel; green). Cell nuclei were stained with DAPI (blue). In the absence of the primary antibody for T1R1 or T1R3 (left panels), there was no detectable staining for the secondary antibody. Scale bar equals 25 μm

    Techniques Used: Expressing, Isolation, Cell Culture, Amplification, SDS Page, Western Blot, Staining

    20) Product Images from "Smurf2 E3 ubiquitin ligase modulates proliferation and invasiveness of breast cancer cells in a CNKSR2 dependent manner"

    Article Title: Smurf2 E3 ubiquitin ligase modulates proliferation and invasiveness of breast cancer cells in a CNKSR2 dependent manner

    Journal: Cell Division

    doi: 10.1186/1747-1028-9-2

    Depletion of Smurf2 accelerates degradation of CNKSR2. (A) Depletion of Smurf2 by siRNA (siSmurf2) leads to decreased CNKSR2 protein levels in MDA-MB-231, MCF-7, SW480, and SCC131 cells. (B) Smurf2 does not affect CNKSR2 transcript level. RNA samples from MDA-MB-231 cells transfected with siSmurf2 were analyzed by qRT-PCR and further by (C) RT-PCR for the indicated transcripts. (D) MDA-MB-231 cells transfected with control siRNA and Smurf2 siRNA were treated with cycloheximide at 100 μg/ml, 48 hours post-transfection. Cells were harvested 0, 1, 2, or 3 h after cycloheximide addition and the cell lysate was subjected to SDS-PAGE followed by immunoblotting with specific antibodies. (E) Plot of CNKSR2 degradation rate was shown in the panel. (F) CNKSR2 depletion does not affect Smurf2 levels.
    Figure Legend Snippet: Depletion of Smurf2 accelerates degradation of CNKSR2. (A) Depletion of Smurf2 by siRNA (siSmurf2) leads to decreased CNKSR2 protein levels in MDA-MB-231, MCF-7, SW480, and SCC131 cells. (B) Smurf2 does not affect CNKSR2 transcript level. RNA samples from MDA-MB-231 cells transfected with siSmurf2 were analyzed by qRT-PCR and further by (C) RT-PCR for the indicated transcripts. (D) MDA-MB-231 cells transfected with control siRNA and Smurf2 siRNA were treated with cycloheximide at 100 μg/ml, 48 hours post-transfection. Cells were harvested 0, 1, 2, or 3 h after cycloheximide addition and the cell lysate was subjected to SDS-PAGE followed by immunoblotting with specific antibodies. (E) Plot of CNKSR2 degradation rate was shown in the panel. (F) CNKSR2 depletion does not affect Smurf2 levels.

    Techniques Used: Multiple Displacement Amplification, Transfection, Quantitative RT-PCR, Reverse Transcription Polymerase Chain Reaction, SDS Page

    21) Product Images from "Dynamic and scalable DNA-based information storage"

    Article Title: Dynamic and scalable DNA-based information storage

    Journal: Nature Communications

    doi: 10.1038/s41467-020-16797-2

    T7-based transcription efficiency can be controlled by surrounding sequences. a An oligo pool that had 1088 distinct sequences was designed to generate ss-dsDNA templates. The first 1024 sequences contained all possible combinations of nucleotides upstream of the promoter sequence (NNNNN-T7, where N is one of four DNA nucleotides), whereas the latter 64 sequences had all possible combinations of nucleotides downstream to the promoter region (T7-NNN). Each sequence contained a barcode to identify the sequence of the variant nucleotides. The template ss-dsDNAs were processed with IVT for 8 h, followed by RT-PCR and next-generation sequencing ( n = 3 for each condition). b Transcription efficiencies of both sequence designs were plotted by normalizing the read count of each transcribed strand to its abundance in the original library. The data was organized from lowest to highest normalized abundance for both designs. c The sequences were further divided into four quartiles based upon normalized transcript abundance and analyzed by the WebLogo tool. d The normalized abundance of each sequence was organized by A/T percentage. P values between each group were calculated using One-Way ANOVA with Tukey–Kramer post-hoc and listed here for statistical significance. NNNNN-T7: p values less than 0.01 for comparisons between 0%–100%, 80%–100% and 20%–80%; p values less than 0.001 for comparisons between 20%–100%, 40%–80%, 40%–100%, 60%–80% and 60%–100%; T7-NNN, p values less than 0.05 for comparisons between 33%–100%, 0%–100% and 0%–66%. e The percent error for each DNA sequence position for the original synthesized database (left) and transcribed database (right). The error rate was calculated by dividing the number of errors of a given type occurring at a nucleotide position by the total number of reads for that sequence (Supplementary Method). Plotted values represent the arithmetic mean, and error bars represent the s.d., of three independent IVT-RT-PCR-NGS samples. Source data are provided as a Source Data file.
    Figure Legend Snippet: T7-based transcription efficiency can be controlled by surrounding sequences. a An oligo pool that had 1088 distinct sequences was designed to generate ss-dsDNA templates. The first 1024 sequences contained all possible combinations of nucleotides upstream of the promoter sequence (NNNNN-T7, where N is one of four DNA nucleotides), whereas the latter 64 sequences had all possible combinations of nucleotides downstream to the promoter region (T7-NNN). Each sequence contained a barcode to identify the sequence of the variant nucleotides. The template ss-dsDNAs were processed with IVT for 8 h, followed by RT-PCR and next-generation sequencing ( n = 3 for each condition). b Transcription efficiencies of both sequence designs were plotted by normalizing the read count of each transcribed strand to its abundance in the original library. The data was organized from lowest to highest normalized abundance for both designs. c The sequences were further divided into four quartiles based upon normalized transcript abundance and analyzed by the WebLogo tool. d The normalized abundance of each sequence was organized by A/T percentage. P values between each group were calculated using One-Way ANOVA with Tukey–Kramer post-hoc and listed here for statistical significance. NNNNN-T7: p values less than 0.01 for comparisons between 0%–100%, 80%–100% and 20%–80%; p values less than 0.001 for comparisons between 20%–100%, 40%–80%, 40%–100%, 60%–80% and 60%–100%; T7-NNN, p values less than 0.05 for comparisons between 33%–100%, 0%–100% and 0%–66%. e The percent error for each DNA sequence position for the original synthesized database (left) and transcribed database (right). The error rate was calculated by dividing the number of errors of a given type occurring at a nucleotide position by the total number of reads for that sequence (Supplementary Method). Plotted values represent the arithmetic mean, and error bars represent the s.d., of three independent IVT-RT-PCR-NGS samples. Source data are provided as a Source Data file.

    Techniques Used: Sequencing, Variant Assay, Reverse Transcription Polymerase Chain Reaction, Next-Generation Sequencing, Synthesized

    22) Product Images from "Absence of germline mono-allelic promoter hypermethylation of the CDH1 gene in gastric cancer patients"

    Article Title: Absence of germline mono-allelic promoter hypermethylation of the CDH1 gene in gastric cancer patients

    Journal: Molecular Cancer

    doi: 10.1186/1476-4598-8-63

    Inverse association between CDH1 promoter methylation level and CDH1 mRNA expression level in human cell lines . (A) Detection of the CDH1 mRNA transcripts in 6 human cell lines by reverse transcription (RT)-polymerase chain reaction (PCR) analysis. mRNA transcripts of the GAPDH , a housekeeping gene, were also amplified as an internal control. M, 100-bp DNA ladder. (B) Map of the CpG sites in the CDH1 promoter. The positions of the CpG sites are indicated by vertical lines. Vertical arrows indicate the location of the -348_-347insA, -161C > A, and -73A > C genetic polymorphisms. +1, transcription start site. (C) Determination of the methylation status of the CpG sites in the CDH1 promoter in 6 human cell lines by bisulfite sequencing analysis. Ten subcloned promoter fragments were sequenced in each cell line. Each horizontal row represents a single allele. The positions of the CpG sites are numbered at the top of the column. Methylated CpG sites are shown as black boxes and unmethylated CpG sites as white boxes.
    Figure Legend Snippet: Inverse association between CDH1 promoter methylation level and CDH1 mRNA expression level in human cell lines . (A) Detection of the CDH1 mRNA transcripts in 6 human cell lines by reverse transcription (RT)-polymerase chain reaction (PCR) analysis. mRNA transcripts of the GAPDH , a housekeeping gene, were also amplified as an internal control. M, 100-bp DNA ladder. (B) Map of the CpG sites in the CDH1 promoter. The positions of the CpG sites are indicated by vertical lines. Vertical arrows indicate the location of the -348_-347insA, -161C > A, and -73A > C genetic polymorphisms. +1, transcription start site. (C) Determination of the methylation status of the CpG sites in the CDH1 promoter in 6 human cell lines by bisulfite sequencing analysis. Ten subcloned promoter fragments were sequenced in each cell line. Each horizontal row represents a single allele. The positions of the CpG sites are numbered at the top of the column. Methylated CpG sites are shown as black boxes and unmethylated CpG sites as white boxes.

    Techniques Used: Methylation, Expressing, Polymerase Chain Reaction, Amplification, Methylation Sequencing

    23) Product Images from "Diagnostic Microbiologic Methods in the GEMS-1 Case/Control Study"

    Article Title: Diagnostic Microbiologic Methods in the GEMS-1 Case/Control Study

    Journal: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America

    doi: 10.1093/cid/cis754

    Gels showing the results of a multiplex polymerase chain reaction (PCR) assay for enteropathogenic Escherichia coli (EPEC), Shiga toxin–producing E. coli , and enterohemorrhagic E. coli (EHEC). Individual isolates from 34 specimens were subjected to a multiplex PCR as described in the text. Each specimen, separated by yellow vertical lines, consists of 3 individual isolates. The yellow values indicate the cycle threshold obtained for each specimen in the real-time PCR used in the initial screening for eae . The amplicons produced by the positive controls, EPEC E2348/69 ( eae and bfpA ) and EHEC EH48 ( stx1 , stx2 , and ehxA ) are also shown. 100 bp DNA ladder was used as a molecular size marker. Abbreviation: NTC, no template control.
    Figure Legend Snippet: Gels showing the results of a multiplex polymerase chain reaction (PCR) assay for enteropathogenic Escherichia coli (EPEC), Shiga toxin–producing E. coli , and enterohemorrhagic E. coli (EHEC). Individual isolates from 34 specimens were subjected to a multiplex PCR as described in the text. Each specimen, separated by yellow vertical lines, consists of 3 individual isolates. The yellow values indicate the cycle threshold obtained for each specimen in the real-time PCR used in the initial screening for eae . The amplicons produced by the positive controls, EPEC E2348/69 ( eae and bfpA ) and EHEC EH48 ( stx1 , stx2 , and ehxA ) are also shown. 100 bp DNA ladder was used as a molecular size marker. Abbreviation: NTC, no template control.

    Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, Produced, Marker

    Appearance of diarrheagenic Escherichia coli amplicons separated by agarose gel electrophoresis. Lane 1, enteropathogenic E. coli ; lane 2, enteroaggregative E. coli ; 3, enterotoxigenic E. coli ; lanes 4 and 5, negative control strains; lane 6, 100 bp DNA ladder (New England Biolabs).
    Figure Legend Snippet: Appearance of diarrheagenic Escherichia coli amplicons separated by agarose gel electrophoresis. Lane 1, enteropathogenic E. coli ; lane 2, enteroaggregative E. coli ; 3, enterotoxigenic E. coli ; lanes 4 and 5, negative control strains; lane 6, 100 bp DNA ladder (New England Biolabs).

    Techniques Used: Agarose Gel Electrophoresis, Negative Control

    Appearance of enteric viral amplicons separated by agarose gel electrophoresis. Lane M, 100 bp DNA ladder (New England Biolabs); lane 1, Norovirus GI (330 bp); lane 2, Norovirus GII positive (387 bp); lane 3, sapovirus (434 bp); lane 4, astrovirus (719 bp).
    Figure Legend Snippet: Appearance of enteric viral amplicons separated by agarose gel electrophoresis. Lane M, 100 bp DNA ladder (New England Biolabs); lane 1, Norovirus GI (330 bp); lane 2, Norovirus GII positive (387 bp); lane 3, sapovirus (434 bp); lane 4, astrovirus (719 bp).

    Techniques Used: Agarose Gel Electrophoresis

    24) Product Images from "Whole-Genome Sequencing in Microbial Forensic Analysis of Gamma-Irradiated Microbial Materials"

    Article Title: Whole-Genome Sequencing in Microbial Forensic Analysis of Gamma-Irradiated Microbial Materials

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.02231-15

    Effect of irradiation on the size of DNA fragments extracted from spores and vegetative cells. (A) Agarose gel electrophoresis. After DNA extraction, samples were diluted to 100 ng/well and small fragments were separated by electrophoresis using a 2%
    Figure Legend Snippet: Effect of irradiation on the size of DNA fragments extracted from spores and vegetative cells. (A) Agarose gel electrophoresis. After DNA extraction, samples were diluted to 100 ng/well and small fragments were separated by electrophoresis using a 2%

    Techniques Used: Irradiation, Agarose Gel Electrophoresis, DNA Extraction, Electrophoresis

    25) Product Images from "Instability of the Octarepeat Region of the Human Prion Protein Gene"

    Article Title: Instability of the Octarepeat Region of the Human Prion Protein Gene

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0026635

    Instability of octarepeats during DNA replication in mismatch repair-deficient XL-1 Red cells. (A) Mutant clones from replication of pOct5 in XL-1 Red E.coli cells. Plasmid DNA samples were prepared from XL-1 Red colonies after transformation with pOct5 and re-transformed into DH5α cells. Plasmid DNAs from the resulting DH5α colonies were digested with Sac II and Spe I and separated on a 2% agarose gel. Shown are plasmid DNAs from 4 DH5α colonies that produced two octarepeat bands of equal molar ratio. (B) Mutant clones from replication of pOct11b in XL-1 Red E.coli cells. Same as in (A) except that pOct11b was used. Shown are plasmid DNAs from 4 colonies that produced two octarepeat bands of equal molar ratio. (C–D) Unusual mutant clones from replication of pOct11b in XL-1 Red E.coli cells. Shown are plasmid DNAs from two pOct11b-transformed XL-1 Red colonies that produced 2–3 octarepeat bands upon digestion with Sac II and Spe I, of which the template-sized band is much stronger than the mutant bands (C). The unequal molar ratio of the octarepeat bands suggests the presence of mixed plasmid DNA species in these colonies. Further transformation of these plasmid DNAs into DH5α cells resulted in separation of the mixed plasmid DNA species and produced colonies that each contained only one of the plasmid DNA species as confirmed by restriction analysis and sequencing (D). For all panels, the octarepeat sequence is indicated above each lane, the arrowhead points to the band whose sequence is shown above the lane, and the black box marks the template-sized Oct5 or Oct11 band from a non-mutant clone. Rep. No., number of repeats; M,100-bp DNA Ladder.
    Figure Legend Snippet: Instability of octarepeats during DNA replication in mismatch repair-deficient XL-1 Red cells. (A) Mutant clones from replication of pOct5 in XL-1 Red E.coli cells. Plasmid DNA samples were prepared from XL-1 Red colonies after transformation with pOct5 and re-transformed into DH5α cells. Plasmid DNAs from the resulting DH5α colonies were digested with Sac II and Spe I and separated on a 2% agarose gel. Shown are plasmid DNAs from 4 DH5α colonies that produced two octarepeat bands of equal molar ratio. (B) Mutant clones from replication of pOct11b in XL-1 Red E.coli cells. Same as in (A) except that pOct11b was used. Shown are plasmid DNAs from 4 colonies that produced two octarepeat bands of equal molar ratio. (C–D) Unusual mutant clones from replication of pOct11b in XL-1 Red E.coli cells. Shown are plasmid DNAs from two pOct11b-transformed XL-1 Red colonies that produced 2–3 octarepeat bands upon digestion with Sac II and Spe I, of which the template-sized band is much stronger than the mutant bands (C). The unequal molar ratio of the octarepeat bands suggests the presence of mixed plasmid DNA species in these colonies. Further transformation of these plasmid DNAs into DH5α cells resulted in separation of the mixed plasmid DNA species and produced colonies that each contained only one of the plasmid DNA species as confirmed by restriction analysis and sequencing (D). For all panels, the octarepeat sequence is indicated above each lane, the arrowhead points to the band whose sequence is shown above the lane, and the black box marks the template-sized Oct5 or Oct11 band from a non-mutant clone. Rep. No., number of repeats; M,100-bp DNA Ladder.

    Techniques Used: Mutagenesis, Clone Assay, Plasmid Preparation, Transformation Assay, Agarose Gel Electrophoresis, Produced, Sequencing

    Mutant plasmids from octarepeat replication in DH5α are all head-to-head dimers. (A) Restriction analysis of replication-mutant plasmids with Spe I, Sac II and Sca I. pOct5 or pOct11b were transformed into DH5α. Plasmid DNAs were prepared from two mutant colonies and two control (non-mutant) colonies each for pOct5 and pOct11b, digested with Spe I, Sac II or Sca I, and separated by agarose gel electrophoresis. All mutant colonies appear to contain a minute amount of monomer plasmids. M1, 100-bp DNA ladder; M2, 1-kb DNA ladder. (B) Diagram of the head-to-head plasmid dimers. The top panel depicts the parental plasmid monomer; the bottom panel depicts the dimer where the newly generated monomer unit is highlighted in thicker lines. The boxes denote the octarepeat inserts.
    Figure Legend Snippet: Mutant plasmids from octarepeat replication in DH5α are all head-to-head dimers. (A) Restriction analysis of replication-mutant plasmids with Spe I, Sac II and Sca I. pOct5 or pOct11b were transformed into DH5α. Plasmid DNAs were prepared from two mutant colonies and two control (non-mutant) colonies each for pOct5 and pOct11b, digested with Spe I, Sac II or Sca I, and separated by agarose gel electrophoresis. All mutant colonies appear to contain a minute amount of monomer plasmids. M1, 100-bp DNA ladder; M2, 1-kb DNA ladder. (B) Diagram of the head-to-head plasmid dimers. The top panel depicts the parental plasmid monomer; the bottom panel depicts the dimer where the newly generated monomer unit is highlighted in thicker lines. The boxes denote the octarepeat inserts.

    Techniques Used: Mutagenesis, Transformation Assay, Plasmid Preparation, Agarose Gel Electrophoresis, Generated

    Instability of octarepeats during PCR amplification by Pwo polymerase. (A) PCR products from the PrP-Oct5 and PrP-Oct11a templates. The octarepeat regions PCR amplified by Pwo polymerase from PrP-Oct5 and PrP-Oct11a with primers HP20 and HP306r were cleaned up and separated on a 2% agarose gel. Bl, blank control. (B) Mutant octarepeat clones from PCR amplification of the PrP-Oct5 template: restriction analysis with Sac II and Spe I. Six mutant clones and one wild type clone are shown. The black box marks the template-sized Oct5 band from a non-mutant clone. (C) Mutant octarepeat clones from PCR amplification of the PrP-Oct11a template: restriction analysis with Sac II and Spe I. Same as in (B) except that PrPOct11a was the template DNA. Eighteen mutant clones and one wild type clone are shown. The black box marks the template-sized Oct11 band from a non-mutant clone. (D) A mutant octarepeat clone containing two octarepeat inserts from PCR amplification of PrP-Oct5. Sac II and Spe I digestion of this mutant plasmid clone produced two octarepeat inserts; one was the wild type Oct5 while the other was a 2-repeat deletion mutant (R1-R2). The arrowhead points to the band whose sequence is shown above the lane. The black box marks the template-sized Oct5 band from a non-mutant clone. (E) Mutant octarepeat clones containing two octarepeat inserts from PCR amplification of PrP-Oct11a. Sac II and Spe I digestion of the 3 mutant clones produced two octarepeat inserts; one was the 11-repeat parental Oct11a in all clones while the other was a mutant octarepeat sequence of varying sizes and sequences. The arrowhead points to the band whose sequence is shown above the lane. The black box marks the template-sized Oct11 band from a non-mutant clone. For all panels, the octarepeat sequence is indicated above each lane; Rep. No., number of repeats; M,100-bp DNA Ladder.
    Figure Legend Snippet: Instability of octarepeats during PCR amplification by Pwo polymerase. (A) PCR products from the PrP-Oct5 and PrP-Oct11a templates. The octarepeat regions PCR amplified by Pwo polymerase from PrP-Oct5 and PrP-Oct11a with primers HP20 and HP306r were cleaned up and separated on a 2% agarose gel. Bl, blank control. (B) Mutant octarepeat clones from PCR amplification of the PrP-Oct5 template: restriction analysis with Sac II and Spe I. Six mutant clones and one wild type clone are shown. The black box marks the template-sized Oct5 band from a non-mutant clone. (C) Mutant octarepeat clones from PCR amplification of the PrP-Oct11a template: restriction analysis with Sac II and Spe I. Same as in (B) except that PrPOct11a was the template DNA. Eighteen mutant clones and one wild type clone are shown. The black box marks the template-sized Oct11 band from a non-mutant clone. (D) A mutant octarepeat clone containing two octarepeat inserts from PCR amplification of PrP-Oct5. Sac II and Spe I digestion of this mutant plasmid clone produced two octarepeat inserts; one was the wild type Oct5 while the other was a 2-repeat deletion mutant (R1-R2). The arrowhead points to the band whose sequence is shown above the lane. The black box marks the template-sized Oct5 band from a non-mutant clone. (E) Mutant octarepeat clones containing two octarepeat inserts from PCR amplification of PrP-Oct11a. Sac II and Spe I digestion of the 3 mutant clones produced two octarepeat inserts; one was the 11-repeat parental Oct11a in all clones while the other was a mutant octarepeat sequence of varying sizes and sequences. The arrowhead points to the band whose sequence is shown above the lane. The black box marks the template-sized Oct11 band from a non-mutant clone. For all panels, the octarepeat sequence is indicated above each lane; Rep. No., number of repeats; M,100-bp DNA Ladder.

