1 kb ladder  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier
Bioz Manufacturer Symbol New England Biolabs manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 97

    Structured Review

    New England Biolabs 1 kb ladder
    Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a <t>1-kb</t> DNA
    1 Kb Ladder, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/1 kb ladder/product/New England Biolabs
    Average 97 stars, based on 23 article reviews
    Price from $9.99 to $1999.99
    1 kb ladder - by Bioz Stars, 2022-09
    97/100 stars

    Images

    1) Product Images from "Edwardsiellosis Caused by Edwardsiella ictaluri in Laboratory Populations of Zebrafish Danio rerio"

    Article Title: Edwardsiellosis Caused by Edwardsiella ictaluri in Laboratory Populations of Zebrafish Danio rerio

    Journal: Journal of aquatic animal health

    doi: 10.1080/08997659.2013.782226

    Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a 1-kb DNA
    Figure Legend Snippet: Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a 1-kb DNA

    Techniques Used: Plasmid Preparation, Isolation, Agarose Gel Electrophoresis

    2) Product Images from "PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes"

    Article Title: PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-8-135

    1% agarose gel electrophoresis of PCR products . PCR products derived from 24 PLUG primer sets were separated using a 1% agarose gel in TAE buffer. Lane numbers correspond to marker numbers indicated in Table 1. M: 2-Log DNA Ladder (New England BioLabs Inc., Ipswich, MA, USA).
    Figure Legend Snippet: 1% agarose gel electrophoresis of PCR products . PCR products derived from 24 PLUG primer sets were separated using a 1% agarose gel in TAE buffer. Lane numbers correspond to marker numbers indicated in Table 1. M: 2-Log DNA Ladder (New England BioLabs Inc., Ipswich, MA, USA).

    Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Derivative Assay, Marker

    3) Product Images from "Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes"

    Article Title: Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes

    Journal: mSphere

    doi: 10.1128/mSphere.00521-17

    Subcellular localization of PRP1 through endogenous tagging. (A) Schematic representation of generating C-terminal endogenously YFP-tagged gPRP1-YFP parasites by single homologous recombination into the RHΔ ku80 parent line. (B) PCR validation of the gPRP1-YFP genotype using the primer pair shown in panel A. Lane M contains 1-kb DNA ladder (New England Biolabs). (C) Live imaging of gPRP1-YFP parasites under intracellular and extracellular conditions as indicated. PC, phase contrast. (D) Live imaging of gPRP1-YFP parasites cotransfected with markers for the IMC (IMC1-mCherry), rhoptries (TLN1-mCherry), and micronemes (MIC8-mCherry). (E) Representative images of intracellular gPRP1-YFP parasites fixed using either 100% methanol (MetOH) or 4% paraformaldehyde (PFA) stained with anti-PRP1 (αPRP1) and anti-GFP (αGFP) antisera as indicated. Note that PFA fixation destroys the costaining of GFP and PRP1 and thus destroys the PRP1 epitope(s) recognized by the specific antiserum.
    Figure Legend Snippet: Subcellular localization of PRP1 through endogenous tagging. (A) Schematic representation of generating C-terminal endogenously YFP-tagged gPRP1-YFP parasites by single homologous recombination into the RHΔ ku80 parent line. (B) PCR validation of the gPRP1-YFP genotype using the primer pair shown in panel A. Lane M contains 1-kb DNA ladder (New England Biolabs). (C) Live imaging of gPRP1-YFP parasites under intracellular and extracellular conditions as indicated. PC, phase contrast. (D) Live imaging of gPRP1-YFP parasites cotransfected with markers for the IMC (IMC1-mCherry), rhoptries (TLN1-mCherry), and micronemes (MIC8-mCherry). (E) Representative images of intracellular gPRP1-YFP parasites fixed using either 100% methanol (MetOH) or 4% paraformaldehyde (PFA) stained with anti-PRP1 (αPRP1) and anti-GFP (αGFP) antisera as indicated. Note that PFA fixation destroys the costaining of GFP and PRP1 and thus destroys the PRP1 epitope(s) recognized by the specific antiserum.