    Techniques Used: Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Mutagenesis, Clone Assay, Plasmid Preparation, Produced, Sequencing

    Instability of octarepeats during DNA replication in DH5α cells. (A) Mutant clones from replication of pOct5 in DH5α cells. pOct5 was transformed into DH5α. Plasmid DNAs were prepared from the resulting colonies, digested with Sac II and Spe I and separated on a 2% agarose gel. Shown are plasmid DNAs from 3 colonies that produced two octarepeat bands of equal molar ratio. (B) Mutant clones from replication of pOct11b in DH5α cells. pOct11b was transformed into DH5α. Plasmid DNAs were prepared from the resulting colonies, digested with Sac II and Spe I and separated on a 2% agarose gel. Shown are plasmid DNAs from 4 colonies that produced two octarepeat bands of equal molar ratio. (C–D) Unusual mutant clones from replication of pOct11b in DH5α cells. Shown are plasmid DNAs from two pOct11b-transformed DH5α colonies that produced 2–3 octarepeat bands upon digestion with Sac II and Spe I, of which the template-sized band is much stronger than the mutant bands (C). The unequal molar ratio of the octarepeat bands suggests the presence in these colonies of mixed plasmid DNA species where each species produced one of the octarepeat bands. Re-transformation of these plasmid DNAs into DH5α cells resulted in separation of the mixed plasmid DNA species and produced colonies that each contained only one plasmid DNA species as confirmed by restriction analysis and sequencing (D). For all panels, the octarepeat sequence is indicated above each lane, the arrowhead points to the band whose sequence is shown above the lane, and the black box marks the template-sized Oct5 or Oct11 band from a non-mutant clone. Rep. No., number of repeats; M,100-bp DNA Ladder.
    Figure Legend Snippet: Instability of octarepeats during DNA replication in DH5α cells. (A) Mutant clones from replication of pOct5 in DH5α cells. pOct5 was transformed into DH5α. Plasmid DNAs were prepared from the resulting colonies, digested with Sac II and Spe I and separated on a 2% agarose gel. Shown are plasmid DNAs from 3 colonies that produced two octarepeat bands of equal molar ratio. (B) Mutant clones from replication of pOct11b in DH5α cells. pOct11b was transformed into DH5α. Plasmid DNAs were prepared from the resulting colonies, digested with Sac II and Spe I and separated on a 2% agarose gel. Shown are plasmid DNAs from 4 colonies that produced two octarepeat bands of equal molar ratio. (C–D) Unusual mutant clones from replication of pOct11b in DH5α cells. Shown are plasmid DNAs from two pOct11b-transformed DH5α colonies that produced 2–3 octarepeat bands upon digestion with Sac II and Spe I, of which the template-sized band is much stronger than the mutant bands (C). The unequal molar ratio of the octarepeat bands suggests the presence in these colonies of mixed plasmid DNA species where each species produced one of the octarepeat bands. Re-transformation of these plasmid DNAs into DH5α cells resulted in separation of the mixed plasmid DNA species and produced colonies that each contained only one plasmid DNA species as confirmed by restriction analysis and sequencing (D). For all panels, the octarepeat sequence is indicated above each lane, the arrowhead points to the band whose sequence is shown above the lane, and the black box marks the template-sized Oct5 or Oct11 band from a non-mutant clone. Rep. No., number of repeats; M,100-bp DNA Ladder.

    Techniques Used: Mutagenesis, Clone Assay, Transformation Assay, Plasmid Preparation, Agarose Gel Electrophoresis, Produced, Sequencing

    Instability of octarepeats during PCR amplification by Taq Polymerase. (A) PCR products from the PrP-Oct5 and PrP-Oct11a templates. The octarepeat regions PCR amplified by Taq polymerase from PrP-Oct5 and PrP-Oct11a with primers HP20 and HP306r were cleaned up and separated on a 2% agarose gel. (B) Mutant octarepeat clones from PCR amplification of the PrP-Oct5 template: restriction analysis with Sac II and Spe I. Six mutant clones and one wild type clone are shown. The black box marks the template-sized Oct5 band from a wild type clone. (C) Mutant octarepeat clones from PCR amplification of the PrP-Oct11a template: restriction analysis with Sac II and Spe I. Same as in (B) except that PrPOct11a was the template. Fifteen mutant clones and one wild type clone are shown. The black box marks the template-sized Oct11 band from a non-mutant clone. (D) A mutant octarepeat clone containing two octarepeat inserts from PCR amplification of PrP-Oct5. Sac II and Spe I digestion of this mutant clone produced two octarepeat inserts; one was the 5-repeat wild type Oct5 while the other was a 2-repeat deletion mutant (R1a-R4). The arrowhead points to the band whose sequence is shown above the lane. The black box marks the template-sized Oct5 band from a non-mutant clone. (E) Mutant octarepeat clones containing two octarepeat inserts from PCR amplification of PrP-Oct11a. Sac II and Spe I digestion of the 10 mutant clones produced two octarepeat inserts; one was the 11-repeat parental Oct11a in all clones while the other was a mutant octarepeat sequence of varying sizes and sequences. The arrowhead points to the band whose sequence is shown above the lane. The black box marks the template-sized Oct11 band from a non-mutant clone. For all panels, the octarepeat sequence is indicated above each lane; Rep. No., number of repeats; M,100-bp DNA Ladder.
    Figure Legend Snippet: Instability of octarepeats during PCR amplification by Taq Polymerase. (A) PCR products from the PrP-Oct5 and PrP-Oct11a templates. The octarepeat regions PCR amplified by Taq polymerase from PrP-Oct5 and PrP-Oct11a with primers HP20 and HP306r were cleaned up and separated on a 2% agarose gel. (B) Mutant octarepeat clones from PCR amplification of the PrP-Oct5 template: restriction analysis with Sac II and Spe I. Six mutant clones and one wild type clone are shown. The black box marks the template-sized Oct5 band from a wild type clone. (C) Mutant octarepeat clones from PCR amplification of the PrP-Oct11a template: restriction analysis with Sac II and Spe I. Same as in (B) except that PrPOct11a was the template. Fifteen mutant clones and one wild type clone are shown. The black box marks the template-sized Oct11 band from a non-mutant clone. (D) A mutant octarepeat clone containing two octarepeat inserts from PCR amplification of PrP-Oct5. Sac II and Spe I digestion of this mutant clone produced two octarepeat inserts; one was the 5-repeat wild type Oct5 while the other was a 2-repeat deletion mutant (R1a-R4). The arrowhead points to the band whose sequence is shown above the lane. The black box marks the template-sized Oct5 band from a non-mutant clone. (E) Mutant octarepeat clones containing two octarepeat inserts from PCR amplification of PrP-Oct11a. Sac II and Spe I digestion of the 10 mutant clones produced two octarepeat inserts; one was the 11-repeat parental Oct11a in all clones while the other was a mutant octarepeat sequence of varying sizes and sequences. The arrowhead points to the band whose sequence is shown above the lane. The black box marks the template-sized Oct11 band from a non-mutant clone. For all panels, the octarepeat sequence is indicated above each lane; Rep. No., number of repeats; M,100-bp DNA Ladder.

    Techniques Used: Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Mutagenesis, Clone Assay, Produced, Sequencing

    26) Product Images from "Interference of Co-Amplified Nuclear Mitochondrial DNA Sequences on the Determination of Human mtDNA Heteroplasmy by Using the SURVEYOR Nuclease and the WAVE HS System"

    Article Title: Interference of Co-Amplified Nuclear Mitochondrial DNA Sequences on the Determination of Human mtDNA Heteroplasmy by Using the SURVEYOR Nuclease and the WAVE HS System

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0092817

    Results from SN/WAVE-HS and DHPLC analysis of the DM#38 amplicon by using total DNA and mtDNA from cells. (A) Results from SN/WAVE-HS analysis. (B) Results from DHPLC analysis. The upper and lower panels of Figure 6A and Figure 6B display the results for 143B cells and the cybrid cells, respectively. In Figure 6A, the results for the DNA samples without (uncut) and with (cut) SN digestion were also compared. ▾ indicates the peaks that appeared in the chromatograms of uncut DNA but were not observed in the chromatograms of the corresponding cut DNA for all DNA samples. ▽ indicates the peaks > 100 bp only present in the chromatograms of the uncut DNA of both total DNA and mtDNA (m), but not the cut DNA. Such peaks for the mtDNA were considerably smaller than those of total DNA. ↓ indicates the peaks
    Figure Legend Snippet: Results from SN/WAVE-HS and DHPLC analysis of the DM#38 amplicon by using total DNA and mtDNA from cells. (A) Results from SN/WAVE-HS analysis. (B) Results from DHPLC analysis. The upper and lower panels of Figure 6A and Figure 6B display the results for 143B cells and the cybrid cells, respectively. In Figure 6A, the results for the DNA samples without (uncut) and with (cut) SN digestion were also compared. ▾ indicates the peaks that appeared in the chromatograms of uncut DNA but were not observed in the chromatograms of the corresponding cut DNA for all DNA samples. ▽ indicates the peaks > 100 bp only present in the chromatograms of the uncut DNA of both total DNA and mtDNA (m), but not the cut DNA. Such peaks for the mtDNA were considerably smaller than those of total DNA. ↓ indicates the peaks

    Techniques Used: Amplification

    PCR products amplified from the DNA of 143B and 143B-ρ 0 cells by using the selected primer pairs. (A) The 17 primer pairs selected from the DM primer set. (B) The 8 primer pairs selected from the SB primer set. A 100-bp DNA ladder and a 1-kb DNA ladder were used as the DNA sizing markers for the testing of the DM primer pairs and SB primer pairs, respectively. N, no-template control; R, DNA of 143B-ρ 0 cells as the template; B, DNA of 143B cells as the template.
    Figure Legend Snippet: PCR products amplified from the DNA of 143B and 143B-ρ 0 cells by using the selected primer pairs. (A) The 17 primer pairs selected from the DM primer set. (B) The 8 primer pairs selected from the SB primer set. A 100-bp DNA ladder and a 1-kb DNA ladder were used as the DNA sizing markers for the testing of the DM primer pairs and SB primer pairs, respectively. N, no-template control; R, DNA of 143B-ρ 0 cells as the template; B, DNA of 143B cells as the template.

    Techniques Used: Polymerase Chain Reaction, Amplification

    27) Product Images from "Lactobacilli with probiotic potential in the prairie vole (Microtus ochrogaster)"

    Article Title: Lactobacilli with probiotic potential in the prairie vole (Microtus ochrogaster)

    Journal: Gut Pathogens

    doi: 10.1186/s13099-015-0082-0

    Random amplified polymorphic DNA (RAPD) analysis of 30 prairie vole Lactobacillus isolates. Amplified fragment patterns for RAPD primer 272 (see text) are shown after electrophoresis on 1.5 % agarose gels. PV010-PV039: Prairie vole Lactobacillus strains PV010-PV039; Lj: L. johnsonii ATCC 33200; LGG: L. rhamnosus GG. M New England BioLabs 2-log DNA ladder
    Figure Legend Snippet: Random amplified polymorphic DNA (RAPD) analysis of 30 prairie vole Lactobacillus isolates. Amplified fragment patterns for RAPD primer 272 (see text) are shown after electrophoresis on 1.5 % agarose gels. PV010-PV039: Prairie vole Lactobacillus strains PV010-PV039; Lj: L. johnsonii ATCC 33200; LGG: L. rhamnosus GG. M New England BioLabs 2-log DNA ladder

    Techniques Used: Amplification, Electrophoresis

    28) Product Images from "Application of Sensitive and Specific Molecular Methods To Uncover Global Dissemination of the Major RDRio Sublineage of the Latin American-Mediterranean Mycobacterium tuberculosis Spoligotype Family ▿ Spoligotype Family ▿ ‡"

    Article Title: Application of Sensitive and Specific Molecular Methods To Uncover Global Dissemination of the Major RDRio Sublineage of the Latin American-Mediterranean Mycobacterium tuberculosis Spoligotype Family ▿ Spoligotype Family ▿ ‡

    Journal:

    doi: 10.1128/JCM.02231-07

    (A) RD Rio multiplex PCR. The presence of a 530-bp band indicates a WT strain, while the presence of an 1,175-bp band indicates an RD Rio strain. Lanes: 1, 100-bp ladder; 2, M. tuberculosis H37Rv; 3 and 4, WT LAM strains; 5 and 6, RD Rio LAM strains; 7,
    Figure Legend Snippet: (A) RD Rio multiplex PCR. The presence of a 530-bp band indicates a WT strain, while the presence of an 1,175-bp band indicates an RD Rio strain. Lanes: 1, 100-bp ladder; 2, M. tuberculosis H37Rv; 3 and 4, WT LAM strains; 5 and 6, RD Rio LAM strains; 7,

    Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Laser Capture Microdissection

    29) Product Images from "Genetic and Mass Spectrometry Analyses of the Unusual Type IV-Like Pili of the Archaeon Methanococcus maripaludis ▿"

    Article Title: Genetic and Mass Spectrometry Analyses of the Unusual Type IV-Like Pili of the Archaeon Methanococcus maripaludis ▿

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.00822-10

    Electron microscopy and SDS-PAGE analysis of purified M. maripaludis pilus samples. (A) Purified M. maripaludis pilus filaments. The sample was negatively stained with 2% phosphotungstic acid (pH 7.0). Bar, 100 nm. (B) Purified M. maripaludis
    Figure Legend Snippet: Electron microscopy and SDS-PAGE analysis of purified M. maripaludis pilus samples. (A) Purified M. maripaludis pilus filaments. The sample was negatively stained with 2% phosphotungstic acid (pH 7.0). Bar, 100 nm. (B) Purified M. maripaludis

    Techniques Used: Electron Microscopy, SDS Page, Purification, Staining

    30) Product Images from "Molecular Analysis of the Enterobacter sakazakii O-Antigen Gene Locus "

    Article Title: Molecular Analysis of the Enterobacter sakazakii O-Antigen Gene Locus

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.02302-07

    Restriction length profiles of rfb -encoding locus of E. sakazakii following MboII digestion. Lane 1, ATCC BAA-894; lane 2, E824; lane 3, E825; lane 4, NCTC 11467; lane 5, NCTC 8155; lane 6, 336; lane 7, 344; lane 8, 109; lane 9, CFS06; lane 10, E787; lane 11, 82; lane 12, 102; lane M1, 100-bp DNA ladder (New England Biolabs, Hertfordshire, England); lane M2, DNA molecular weight marker XVI (Roche, Mannheim, Germany). Black and gray boxes indicate profiles of strains corresponding to O:1 and O:2 serotypes, respectively.
    Figure Legend Snippet: Restriction length profiles of rfb -encoding locus of E. sakazakii following MboII digestion. Lane 1, ATCC BAA-894; lane 2, E824; lane 3, E825; lane 4, NCTC 11467; lane 5, NCTC 8155; lane 6, 336; lane 7, 344; lane 8, 109; lane 9, CFS06; lane 10, E787; lane 11, 82; lane 12, 102; lane M1, 100-bp DNA ladder (New England Biolabs, Hertfordshire, England); lane M2, DNA molecular weight marker XVI (Roche, Mannheim, Germany). Black and gray boxes indicate profiles of strains corresponding to O:1 and O:2 serotypes, respectively.

    Techniques Used: Molecular Weight, Marker

    A 1.5% agarose gel image of specific-serotype O:1 (top panel) or serotype O:2 (bottom panel) amplicons, generated by PCR. Lane 1, CFS131; lane 2, E824; lane 3, CFS06; lane 4, 44; lane 5, 93; lane 6, E891; lane 7, E784; lane 8, CFS153; lane 9, 88; lane 10, 305N; lane 11, ATCC BAA 893; lane 12, ATCC BAA 894; lane 13, E899; lane 14, 343; lane 15, 80; lane 16, E775; lane 17, 71; lane 18, E846; lane 19, E830; lane 20, 228N; lane 21, CFS136; lane 22, CFS149; lane 23, no-template control; lane M, 100-bp DNA ladder (New England Biolabs, Hertfordshire, England). Dashed-line box indicates serotype O:1 strains, while continuous-line box indicates serotype O:2 strains.
    Figure Legend Snippet: A 1.5% agarose gel image of specific-serotype O:1 (top panel) or serotype O:2 (bottom panel) amplicons, generated by PCR. Lane 1, CFS131; lane 2, E824; lane 3, CFS06; lane 4, 44; lane 5, 93; lane 6, E891; lane 7, E784; lane 8, CFS153; lane 9, 88; lane 10, 305N; lane 11, ATCC BAA 893; lane 12, ATCC BAA 894; lane 13, E899; lane 14, 343; lane 15, 80; lane 16, E775; lane 17, 71; lane 18, E846; lane 19, E830; lane 20, 228N; lane 21, CFS136; lane 22, CFS149; lane 23, no-template control; lane M, 100-bp DNA ladder (New England Biolabs, Hertfordshire, England). Dashed-line box indicates serotype O:1 strains, while continuous-line box indicates serotype O:2 strains.

    Techniques Used: Agarose Gel Electrophoresis, Generated, Polymerase Chain Reaction

    31) Product Images from "Methods for targeted mutagenesis in zebrafish using TALENs"

    Article Title: Methods for targeted mutagenesis in zebrafish using TALENs

    Journal: Methods (San Diego, Calif.)

    doi: 10.1016/j.ymeth.2014.04.009

    A representation of T7EI assay results. T7EI assay was performed as described in Section 6.2.1 using single embryo lysis from six nuclease-injected embryos (marked as #1–6) and two uninjected embryos (marked as “U”). An agarose gel image of the results is shown. While the parent amplicons from the uninjected embryos remained intact after the assay, some portions of the parent amplicons from the injected embryos were cleaved by T7EI into two bands of expected sizes. The “fraction cleaved” and the “% modification” calculated according to the protocol are shown at the bottom of each lane. M, 100 bp DNA ladder (New England Biolabs).
    Figure Legend Snippet: A representation of T7EI assay results. T7EI assay was performed as described in Section 6.2.1 using single embryo lysis from six nuclease-injected embryos (marked as #1–6) and two uninjected embryos (marked as “U”). An agarose gel image of the results is shown. While the parent amplicons from the uninjected embryos remained intact after the assay, some portions of the parent amplicons from the injected embryos were cleaved by T7EI into two bands of expected sizes. The “fraction cleaved” and the “% modification” calculated according to the protocol are shown at the bottom of each lane. M, 100 bp DNA ladder (New England Biolabs).

    Techniques Used: T7EI Assay, Lysis, Injection, Agarose Gel Electrophoresis, Modification

    32) Product Images from "ADH1B, ALDH2, GSTM1 and GSTT1 Gene Polymorphic Frequencies among Alcoholics and Controls in the Arcadian Population of Central India"

    Article Title: ADH1B, ALDH2, GSTM1 and GSTT1 Gene Polymorphic Frequencies among Alcoholics and Controls in the Arcadian Population of Central India

    Journal: Asian Pacific Journal of Cancer Prevention : APJCP

    doi: 10.22034/APJCP.2018.19.3.725

    For ALDH2 Genotyping–Lane L, 100bp DNA Ladder; Lane 1–2, Digested fragments of 90bp and 18bp bands; Lane 3–6, One uncut (119bp) with two digested fragments (90bp and 18bp); Lane 7, Undigested band (119bp).
    Figure Legend Snippet: For ALDH2 Genotyping–Lane L, 100bp DNA Ladder; Lane 1–2, Digested fragments of 90bp and 18bp bands; Lane 3–6, One uncut (119bp) with two digested fragments (90bp and 18bp); Lane 7, Undigested band (119bp).

    Techniques Used:

    For ADH1B Genotyping–Lane L, 100bp DNA Ladder; Lane 1–7, Undigested 155bp bands for ADH1B.
    Figure Legend Snippet: For ADH1B Genotyping–Lane L, 100bp DNA Ladder; Lane 1–7, Undigested 155bp bands for ADH1B.

    Techniques Used:

    GSTM1 Genotyping; Lane L, 100bp DNA Ladder; Lane 1, Null allele for GSTM1; Lane 2–6, Positive allele for GSTM1 (215bp).
    Figure Legend Snippet: GSTM1 Genotyping; Lane L, 100bp DNA Ladder; Lane 1, Null allele for GSTM1; Lane 2–6, Positive allele for GSTM1 (215bp).