    Techniques Used: Homologous Recombination, Polymerase Chain Reaction, Imaging, Staining

    4) Product Images from "Functional and Structural Characterization of Novel Type of Linker Connecting Capsid and Nucleocapsid Protein Domains in Murine Leukemia Virus *"

    Article Title: Functional and Structural Characterization of Novel Type of Linker Connecting Capsid and Nucleocapsid Protein Domains in Murine Leukemia Virus *

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M116.746461

    EMSA. The indicated proteins were incubated with a 1-kb DNA ladder, and the sample aliquots were then treated with proteinase K. All the samples were analyzed by agarose gel electrophoresis. Lanes: L : 1-kb DNA ladder; 1 : the tested proteins without the
    Figure Legend Snippet: EMSA. The indicated proteins were incubated with a 1-kb DNA ladder, and the sample aliquots were then treated with proteinase K. All the samples were analyzed by agarose gel electrophoresis. Lanes: L : 1-kb DNA ladder; 1 : the tested proteins without the

    Techniques Used: Incubation, Agarose Gel Electrophoresis

    5) Product Images from "In Situ Transfection by Controlled Release of Lipoplexes using Acoustic Droplet Vaporization"

    Article Title: In Situ Transfection by Controlled Release of Lipoplexes using Acoustic Droplet Vaporization

    Journal: Advanced healthcare materials

    doi: 10.1002/adhm.201600008

    Gel electrophoresis confirming stability of plasmid after ultrasound exposures. Lane 1) pDNA; lane 2) sonicated pDNA; lane 3) lipoplex; lane 4) sonicated lipoplex; lane 5) emulsified lipoplex released by ultrasound (3.5 MHz, mechanical index (MI) = 2.5, 10 Hz pulse repetition frequency (PRF), 30 cycles); lane 6) 1 kb linear DNA ladder marker. The mass of pDNA was equivalent in all lanes.
    Figure Legend Snippet: Gel electrophoresis confirming stability of plasmid after ultrasound exposures. Lane 1) pDNA; lane 2) sonicated pDNA; lane 3) lipoplex; lane 4) sonicated lipoplex; lane 5) emulsified lipoplex released by ultrasound (3.5 MHz, mechanical index (MI) = 2.5, 10 Hz pulse repetition frequency (PRF), 30 cycles); lane 6) 1 kb linear DNA ladder marker. The mass of pDNA was equivalent in all lanes.

    Techniques Used: Nucleic Acid Electrophoresis, Plasmid Preparation, Sonication, Marker

    6) Product Images from "Evolution of the Plant Reproduction Master Regulators LFY and the MADS Transcription Factors: The Role of Protein Structure in the Evolutionary Development of the Flower"

    Article Title: Evolution of the Plant Reproduction Master Regulators LFY and the MADS Transcription Factors: The Role of Protein Structure in the Evolutionary Development of the Flower