    Techniques Used:

    33) Product Images from "Pathogenomics Characterization of an Emerging Fungal Pathogen, Fusarium oxysporum f. sp. lycopersici in Greenhouse Tomato Production Systems"

    Article Title: Pathogenomics Characterization of an Emerging Fungal Pathogen, Fusarium oxysporum f. sp. lycopersici in Greenhouse Tomato Production Systems

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2020.01995

    Differentiation of Fusarium oxysporum f. sp. lycopersici race 3 from race 1 isolates collected from tomato-grown in greenhouses in North Carolina by polymerase chain reaction (PCR) assay targeting the SIX3 gene and sequence alignments. The Maximum-likelihood phylogenetic trees were generated from the SIX3 gene sequences of the representative isolates and outgroup isolate “Ara1” of F. odoratissimum sequences were downloaded from the National Center for Biotechnology Information database GenBank ( http://www.ncbi.nlm.nih.gov/genbank ). The tree topology was obtained through maximum-likelihood with 1,000 replications using the Tamura-Nei DNA substitution model. Parsimony bootstrap values ( > 80%) are shown above the branches. The clade of each isolate is also presented in Table 1 . Sequences of two isolates Fu 12 and Fu 17 were not included due to short lengths. Nonpathogenic isolate Fu 6 did not have an amplicon corresponding to the SIX3 gene.
    Figure Legend Snippet: Differentiation of Fusarium oxysporum f. sp. lycopersici race 3 from race 1 isolates collected from tomato-grown in greenhouses in North Carolina by polymerase chain reaction (PCR) assay targeting the SIX3 gene and sequence alignments. The Maximum-likelihood phylogenetic trees were generated from the SIX3 gene sequences of the representative isolates and outgroup isolate “Ara1” of F. odoratissimum sequences were downloaded from the National Center for Biotechnology Information database GenBank ( http://www.ncbi.nlm.nih.gov/genbank ). The tree topology was obtained through maximum-likelihood with 1,000 replications using the Tamura-Nei DNA substitution model. Parsimony bootstrap values ( > 80%) are shown above the branches. The clade of each isolate is also presented in Table 1 . Sequences of two isolates Fu 12 and Fu 17 were not included due to short lengths. Nonpathogenic isolate Fu 6 did not have an amplicon corresponding to the SIX3 gene.

    Techniques Used: Polymerase Chain Reaction, Sequencing, Generated, Amplification

    34) Product Images from "A Partial Gene Deletion of SLC45A2 Causes Oculocutaneous Albinism in Doberman Pinscher Dogs"

    Article Title: A Partial Gene Deletion of SLC45A2 Causes Oculocutaneous Albinism in Doberman Pinscher Dogs

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0092127

    Lack of exclusion of SLC45A2 with white Doberman pinschers as assessed by genotyping microsatellites by agarose gel electrophoresis. 2.0% agarose gel comparisons of (A) SLC45A2 microsatellite marker 1 (192 kb upstream of SLC45A2 ), white Doberman pinschers (WDPs, left hand portions of panel A) and standard color Doberman pinschers (SDPs, right hand portion of panel A) and (B) SLC45A2 microsatellite marker 2 (46 kb downstream of SLC45A2 ), for WDPs and SDPs. Note the high variability in the markers in the SDPs compared with the almost complete lack of variation seen for WDPs (the extra band seen in lane 1 is a heteroduplex band caused by a one-step tetranucleotide repeat mutation [see Table S2 ]). Lanes for the two gels in each panel: L, 100 bp DNA ladder (New England Biolabs, Inc.), WDP lanes 1–14, WDP samples 1–14; SDP lanes: L, 100 bp DNA ladder, lanes 1–12, SDP samples 1–12. Samples in these gels correspond to those in Table S3 , which contains the high resolution genotyping data.
    Figure Legend Snippet: Lack of exclusion of SLC45A2 with white Doberman pinschers as assessed by genotyping microsatellites by agarose gel electrophoresis. 2.0% agarose gel comparisons of (A) SLC45A2 microsatellite marker 1 (192 kb upstream of SLC45A2 ), white Doberman pinschers (WDPs, left hand portions of panel A) and standard color Doberman pinschers (SDPs, right hand portion of panel A) and (B) SLC45A2 microsatellite marker 2 (46 kb downstream of SLC45A2 ), for WDPs and SDPs. Note the high variability in the markers in the SDPs compared with the almost complete lack of variation seen for WDPs (the extra band seen in lane 1 is a heteroduplex band caused by a one-step tetranucleotide repeat mutation [see Table S2 ]). Lanes for the two gels in each panel: L, 100 bp DNA ladder (New England Biolabs, Inc.), WDP lanes 1–14, WDP samples 1–14; SDP lanes: L, 100 bp DNA ladder, lanes 1–12, SDP samples 1–12. Samples in these gels correspond to those in Table S3 , which contains the high resolution genotyping data.

    Techniques Used: Agarose Gel Electrophoresis, Marker, Mutagenesis

    35) Product Images from "Genomic Analysis of Blastocystis hominis Strains Isolated from Two Long-Term Health Care Facilities"

    Article Title: Genomic Analysis of Blastocystis hominis Strains Isolated from Two Long-Term Health Care Facilities

    Journal: Journal of Clinical Microbiology

    doi:

    The specificity of four diagnostic primers was tested against other intestinal protozoa and a yeast. Lanes 1 to 7 were amplified by using primer sets SB227, lanes 8 to 14 were amplified with SB228, lanes 15 to 21 were amplified with SB229, and lanes 22 to 28 were amplified with SB332. Only positive controls (lanes 7, 14, 21, and 28) showed a single band. Lanes: MM, molecular marker of a 100-bp ladder; 1, 8, 15, and 22, E. histolytica ; 2, 9, 16, and 23, E. moshkovskii ; 3, 10, 17, and 24, G. intestinalis ; 4, 11, 18, and 25, C. muris ; 5, 12, 19, and 26, C. parvum ; 6, 13, 20, and 27, S. cerevisiae ; 7 and 14, HV93-13; 21, HV96A-26; 28, HJ96AS-1.
    Figure Legend Snippet: The specificity of four diagnostic primers was tested against other intestinal protozoa and a yeast. Lanes 1 to 7 were amplified by using primer sets SB227, lanes 8 to 14 were amplified with SB228, lanes 15 to 21 were amplified with SB229, and lanes 22 to 28 were amplified with SB332. Only positive controls (lanes 7, 14, 21, and 28) showed a single band. Lanes: MM, molecular marker of a 100-bp ladder; 1, 8, 15, and 22, E. histolytica ; 2, 9, 16, and 23, E. moshkovskii ; 3, 10, 17, and 24, G. intestinalis ; 4, 11, 18, and 25, C. muris ; 5, 12, 19, and 26, C. parvum ; 6, 13, 20, and 27, S. cerevisiae ; 7 and 14, HV93-13; 21, HV96A-26; 28, HJ96AS-1.

    Techniques Used: Diagnostic Assay, Amplification, Marker

    36) Product Images from "TRIM25 binds RNA to modulate cellular anti-viral defense"

    Article Title: TRIM25 binds RNA to modulate cellular anti-viral defense

    Journal: Journal of molecular biology

    doi: 10.1016/j.jmb.2018.10.003

    RNA enhances TRIM25’s catalytic activity in vitro . ( a ]. Reactions contained 100 nM E1, 40 μM Ub, and 5 mM Mg-ATP. ( b ) TRIM25 purified in the absence of PEI treatment was pre-incubated with RNase A (lanes 5 and 9), DNase I (lanes 4 and 8), or buffer control (lanes 3 and 7) prior to setting up ubiquitination assays. ( c ) TRIM25 purified with PEI treatment was pre-incubated with 500 ng of dsRNA (lanes 4 and 8), 500 ng of dsDNA (lanes 5 and 9), or buffer control (lanes 3 and 7) prior to ubiquitination assays. ( d ) TRIM25 purified with PEI treatment was pre-incubated with the indicated concentrations of 14, 28, or 56-bp dsRNA prior to ubiquitination with Ube2N/Ube2V2 as E2.
    Figure Legend Snippet: RNA enhances TRIM25’s catalytic activity in vitro . ( a ]. Reactions contained 100 nM E1, 40 μM Ub, and 5 mM Mg-ATP. ( b ) TRIM25 purified in the absence of PEI treatment was pre-incubated with RNase A (lanes 5 and 9), DNase I (lanes 4 and 8), or buffer control (lanes 3 and 7) prior to setting up ubiquitination assays. ( c ) TRIM25 purified with PEI treatment was pre-incubated with 500 ng of dsRNA (lanes 4 and 8), 500 ng of dsDNA (lanes 5 and 9), or buffer control (lanes 3 and 7) prior to ubiquitination assays. ( d ) TRIM25 purified with PEI treatment was pre-incubated with the indicated concentrations of 14, 28, or 56-bp dsRNA prior to ubiquitination with Ube2N/Ube2V2 as E2.

    Techniques Used: Activity Assay, In Vitro, Purification, Incubation

    37) Product Images from "Relative Ability of Orally Administered Lactobacillus murinus To Predominate and Persist in the Porcine Gastrointestinal Tract"

    Article Title: Relative Ability of Orally Administered Lactobacillus murinus To Predominate and Persist in the Porcine Gastrointestinal Tract

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.70.4.1895-1906.2004

    (A) Excretion of administered strains in pigs fed ∼10 10 CFU of each of the porcine cultures/day. L. salivarius DPC6005 Rif r (♦), P. pentosaceus DPC6006 Rif r (▪), L. pentosus DPC6004 Rif r (▴), L. murinus DPC6002 Rif r (X), L. murinus DPC6003 Rif r (*), or a combination of all five cultures (•) was fed from day 1 to 22, where day 1 represents the first day of culture administration. Values are means of the results from 4 pigs (except for the L. murinus DPC6002 treatment, where values are the means of the results from 3 pigs), with standard errors of the means indicated by vertical bars. (B) RAPD fingerprints (generated with R1 primer) of representative fecal isolates obtained from selected pigs on day 15 of oral administration of these porcine cultures individually (lanes 2 to 6, 9 to 13, 15 to 18, 20 to 24, and 26 to 30) compared with RAPD fingerprints of the relevant administered strains (lanes 1, 8, 14, 19, and 25, respectively). Lanes 7 and 31 contain a 100-bp ladder. (C) RAPD fingerprints (generated with R2 primer) of representative fecal isolates obtained from selected pigs on day 15 of oral administration of a combination of all five porcine cultures (lanes 6 to 15) compared with RAPD fingerprints of each of the strains administered in the mixture (lanes 1 to 5). Lane 16 contains a 100-bp ladder.
    Figure Legend Snippet: (A) Excretion of administered strains in pigs fed ∼10 10 CFU of each of the porcine cultures/day. L. salivarius DPC6005 Rif r (♦), P. pentosaceus DPC6006 Rif r (▪), L. pentosus DPC6004 Rif r (▴), L. murinus DPC6002 Rif r (X), L. murinus DPC6003 Rif r (*), or a combination of all five cultures (•) was fed from day 1 to 22, where day 1 represents the first day of culture administration. Values are means of the results from 4 pigs (except for the L. murinus DPC6002 treatment, where values are the means of the results from 3 pigs), with standard errors of the means indicated by vertical bars. (B) RAPD fingerprints (generated with R1 primer) of representative fecal isolates obtained from selected pigs on day 15 of oral administration of these porcine cultures individually (lanes 2 to 6, 9 to 13, 15 to 18, 20 to 24, and 26 to 30) compared with RAPD fingerprints of the relevant administered strains (lanes 1, 8, 14, 19, and 25, respectively). Lanes 7 and 31 contain a 100-bp ladder. (C) RAPD fingerprints (generated with R2 primer) of representative fecal isolates obtained from selected pigs on day 15 of oral administration of a combination of all five porcine cultures (lanes 6 to 15) compared with RAPD fingerprints of each of the strains administered in the mixture (lanes 1 to 5). Lane 16 contains a 100-bp ladder.

    Techniques Used: Generated

    38) Product Images from "Identification of mutations in the c-mpl gene in congenital amegakaryocytic thrombocytopenia"

    Article Title: Identification of mutations in the c-mpl gene in congenital amegakaryocytic thrombocytopenia

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi:

    c-mpl gene mutations in the family with CAMT. ( A ) A pedigree of the family. Circles represent females and squares males. Half-shaded (left side of the symbol) symbols represent carriers of the Q186X mutation, and half-hatched (right side of the symbol) symbols represent carriers of the 1,499 delT mutation. The proband is II-1. ( B ) Verification of the C-to-T mutation at cDNA position 556 by PCR amplification and restriction-enzyme analysis. PCR products of exon 4 were digested with Pvu II and checked by agarose gel electrophoresis. The 380-bp PCR product of exon 4 is cleaved to 175-bp, 105-bp, and 100-bp fragments by Pvu II. The Q186X mutation abolishes one of two Pvu II sites, resulting in 275-bp and 105-bp fragments. The patient (lane 2), her mother (lane 4), and her brother (lane 5) possess this mutation in one allele, whereas her father (lane 3) and her sister (lane 6) do not have this mutation. Lane 1 shows the molecular size marker. ( C ) Restriction-enzyme analysis of the 1,499 delT. The 265-bp PCR product of exon 10 is cleaved to 162-bp, 70-bp, and 33-bp fragments by Bfa I. The 1,499 delT abolishes one of two Bfa I sites, resulting in 195-bp and 70-bp fragments (70-bp and 33-bp bands are not shown). Although the patient (lane 2) and her father (lane 3) have this mutation in one allele, her mother (lane 4), her brother (lane 5), and her sister (lane 6) do not have this mutation. Lane 1 shows the molecular size marker.
    Figure Legend Snippet: c-mpl gene mutations in the family with CAMT. ( A ) A pedigree of the family. Circles represent females and squares males. Half-shaded (left side of the symbol) symbols represent carriers of the Q186X mutation, and half-hatched (right side of the symbol) symbols represent carriers of the 1,499 delT mutation. The proband is II-1. ( B ) Verification of the C-to-T mutation at cDNA position 556 by PCR amplification and restriction-enzyme analysis. PCR products of exon 4 were digested with Pvu II and checked by agarose gel electrophoresis. The 380-bp PCR product of exon 4 is cleaved to 175-bp, 105-bp, and 100-bp fragments by Pvu II. The Q186X mutation abolishes one of two Pvu II sites, resulting in 275-bp and 105-bp fragments. The patient (lane 2), her mother (lane 4), and her brother (lane 5) possess this mutation in one allele, whereas her father (lane 3) and her sister (lane 6) do not have this mutation. Lane 1 shows the molecular size marker. ( C ) Restriction-enzyme analysis of the 1,499 delT. The 265-bp PCR product of exon 10 is cleaved to 162-bp, 70-bp, and 33-bp fragments by Bfa I. The 1,499 delT abolishes one of two Bfa I sites, resulting in 195-bp and 70-bp fragments (70-bp and 33-bp bands are not shown). Although the patient (lane 2) and her father (lane 3) have this mutation in one allele, her mother (lane 4), her brother (lane 5), and her sister (lane 6) do not have this mutation. Lane 1 shows the molecular size marker.

    Techniques Used: Mutagenesis, Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Marker

    39) Product Images from "The gene silencing protein MORC-1 topologically entraps DNA and forms multimeric assemblies to cause DNA compaction."

    Article Title: The gene silencing protein MORC-1 topologically entraps DNA and forms multimeric assemblies to cause DNA compaction.

    Journal: Molecular cell

    doi: 10.1016/j.molcel.2019.07.032

    MORC-1 is a DNA binding protein. (A) Protein ([MORC-1] = 100 nM, 200 nM, 400 nM, 800 nM) was incubated with 32P labeled 250 bp DNA probe derived from λ-DNA and run on a 3% agarose gel, then dried before exposure to a phophor screen. (B) 200 nM MORC-1 was added to 0.5 nM 32P labeled 250 bp λ-DNA that was premixed with cold 250 bp λ-DNA, 250 bp scrambled DNA, or 50 bp λ-DNA probe (1 nM, 10 nM, 20 nM, 50 nM) and processed as described above. .
    Figure Legend Snippet: MORC-1 is a DNA binding protein. (A) Protein ([MORC-1] = 100 nM, 200 nM, 400 nM, 800 nM) was incubated with 32P labeled 250 bp DNA probe derived from λ-DNA and run on a 3% agarose gel, then dried before exposure to a phophor screen. (B) 200 nM MORC-1 was added to 0.5 nM 32P labeled 250 bp λ-DNA that was premixed with cold 250 bp λ-DNA, 250 bp scrambled DNA, or 50 bp λ-DNA probe (1 nM, 10 nM, 20 nM, 50 nM) and processed as described above. .

    Techniques Used: Binding Assay, Incubation, Labeling, Derivative Assay, Agarose Gel Electrophoresis

    40) Product Images from "Evaluation of the Broad-Range PCR-Electrospray Ionization Mass Spectrometry (PCR/ESI-MS) System and Virus Microarrays for Virus Detection"

    Article Title: Evaluation of the Broad-Range PCR-Electrospray Ionization Mass Spectrometry (PCR/ESI-MS) System and Virus Microarrays for Virus Detection

    Journal: Viruses

    doi: 10.3390/v6051876

    Determination of retrovirus LOD using RT-PCR assays. Total RNA was extracted from each virus dilution to create XMRV and SFV-1 RNA panels (10 0 –10 −7 ) in the absence and presence of 10 5 or 10 4 cell equivalents of Sf9 total nucleic acids as described in Materials and Methods. A subset of the RNA panels (10 −3 –10 −6 ) was subjected to nested RT-PCR assays. An RT minus (−RT) control of the samples shows the absence of residual cellular DNA and the negative, no template control for the PCR shows the absence of contamination in the assay. ( a ) XMRV gag primers; ( b ) SFV-1 gag primers. The size of fragments in the 100 bp marker (M) is indicated in base pairs (bp).
    Figure Legend Snippet: Determination of retrovirus LOD using RT-PCR assays. Total RNA was extracted from each virus dilution to create XMRV and SFV-1 RNA panels (10 0 –10 −7 ) in the absence and presence of 10 5 or 10 4 cell equivalents of Sf9 total nucleic acids as described in Materials and Methods. A subset of the RNA panels (10 −3 –10 −6 ) was subjected to nested RT-PCR assays. An RT minus (−RT) control of the samples shows the absence of residual cellular DNA and the negative, no template control for the PCR shows the absence of contamination in the assay. ( a ) XMRV gag primers; ( b ) SFV-1 gag primers. The size of fragments in the 100 bp marker (M) is indicated in base pairs (bp).

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Marker

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    Article Snippet: After electrophoresis, gel was stained with ethidium bromide (0.5 μg/ml) for 1 h, destained with TAE buffer and photographed. .. For Electrophoretic mobility shift assay ( EMSA) on polyacrylamide gel, 100 ng of 30 bp DNA was 5′-end labeled with [γ-32 P] ATP using T4 polynucleotide kinase (NEB). .. Different concentrations of rLdACT were mixed with ∼5 pmol of 5′-end-labeled and purified DNA fragments in a total volume of 20 μl in 20 mM Tris–HCl, 0.1 mM EDTA, pH 7.5 and incubated for 30 min at 25°C.

    Labeling:

    Article Title: Leishmania actin binds and nicks kDNA as well as inhibits decatenation activity of type II topoisomerase
    Article Snippet: After electrophoresis, gel was stained with ethidium bromide (0.5 μg/ml) for 1 h, destained with TAE buffer and photographed. .. For Electrophoretic mobility shift assay ( EMSA) on polyacrylamide gel, 100 ng of 30 bp DNA was 5′-end labeled with [γ-32 P] ATP using T4 polynucleotide kinase (NEB). .. Different concentrations of rLdACT were mixed with ∼5 pmol of 5′-end-labeled and purified DNA fragments in a total volume of 20 μl in 20 mM Tris–HCl, 0.1 mM EDTA, pH 7.5 and incubated for 30 min at 25°C.

    Mutagenesis:

    Article Title: A selectable, plasmid-based system to generate CRISPR/Cas9 gene edited and knock-in mosquito cell lines
    Article Snippet: PCRs were amplified from genomic DNA using primers RU-O-22929 and RU-O-24042 for U4.4 cells (full-length PCR product = 353 bp, digested = ~ 330 bp + ~ 23 bp); primers RU-O-22776 and RU-O-22777 were used for Aag2 cells (full-length PCR product = 412 bp, digested = ~ 179 bp + ~ 231 bp). .. PCRs were screened for editing efficiency using the Surveyor Mutation Detection Kit (IDT) according to the manufacturer’s instructions, and treated amplicons were visualized on ~ 1% agarose gels with 100 bp DNA ladder (NEB) and SYBR Gold (Thermo Fisher Scientific). .. Single cell cloningFor bulk CRISPR/Cas9-transfected cells with apparent editing, we isolated single cells to establish clonal edited cell lines.

    Polymerase Chain Reaction:

    Article Title: ADH1B, ALDH2, GSTM1 and GSTT1 Gene Polymorphic Frequencies among Alcoholics and Controls in the Arcadian Population of Central India
    Article Snippet: .. After PCR, amplicons size with the help of 100bp DNA ladder (NEB, US) were analyzed by gel electrophoresis using ethidium bromide (EtBr) stained (10mg/ml) 2% AG (Sigma). ..

    Article Title: Identification of UDP Glycosyltransferase 3A1 as a UDPN-Acetylglucosaminyltransferase *
    Article Snippet: The cycling parameters consisted of one cycle at 95 °C for 15 min and then 40 cycles of 95 °C for 10 s, 55 °C for 15 s, and 72 °C for 20 s. Transcript copy number was determined using UGT3A1 plasmid as standard. .. At the end of 40 cycles, the integrity of PCR products was assessed by electrophoresis on a 1.5% agarose gel with 100-bp DNA markers (New England Biolabs) as a reference to estimate molecular size. .. The DNA was visualized by staining with ethidium bromide.