    Journal: Frontiers in Plant Science

    doi: 10.3389/fpls.2015.01193

    Electrophoretic mobility shift assay (EMSA) for SEP3 and AG. (A) Comparison of the oligomerisation state of SEP3 wild type, dimerisation and tetramerisation mutants with AG using a 121 bp DNA fragment of the SOC1 promoter comprising two CArG boxes. Lane 1 corresponds to DNA alone, lane 2 SEP3 wild type, lane 3 SEP3 L171A , lane 4 SEP3 L115R , lane 5 SEP3 ΔC truncation mutant, lane 6 AG, lane 7 SEP3 + AG, lane 8 SEP3 L171A + AG, lane 9 SEP3 L115R + AG, lane 10 SEP3 ΔC + AG. Putative tetramer and dimer are indicated by arrows. The truncation mutant in lane 5 likely has one or two dimers bound to DNA as indicated above the bands by a single (one dimer bound) or double (two dimers bound) asterix. A faint highly retarded band corresponding to bound tetramers or tetramer-induced DNA-looping was noted in lanes 7 and 9 and indicated. (B) EMSAs run with either CArG box 1 (left) or CArG box 2 (right) mutated (see Materials and Methods). Proteins are as per (A) . A faint band for SEP3 wild type and SEP3 L171A was noted running as per the tetramer band in (A) , suggesting homotetramer formation on a single CArG box site. All proteins were produced via in vitro transcription translation using equivalent amounts of template DNA and equivolumes of the reaction mixture were added to the final binding reaction. DNA was approximately 5–10 nM and labeled with DY-682 (A) or Cy5 (B) for imaging.
    Figure Legend Snippet: Electrophoretic mobility shift assay (EMSA) for SEP3 and AG. (A) Comparison of the oligomerisation state of SEP3 wild type, dimerisation and tetramerisation mutants with AG using a 121 bp DNA fragment of the SOC1 promoter comprising two CArG boxes. Lane 1 corresponds to DNA alone, lane 2 SEP3 wild type, lane 3 SEP3 L171A , lane 4 SEP3 L115R , lane 5 SEP3 ΔC truncation mutant, lane 6 AG, lane 7 SEP3 + AG, lane 8 SEP3 L171A + AG, lane 9 SEP3 L115R + AG, lane 10 SEP3 ΔC + AG. Putative tetramer and dimer are indicated by arrows. The truncation mutant in lane 5 likely has one or two dimers bound to DNA as indicated above the bands by a single (one dimer bound) or double (two dimers bound) asterix. A faint highly retarded band corresponding to bound tetramers or tetramer-induced DNA-looping was noted in lanes 7 and 9 and indicated. (B) EMSAs run with either CArG box 1 (left) or CArG box 2 (right) mutated (see Materials and Methods). Proteins are as per (A) . A faint band for SEP3 wild type and SEP3 L171A was noted running as per the tetramer band in (A) , suggesting homotetramer formation on a single CArG box site. All proteins were produced via in vitro transcription translation using equivalent amounts of template DNA and equivolumes of the reaction mixture were added to the final binding reaction. DNA was approximately 5–10 nM and labeled with DY-682 (A) or Cy5 (B) for imaging.

    Techniques Used: Electrophoretic Mobility Shift Assay, Mutagenesis, Produced, In Vitro, Binding Assay, Labeling, Imaging

    7) Product Images from "Assessment of corn starch as substitute for agarose in DNA gel electrophoresis"

    Article Title: Assessment of corn starch as substitute for agarose in DNA gel electrophoresis

    Journal: BMC Research Notes

    doi: 10.1186/s13104-021-05483-1

    Migration of loaded DNA ladder (DL) and DNA sample (DS) on corn starch gel. a Shows the loaded samples (DNA + Apex Safe DNA loading dye), and the 1 kb DNA ladder (DL) on the starch gel at the onset. b Shows a migration of samples and DL 10 min after we started running the gel. c Shows migration of samples and DL at 30 min after we started running the gel. d Shows migration of samples and DL at 90 min after we started running the gel
    Figure Legend Snippet: Migration of loaded DNA ladder (DL) and DNA sample (DS) on corn starch gel. a Shows the loaded samples (DNA + Apex Safe DNA loading dye), and the 1 kb DNA ladder (DL) on the starch gel at the onset. b Shows a migration of samples and DL 10 min after we started running the gel. c Shows migration of samples and DL at 30 min after we started running the gel. d Shows migration of samples and DL at 90 min after we started running the gel

    Techniques Used: Migration

    Comparison of gels viewed under blue light. a Corn starch gel viewed under blue light with no bands seen. b Agarose gel viewed under blue light showing DNA bands. The first and the last 2 lanes show the 1 kb DNA ladder whereas the middle samples show the DNA bands around the expected molecular weight of about 300 base pairs
    Figure Legend Snippet: Comparison of gels viewed under blue light. a Corn starch gel viewed under blue light with no bands seen. b Agarose gel viewed under blue light showing DNA bands. The first and the last 2 lanes show the 1 kb DNA ladder whereas the middle samples show the DNA bands around the expected molecular weight of about 300 base pairs

    Techniques Used: Agarose Gel Electrophoresis, Molecular Weight

    8) Product Images from "The distribution of DNA translocation times in solid-state nanopores"

    Article Title: The distribution of DNA translocation times in solid-state nanopores