    Nucleic Acid Electrophoresis:

    Article Title: ADH1B, ALDH2, GSTM1 and GSTT1 Gene Polymorphic Frequencies among Alcoholics and Controls in the Arcadian Population of Central India
    Article Snippet: .. After PCR, amplicons size with the help of 100bp DNA ladder (NEB, US) were analyzed by gel electrophoresis using ethidium bromide (EtBr) stained (10mg/ml) 2% AG (Sigma). ..

    Staining:

    Article Title: ADH1B, ALDH2, GSTM1 and GSTT1 Gene Polymorphic Frequencies among Alcoholics and Controls in the Arcadian Population of Central India
    Article Snippet: .. After PCR, amplicons size with the help of 100bp DNA ladder (NEB, US) were analyzed by gel electrophoresis using ethidium bromide (EtBr) stained (10mg/ml) 2% AG (Sigma). ..

    Marker:

    Article Title: Identification of Coupling and Repulsion Phase DNA Marker Associated With an Allele of a Gene Conferring Host Plant Resistance to Pigeonpea sterility mosaic virus (PPSMV) in Pigeonpea (Cajanus cajan L. Millsp.)
    Article Snippet: The agarose gels were stained with 1 μg ml−1 ethidium bromide, visualized under UV light and photographed on a digital gel-documentation system. .. The molecular weights of the short decamer random DNA marker products were estimated with a 100-bp DNA ladder (New England BioLabs, MA, USA). ..

    Article Title: Simple and Reliable Multiplex PCR Assay for Surveillance Isolates of Vancomycin-Resistant Enterococci
    Article Snippet: PCR products were analyzed on a 1.5% SeaKem ME agarose gel (FMC BioProducts, Rockland, Maine) with 0.5× Tris-borate-EDTA buffer. .. A 100-bp DNA ladder (New England Biolabs, Beverly, Mass.) was used as the molecular size marker. .. The gels were stained with ethidium bromide and photographed under UV light.

    Article Title: Relationship Between Chromatin Structure and Sensitivity to Molecularly Targeted Auger Electron Radiation Therapy
    Article Snippet: .. DNA was purified, separated alongside a 100-bp marker (New England Biolabs, Hitchin, UK) by electrophoresis in 1.2% agarose gel containing ethidium bromide, and visualized by ultraviolet transillumination. ..

    Purification:

    Article Title: Relationship Between Chromatin Structure and Sensitivity to Molecularly Targeted Auger Electron Radiation Therapy
    Article Snippet: .. DNA was purified, separated alongside a 100-bp marker (New England Biolabs, Hitchin, UK) by electrophoresis in 1.2% agarose gel containing ethidium bromide, and visualized by ultraviolet transillumination. ..

    Electrophoresis:

    Article Title: Relationship Between Chromatin Structure and Sensitivity to Molecularly Targeted Auger Electron Radiation Therapy
    Article Snippet: .. DNA was purified, separated alongside a 100-bp marker (New England Biolabs, Hitchin, UK) by electrophoresis in 1.2% agarose gel containing ethidium bromide, and visualized by ultraviolet transillumination. ..

    Article Title: Identification of UDP Glycosyltransferase 3A1 as a UDPN-Acetylglucosaminyltransferase *
    Article Snippet: The cycling parameters consisted of one cycle at 95 °C for 15 min and then 40 cycles of 95 °C for 10 s, 55 °C for 15 s, and 72 °C for 20 s. Transcript copy number was determined using UGT3A1 plasmid as standard. .. At the end of 40 cycles, the integrity of PCR products was assessed by electrophoresis on a 1.5% agarose gel with 100-bp DNA markers (New England Biolabs) as a reference to estimate molecular size. .. The DNA was visualized by staining with ethidium bromide.

    Agarose Gel Electrophoresis:

    Article Title: Relationship Between Chromatin Structure and Sensitivity to Molecularly Targeted Auger Electron Radiation Therapy
    Article Snippet: .. DNA was purified, separated alongside a 100-bp marker (New England Biolabs, Hitchin, UK) by electrophoresis in 1.2% agarose gel containing ethidium bromide, and visualized by ultraviolet transillumination. ..

    Article Title: Identification of UDP Glycosyltransferase 3A1 as a UDPN-Acetylglucosaminyltransferase *
    Article Snippet: The cycling parameters consisted of one cycle at 95 °C for 15 min and then 40 cycles of 95 °C for 10 s, 55 °C for 15 s, and 72 °C for 20 s. Transcript copy number was determined using UGT3A1 plasmid as standard. .. At the end of 40 cycles, the integrity of PCR products was assessed by electrophoresis on a 1.5% agarose gel with 100-bp DNA markers (New England Biolabs) as a reference to estimate molecular size. .. The DNA was visualized by staining with ethidium bromide.

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    New England Biolabs bp dna
    ( A ) ChIP analysis using anti-rLdACT antibodies showed the in vivo association of LdACT with chromatin and kDNA network. ( a ) and ( b ) are the agarose gels of PCR products after ChIP assay, showing the association of LdACT with nuclear <t>DNA</t> and kDNA, respectively. Lanes are marked on the top with their respective antibodies used in the ChIP assay and arrows indicated the genes amplified after pull down. An irrelevant, non-DNA associating antibody, GRP78, was used as a negative control, whereas, antibodies against DNA polβ, and UMSBP (universal minicircle sequence-binding protein), were used as positive controls for nuclear DNA and kDNA respectively. LdPFN, Leishmania profilin; NM12/17, specific minicircle primers. ( B ) Agarose gel shift assay of supercoiled and linearized pBR322 (400 ng each) in the presence of rLdACT (0.5 2.0 μM), and β- and γ-actins (0.5 2.0 μM) as indicated on the top of the gels. Lane M, shows 1 kb DNA ladder; FI: supercoiled form, FII: relaxed form, FIII: linearized form of DNA. ( C ) Autoradiogram of <t>EMSA</t> on polyacrylamide gel of 32 P end-labelled 30 bp DNA probe in the presence of increasing concentration of rLdACT (0.1–0.6 μM).
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    ( A ) ChIP analysis using anti-rLdACT antibodies showed the in vivo association of LdACT with chromatin and kDNA network. ( a ) and ( b ) are the agarose gels of PCR products after ChIP assay, showing the association of LdACT with nuclear DNA and kDNA, respectively. Lanes are marked on the top with their respective antibodies used in the ChIP assay and arrows indicated the genes amplified after pull down. An irrelevant, non-DNA associating antibody, GRP78, was used as a negative control, whereas, antibodies against DNA polβ, and UMSBP (universal minicircle sequence-binding protein), were used as positive controls for nuclear DNA and kDNA respectively. LdPFN, Leishmania profilin; NM12/17, specific minicircle primers. ( B ) Agarose gel shift assay of supercoiled and linearized pBR322 (400 ng each) in the presence of rLdACT (0.5 2.0 μM), and β- and γ-actins (0.5 2.0 μM) as indicated on the top of the gels. Lane M, shows 1 kb DNA ladder; FI: supercoiled form, FII: relaxed form, FIII: linearized form of DNA. ( C ) Autoradiogram of EMSA on polyacrylamide gel of 32 P end-labelled 30 bp DNA probe in the presence of increasing concentration of rLdACT (0.1–0.6 μM).

    Journal: Nucleic Acids Research

    Article Title: Leishmania actin binds and nicks kDNA as well as inhibits decatenation activity of type II topoisomerase

    doi: 10.1093/nar/gkq051

    Figure Lengend Snippet: ( A ) ChIP analysis using anti-rLdACT antibodies showed the in vivo association of LdACT with chromatin and kDNA network. ( a ) and ( b ) are the agarose gels of PCR products after ChIP assay, showing the association of LdACT with nuclear DNA and kDNA, respectively. Lanes are marked on the top with their respective antibodies used in the ChIP assay and arrows indicated the genes amplified after pull down. An irrelevant, non-DNA associating antibody, GRP78, was used as a negative control, whereas, antibodies against DNA polβ, and UMSBP (universal minicircle sequence-binding protein), were used as positive controls for nuclear DNA and kDNA respectively. LdPFN, Leishmania profilin; NM12/17, specific minicircle primers. ( B ) Agarose gel shift assay of supercoiled and linearized pBR322 (400 ng each) in the presence of rLdACT (0.5 2.0 μM), and β- and γ-actins (0.5 2.0 μM) as indicated on the top of the gels. Lane M, shows 1 kb DNA ladder; FI: supercoiled form, FII: relaxed form, FIII: linearized form of DNA. ( C ) Autoradiogram of EMSA on polyacrylamide gel of 32 P end-labelled 30 bp DNA probe in the presence of increasing concentration of rLdACT (0.1–0.6 μM).

    Article Snippet: For Electrophoretic mobility shift assay ( EMSA) on polyacrylamide gel, 100 ng of 30 bp DNA was 5′-end labeled with [γ-32 P] ATP using T4 polynucleotide kinase (NEB).

    Techniques: Chromatin Immunoprecipitation, In Vivo, Polymerase Chain Reaction, Amplification, Negative Control, Sequencing, Binding Assay, Agarose Gel Electrophoresis, Shift Assay, Concentration Assay

    ( A ) Agarose gel (0.5%), showing the time dependent nicking of kDNA by rLdACT (4.0 μM) which revealed the existence of major nicked DNA and minor concatenated minicircle species. ( B ) Agarose gel, showing rLdACT mediated decatenation of the kDNA network in the presence or absence of anti-rLdACT antibodies. DM, decatenated kDNA marker (Topogen). ( C ) Agarose gel (1.0%), showing rLdACT mediated decatenation of kDNA network with rLdACT in the presence or absence of DNase-1 and its inhibitor EDTA, which completely rules out the possibility of DNA nicking by some contaminating nuclease. ( D ) Agarose gel (1.0%), showing requirement of rLdACT in its polymeric state for its kDNA decatenation activity. ( E ): ( a ), Agarose gel (1.0%), showing requirement of ATP in the rLdACT mediated kDNA decatenation process. ( b ), Graph, showing ATP dependence of rLdACT-mediated kDNA decatenation. ( F ) ( a ), Agarose gel (1.0%), showing rLdACT-mediated decatenation of kDNA in the presence of non-hydrolysable analogs of ATP. ( b ) Graph, showing relative inhibition of rLdACT mediated decatenation of kDNA network in the presence of non-hydrolysable ATP analogs when plotted with the increasing concentration of rLdACT.