    Journal: Journal of Physics

    doi: 10.1088/0953-8984/22/45/454129

    (A) Event distribution plot of 3 kbp (L C =1020 nm) DNA translocation as a function of solution viscosity in 1.5 M KCl, pH 7.5, and ψ=120 mV. Insert, left axis: the uncertainty in determine DNA chain length due to random walk ΔL/L DNA ( ); right axis: the relative blockade current ΔI/I 0 (◆). The error bars are smaller than the symbols. (B) The drifting speed, (C) the diffusion constant, and (D) the calculated drag force as a function of viscosity.
    Figure Legend Snippet: (A) Event distribution plot of 3 kbp (L C =1020 nm) DNA translocation as a function of solution viscosity in 1.5 M KCl, pH 7.5, and ψ=120 mV. Insert, left axis: the uncertainty in determine DNA chain length due to random walk ΔL/L DNA ( ); right axis: the relative blockade current ΔI/I 0 (◆). The error bars are smaller than the symbols. (B) The drifting speed, (C) the diffusion constant, and (D) the calculated drag force as a function of viscosity.

    Techniques Used: Translocation Assay, Diffusion-based Assay

    (A) Illustration of linear DNA translocation experiment. (B) Typical 3 kbp DNA translocation events in a 8±2 nm diameter pore in 1.5 MKCl with 30% glycerol at pH 7.5. (C) All events distribution plot of current drop ΔI b vs translocation times t d . (D) Selected linear translocation events plot from the data shown in (C).
    Figure Legend Snippet: (A) Illustration of linear DNA translocation experiment. (B) Typical 3 kbp DNA translocation events in a 8±2 nm diameter pore in 1.5 MKCl with 30% glycerol at pH 7.5. (C) All events distribution plot of current drop ΔI b vs translocation times t d . (D) Selected linear translocation events plot from the data shown in (C).

    Techniques Used: Translocation Assay

    (A) Event distribution plot of 3 kbp DNA translocation as a function of applied voltage. Insert, left axis: the uncertainty in determine DNA chain length due to random walk ΔL/L DNA ( ); right axis: the relative blockade current ΔI/I 0 (◆). The error bars are smaller than the symbols. (B) The drifting speed, (C) the diffusion constant, and (D) the calculated drag force as a function of voltage. The experiment was performed in 1.6 M KCl with 20% glycerol at pH 7.5 in a 8±2 nm silicon nitride pore.
    Figure Legend Snippet: (A) Event distribution plot of 3 kbp DNA translocation as a function of applied voltage. Insert, left axis: the uncertainty in determine DNA chain length due to random walk ΔL/L DNA ( ); right axis: the relative blockade current ΔI/I 0 (◆). The error bars are smaller than the symbols. (B) The drifting speed, (C) the diffusion constant, and (D) the calculated drag force as a function of voltage. The experiment was performed in 1.6 M KCl with 20% glycerol at pH 7.5 in a 8±2 nm silicon nitride pore.

    Techniques Used: Translocation Assay, Diffusion-based Assay

    (A) Event distribution plot of translocation of a DNA ladder (λ cut) that contains a mixture of ~2.17, 4.36, 6.56, 9.42, and 23 kbp DNA. The experiment was performed in 1.0 M KCl with no glycerol. More than 20,000 events are in this event distribution plot. (B) The experiment was performed in 1.6 M KCl with 20% glycerol. Both sets of data were recorded with low pass filter set at 100 kHz. The fitted drifting speed (C) and the diffusion constants (D) as a function of the DNA chain length. All data are measured with 10±2 nm silicon nitride pores and the applied voltage was 120 mV. The error bars for drifting speed in panel C are smaller than the markers for all the data points.
    Figure Legend Snippet: (A) Event distribution plot of translocation of a DNA ladder (λ cut) that contains a mixture of ~2.17, 4.36, 6.56, 9.42, and 23 kbp DNA. The experiment was performed in 1.0 M KCl with no glycerol. More than 20,000 events are in this event distribution plot. (B) The experiment was performed in 1.6 M KCl with 20% glycerol. Both sets of data were recorded with low pass filter set at 100 kHz. The fitted drifting speed (C) and the diffusion constants (D) as a function of the DNA chain length. All data are measured with 10±2 nm silicon nitride pores and the applied voltage was 120 mV. The error bars for drifting speed in panel C are smaller than the markers for all the data points.

    Techniques Used: Translocation Assay, Diffusion-based Assay

    9) Product Images from "Micropropagation, encapsulation, physiological, and genetic homogeneity assessment in Casuarina equisetifolia"

    Article Title: Micropropagation, encapsulation, physiological, and genetic homogeneity assessment in Casuarina equisetifolia

    Journal: Frontiers in Plant Science

    doi: 10.3389/fpls.2022.905444

    DNA profiles of the mother (Lane M) with DNA ladder (lane L) and micropropagated plants (Lanes 1–9). (A) RAPD (OPU-08). (B) ISSR (UBC-812).
    Figure Legend Snippet: DNA profiles of the mother (Lane M) with DNA ladder (lane L) and micropropagated plants (Lanes 1–9). (A) RAPD (OPU-08). (B) ISSR (UBC-812).

    Techniques Used:

    10) Product Images from "Mitochondrial nicotinamide adenine dinucleotide hydride dehydrogenase (NADH) subunit 4 (MTND4) polymorphisms and their association with male infertility"

    Article Title: Mitochondrial nicotinamide adenine dinucleotide hydride dehydrogenase (NADH) subunit 4 (MTND4) polymorphisms and their association with male infertility

    Journal: Journal of Assisted Reproduction and Genetics

    doi: 10.1007/s10815-021-02199-w

    Representative gel electrophoresis on 1% agarose gel of PCR products for the amplification of the MTND4 gene (1432 Bp). Lane M: DNA ladder (100–10,000 bp) (NE Biolabs, USA), lanes 1-18: PCR sample products, lane -ve: negative control. Electrophoresis was carried out at 100 V for 45 min. Gels were stained with red-safe stain and then DNA was visualized by ultra-violet (UV) transilluminator using Image LabTM Software (BIO-RAD, USA)
    Figure Legend Snippet: Representative gel electrophoresis on 1% agarose gel of PCR products for the amplification of the MTND4 gene (1432 Bp). Lane M: DNA ladder (100–10,000 bp) (NE Biolabs, USA), lanes 1-18: PCR sample products, lane -ve: negative control. Electrophoresis was carried out at 100 V for 45 min. Gels were stained with red-safe stain and then DNA was visualized by ultra-violet (UV) transilluminator using Image LabTM Software (BIO-RAD, USA)

    Techniques Used: Nucleic Acid Electrophoresis, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification, Negative Control, Electrophoresis, Staining, Software

    11) Product Images from "Assessment of corn starch as substitute for agarose in DNA gel electrophoresis"

    Article Title: Assessment of corn starch as substitute for agarose in DNA gel electrophoresis

    Journal: BMC Research Notes

    doi: 10.1186/s13104-021-05483-1

    Migration of loaded DNA ladder (DL) and DNA sample (DS) on corn starch gel. a Shows the loaded samples (DNA + Apex Safe DNA loading dye), and the 1 kb DNA ladder (DL) on the starch gel at the onset. b Shows a migration of samples and DL 10 min after we started running the gel. c Shows migration of samples and DL at 30 min after we started running the gel. d Shows migration of samples and DL at 90 min after we started running the gel
    Figure Legend Snippet: Migration of loaded DNA ladder (DL) and DNA sample (DS) on corn starch gel. a Shows the loaded samples (DNA + Apex Safe DNA loading dye), and the 1 kb DNA ladder (DL) on the starch gel at the onset. b Shows a migration of samples and DL 10 min after we started running the gel. c Shows migration of samples and DL at 30 min after we started running the gel. d Shows migration of samples and DL at 90 min after we started running the gel

    Techniques Used: Migration

    Comparison of gels viewed under blue light. a Corn starch gel viewed under blue light with no bands seen. b Agarose gel viewed under blue light showing DNA bands. The first and the last 2 lanes show the 1 kb DNA ladder whereas the middle samples show the DNA bands around the expected molecular weight of about 300 base pairs
    Figure Legend Snippet: Comparison of gels viewed under blue light. a Corn starch gel viewed under blue light with no bands seen. b Agarose gel viewed under blue light showing DNA bands. The first and the last 2 lanes show the 1 kb DNA ladder whereas the middle samples show the DNA bands around the expected molecular weight of about 300 base pairs