    Journal: Nucleic Acids Research

    Article Title: Leishmania actin binds and nicks kDNA as well as inhibits decatenation activity of type II topoisomerase

    doi: 10.1093/nar/gkq051

    Figure Lengend Snippet: ( A ) Agarose gel (0.5%), showing the time dependent nicking of kDNA by rLdACT (4.0 μM) which revealed the existence of major nicked DNA and minor concatenated minicircle species. ( B ) Agarose gel, showing rLdACT mediated decatenation of the kDNA network in the presence or absence of anti-rLdACT antibodies. DM, decatenated kDNA marker (Topogen). ( C ) Agarose gel (1.0%), showing rLdACT mediated decatenation of kDNA network with rLdACT in the presence or absence of DNase-1 and its inhibitor EDTA, which completely rules out the possibility of DNA nicking by some contaminating nuclease. ( D ) Agarose gel (1.0%), showing requirement of rLdACT in its polymeric state for its kDNA decatenation activity. ( E ): ( a ), Agarose gel (1.0%), showing requirement of ATP in the rLdACT mediated kDNA decatenation process. ( b ), Graph, showing ATP dependence of rLdACT-mediated kDNA decatenation. ( F ) ( a ), Agarose gel (1.0%), showing rLdACT-mediated decatenation of kDNA in the presence of non-hydrolysable analogs of ATP. ( b ) Graph, showing relative inhibition of rLdACT mediated decatenation of kDNA network in the presence of non-hydrolysable ATP analogs when plotted with the increasing concentration of rLdACT.

    Article Snippet: For Electrophoretic mobility shift assay ( EMSA) on polyacrylamide gel, 100 ng of 30 bp DNA was 5′-end labeled with [γ-32 P] ATP using T4 polynucleotide kinase (NEB).

    Techniques: Agarose Gel Electrophoresis, Marker, Activity Assay, Inhibition, Concentration Assay

    ( A ) Agarose gel, showing supercoiled pBR322 DNA (400 ng) relaxation separately with rLdACT (0.5 1.0 μM) and E. coli Topo I. Image presented is the negative of original gel image. ( B ) Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT in the presence or absence of anti-rLdACT antibodies, showing specificity of nicking activity associated with rLdACT. ( C ) Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT (0.5 1.0 μM) in the presence or absence of DNase-1 and its inhibitor EDTA which further eliminates the possibility of DNA nicking by contaminating nuclease. ( D ): a and b, Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT in the presence of ATP and its non-hydrolysable ATP analogs as indicated on the top of the gel. ( E ) Graph showing the requirement of ATP in its hydrolysable form during rLdACT mediated relaxation of supercoiled pBR322 DNA. ( F ) Agarose gel, showing requirement of rLdACT (0.5 2.0 μM) in its polymeric state for its scDNA-relaxation activity. ( G ) Graph, representing rLdACT (1.0 μM) mediated relaxation of supercoiled pBR322 DNA in the presence of increasing concentration of NaCl, inset shows the relative % inhibition of rLdACT mediated relaxation of supercoiled pBR322 DNA in presence of 50 mM salts having different ionization constant (Ksp) as indicated on the top of the bars. ( H ) Dynamic light scattering measurements of rLdACT (1.0 μM) showing insignificant effect of 0.2 M NaCl on the polymerized state of rLdACT after complete polymerization.

    Journal: Nucleic Acids Research

    Article Title: Leishmania actin binds and nicks kDNA as well as inhibits decatenation activity of type II topoisomerase

    doi: 10.1093/nar/gkq051

    Figure Lengend Snippet: ( A ) Agarose gel, showing supercoiled pBR322 DNA (400 ng) relaxation separately with rLdACT (0.5 1.0 μM) and E. coli Topo I. Image presented is the negative of original gel image. ( B ) Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT in the presence or absence of anti-rLdACT antibodies, showing specificity of nicking activity associated with rLdACT. ( C ) Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT (0.5 1.0 μM) in the presence or absence of DNase-1 and its inhibitor EDTA which further eliminates the possibility of DNA nicking by contaminating nuclease. ( D ): a and b, Agarose gel electrophoresis of supercoiled pBR322 DNA (400 ng) with rLdACT in the presence of ATP and its non-hydrolysable ATP analogs as indicated on the top of the gel. ( E ) Graph showing the requirement of ATP in its hydrolysable form during rLdACT mediated relaxation of supercoiled pBR322 DNA. ( F ) Agarose gel, showing requirement of rLdACT (0.5 2.0 μM) in its polymeric state for its scDNA-relaxation activity. ( G ) Graph, representing rLdACT (1.0 μM) mediated relaxation of supercoiled pBR322 DNA in the presence of increasing concentration of NaCl, inset shows the relative % inhibition of rLdACT mediated relaxation of supercoiled pBR322 DNA in presence of 50 mM salts having different ionization constant (Ksp) as indicated on the top of the bars. ( H ) Dynamic light scattering measurements of rLdACT (1.0 μM) showing insignificant effect of 0.2 M NaCl on the polymerized state of rLdACT after complete polymerization.

    Article Snippet: For Electrophoretic mobility shift assay ( EMSA) on polyacrylamide gel, 100 ng of 30 bp DNA was 5′-end labeled with [γ-32 P] ATP using T4 polynucleotide kinase (NEB).

    Techniques: Agarose Gel Electrophoresis, Activity Assay, Concentration Assay, Inhibition

    Agarose gel electrophoresis of the nPCR products. (1) 100-bp ladder; (2) OP with S. epidermidis DNA; (3) OP with P. mirabilis DNA; (4) IP with S. epidermidis DNA; (5) IP with P. mirabilis DNA; and (6) Negative control

    Journal: Strategies in Trauma and Limb Reconstruction

    Article Title: Titanium Kirschner Wires Resist Biofilms Better Than Stainless Steel and Hydroxyapatite-coated Wires: An In Vitro Study

    doi: 10.5005/jp-journals-10080-1426

    Figure Lengend Snippet: Agarose gel electrophoresis of the nPCR products. (1) 100-bp ladder; (2) OP with S. epidermidis DNA; (3) OP with P. mirabilis DNA; (4) IP with S. epidermidis DNA; (5) IP with P. mirabilis DNA; and (6) Negative control

    Article Snippet: Amplicons of approximately 700 bp [outer primer (OP)] and 300 bp [inner primer (IP)] were expected and compared against a 100-bp ladder (New England Biolabs: Hertfordshire, UK).

    Techniques: Agarose Gel Electrophoresis, Negative Control

    Agarose gel electrophoresis of the nPCR products by species. (1) 100-bp ladder; (2) OP S. epidermidis ; (3) OP S. epidermidis ; (4) OP S. epidermidis ; (5) OP S. aureus ; (6) OP S. aureus ; (7) OP P. mirabilis ; (8) OP P. mirabilis ; (9) OP negative control; (10) IP S. epidermidis ; (11) IP S. epidermidis ; (12) IP S. epidermidis ; (13) IP S. aureus ; (14) IP S. aureus ; (15) IP P. mirabilis ; (16) IP P. mirabilis ; and (17) IP negative control

    Journal: Strategies in Trauma and Limb Reconstruction

    Article Title: Titanium Kirschner Wires Resist Biofilms Better Than Stainless Steel and Hydroxyapatite-coated Wires: An In Vitro Study

    doi: 10.5005/jp-journals-10080-1426

    Figure Lengend Snippet: Agarose gel electrophoresis of the nPCR products by species. (1) 100-bp ladder; (2) OP S. epidermidis ; (3) OP S. epidermidis ; (4) OP S. epidermidis ; (5) OP S. aureus ; (6) OP S. aureus ; (7) OP P. mirabilis ; (8) OP P. mirabilis ; (9) OP negative control; (10) IP S. epidermidis ; (11) IP S. epidermidis ; (12) IP S. epidermidis ; (13) IP S. aureus ; (14) IP S. aureus ; (15) IP P. mirabilis ; (16) IP P. mirabilis ; and (17) IP negative control

    Article Snippet: Amplicons of approximately 700 bp [outer primer (OP)] and 300 bp [inner primer (IP)] were expected and compared against a 100-bp ladder (New England Biolabs: Hertfordshire, UK).

    Techniques: Agarose Gel Electrophoresis, Negative Control

    Detection of UGT3A1 transcripts in a human tissue RNA panel. UGT3A1 RNA was amplified by reverse transcription-PCR over 40 cycles and detected by electrophoresis in a 1.5% agarose gel, stained with ethidium bromide. The 100-bp DNA markers are shown

    Journal: The Journal of Biological Chemistry

    Article Title: Identification of UDP Glycosyltransferase 3A1 as a UDPN-Acetylglucosaminyltransferase *

    doi: 10.1074/jbc.M807961200

    Figure Lengend Snippet: Detection of UGT3A1 transcripts in a human tissue RNA panel. UGT3A1 RNA was amplified by reverse transcription-PCR over 40 cycles and detected by electrophoresis in a 1.5% agarose gel, stained with ethidium bromide. The 100-bp DNA markers are shown

    Article Snippet: At the end of 40 cycles, the integrity of PCR products was assessed by electrophoresis on a 1.5% agarose gel with 100-bp DNA markers (New England Biolabs) as a reference to estimate molecular size.

    Techniques: Amplification, Polymerase Chain Reaction, Electrophoresis, Agarose Gel Electrophoresis, Staining

    Clonogenic survival for (A, B) MDA-MB-468 and (C, D) 231-H2N cells. Cells were incubated with suberoylanilide hydroxamic acid (SAHA) followed by (A, C) IR, (B, D) 111 In-DTPA-hEGF (30 MBq/μg; 100 pM or 0–67 MBq/μg; 12 nM, respectively) or DTPA-hEGF (100 pM or 12 nM). Results are means ± SEM of three experiments or means ± SEM of triplicates in one experiment. Error bars are too small to be seen in (A and D).

    Journal: International journal of radiation oncology, biology, physics

    Article Title: Relationship Between Chromatin Structure and Sensitivity to Molecularly Targeted Auger Electron Radiation Therapy

    doi: 10.1016/j.ijrobp.2011.09.051

    Figure Lengend Snippet: Clonogenic survival for (A, B) MDA-MB-468 and (C, D) 231-H2N cells. Cells were incubated with suberoylanilide hydroxamic acid (SAHA) followed by (A, C) IR, (B, D) 111 In-DTPA-hEGF (30 MBq/μg; 100 pM or 0–67 MBq/μg; 12 nM, respectively) or DTPA-hEGF (100 pM or 12 nM). Results are means ± SEM of three experiments or means ± SEM of triplicates in one experiment. Error bars are too small to be seen in (A and D).

    Article Snippet: DNA was purified, separated alongside a 100-bp marker (New England Biolabs, Hitchin, UK) by electrophoresis in 1.2% agarose gel containing ethidium bromide, and visualized by ultraviolet transillumination.

    Techniques: Multiple Displacement Amplification, Incubation