    Techniques Used: Agarose Gel Electrophoresis, Molecular Weight

    12) Product Images from "High-Throughput RNA Sequencing of Mosaic Infected and Non-Infected Apple (Malus × domestica Borkh.) Cultivars: From Detection to the Reconstruction of Whole Genome of Viruses and Viroid"

    Article Title: High-Throughput RNA Sequencing of Mosaic Infected and Non-Infected Apple (Malus × domestica Borkh.) Cultivars: From Detection to the Reconstruction of Whole Genome of Viruses and Viroid

    Journal: Plants

    doi: 10.3390/plants11050675

    The PCR products from amplified region of viruses ( a ) ApNMV, ( b ) ApMV, ( c ) ASPV, ( d ) ASGV, ( e ) AHVd, ( f ) ACLSV L-1kb Ladder, OS: Oregon spur, GD: Golden Delicious, RF: Red Fuji.
    Figure Legend Snippet: The PCR products from amplified region of viruses ( a ) ApNMV, ( b ) ApMV, ( c ) ASPV, ( d ) ASGV, ( e ) AHVd, ( f ) ACLSV L-1kb Ladder, OS: Oregon spur, GD: Golden Delicious, RF: Red Fuji.

    Techniques Used: Polymerase Chain Reaction, Amplification

    13) Product Images from "Targeted mutagenesis in a human-parasitic nematode"

    Article Title: Targeted mutagenesis in a human-parasitic nematode

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1006675

    CRISPR-mediated homology-directed repair of Ss-unc-22 . ( A ) Strategy for HDR at Ss-unc-22 target site #2. unc F 1 iL3s that displayed both the nicotine-twitching phenotype and red fluorescence were selected as candidates for HDR and were genotyped using the primer sets indicated. 5’ and 3’ integration primer pairs amplify only following successful integration of Ss-act-2 :: mRFPmars into site #2. HA = homology arm. ( B ) Representative DIC + epifluorescence overlays of unc F 1 iL3s expressing Ss-act-2 :: mRFPmars . Top, iL3 expressing mRFPmars (sparse expression indicated by the arrow) from an extrachromosomal array. Bottom, iL3 expressing mRFPmars following HDR, showing near-uniform mRFPmars expression in the body wall. For both images, anterior is to the left. Scale bar = 50 μm. ( C ) Representative genotypes of a wild-type iL3 and unc F 1 iL3s expressing mRFPmars . Genomic DNA from individual iL3s was split into four reactions: ctrl. = control reaction amplifying 416 bp of the first exon of the Ss-act-2 gene to confirm the presence of genomic DNA; wt = reaction for the wild-type locus of site #2 where primer R1 overlaps the predicted CRISPR cut site; 5’ = reaction for insertion of the 5’ border of the integrated cassette; 3’ = reaction for insertion of the 3’ border of the integrated cassette. For genotypes: array = red unc F 1 iL3s that showed no evidence of integration; integrated = red unc F 1 iL3s with successful HDR. Some integrated iL3s had putative homozygous disruptions of Ss-unc-22 site #2 ( e . g . iL3s #4 and #7, which lacked the wt band). Asterisks indicate genotypes for iL3s shown in B . Size markers = 2 kb, 1.5 kb, 1 kb, and 500 bp from top to bottom.
    Figure Legend Snippet: CRISPR-mediated homology-directed repair of Ss-unc-22 . ( A ) Strategy for HDR at Ss-unc-22 target site #2. unc F 1 iL3s that displayed both the nicotine-twitching phenotype and red fluorescence were selected as candidates for HDR and were genotyped using the primer sets indicated. 5’ and 3’ integration primer pairs amplify only following successful integration of Ss-act-2 :: mRFPmars into site #2. HA = homology arm. ( B ) Representative DIC + epifluorescence overlays of unc F 1 iL3s expressing Ss-act-2 :: mRFPmars . Top, iL3 expressing mRFPmars (sparse expression indicated by the arrow) from an extrachromosomal array. Bottom, iL3 expressing mRFPmars following HDR, showing near-uniform mRFPmars expression in the body wall. For both images, anterior is to the left. Scale bar = 50 μm. ( C ) Representative genotypes of a wild-type iL3 and unc F 1 iL3s expressing mRFPmars . Genomic DNA from individual iL3s was split into four reactions: ctrl. = control reaction amplifying 416 bp of the first exon of the Ss-act-2 gene to confirm the presence of genomic DNA; wt = reaction for the wild-type locus of site #2 where primer R1 overlaps the predicted CRISPR cut site; 5’ = reaction for insertion of the 5’ border of the integrated cassette; 3’ = reaction for insertion of the 3’ border of the integrated cassette. For genotypes: array = red unc F 1 iL3s that showed no evidence of integration; integrated = red unc F 1 iL3s with successful HDR. Some integrated iL3s had putative homozygous disruptions of Ss-unc-22 site #2 ( e . g . iL3s #4 and #7, which lacked the wt band). Asterisks indicate genotypes for iL3s shown in B . Size markers = 2 kb, 1.5 kb, 1 kb, and 500 bp from top to bottom.

    Techniques Used: CRISPR, Fluorescence, Activated Clotting Time Assay, Expressing

    CRISPR-mediated mutagenesis of Ss-unc-22 results in putative deletion of the target locus. ( A ) Representative gel of wild-type iL3s (top) or unc F 1 iL3s from RNP injections at site #3 (bottom). Genomic DNA from each iL3 was split into two reactions: ctrl. = control reaction amplifying 416 bp of the first exon of the Ss-act-2 gene to confirm the presence of genomic DNA; u22 = reaction amplifying 660 bp around site #3. Size markers = 1.5 kb, 1 kb, and 500 bp from top to bottom. ( B ) The Ss-unc-22 region is significantly depleted in unc F 1 iL3s. Left: relative quantity analysis of PCR products. All control bands and all u22 bands were quantified relative to their respective reference bands, denoted by asterisks in A . Values > 1 indicate more PCR product than the reference while values
    Figure Legend Snippet: CRISPR-mediated mutagenesis of Ss-unc-22 results in putative deletion of the target locus. ( A ) Representative gel of wild-type iL3s (top) or unc F 1 iL3s from RNP injections at site #3 (bottom). Genomic DNA from each iL3 was split into two reactions: ctrl. = control reaction amplifying 416 bp of the first exon of the Ss-act-2 gene to confirm the presence of genomic DNA; u22 = reaction amplifying 660 bp around site #3. Size markers = 1.5 kb, 1 kb, and 500 bp from top to bottom. ( B ) The Ss-unc-22 region is significantly depleted in unc F 1 iL3s. Left: relative quantity analysis of PCR products. All control bands and all u22 bands were quantified relative to their respective reference bands, denoted by asterisks in A . Values > 1 indicate more PCR product than the reference while values

    Techniques Used: CRISPR, Mutagenesis, Activated Clotting Time Assay, Polymerase Chain Reaction

    14) Product Images from "Direct observation of single flexible polymers using single stranded DNA"

    Article Title: Direct observation of single flexible polymers using single stranded DNA

    Journal: Soft matter

    doi: 10.1039/C1SM05297G

    Direct visualization of fluorescently labelled ssDNA molecules using fluorescence microscopy. Single molecules of ssDNA and ds-λ-DNA are shown for (a) stretched and (b) coiled configurations. ssDNA (Sequence 1) with variable dye-labelling ratios are imaged.
    Figure Legend Snippet: Direct visualization of fluorescently labelled ssDNA molecules using fluorescence microscopy. Single molecules of ssDNA and ds-λ-DNA are shown for (a) stretched and (b) coiled configurations. ssDNA (Sequence 1) with variable dye-labelling ratios are imaged.

    Techniques Used: Fluorescence, Microscopy, Sequencing

    15) Product Images from "Single Molecule Hydrodynamic Separation Allows Sensitive and Quantitative Analysis of DNA Conformation and Binding Interactions in Free Solution"

    Article Title: Single Molecule Hydrodynamic Separation Allows Sensitive and Quantitative Analysis of DNA Conformation and Binding Interactions in Free Solution

    Journal: Journal of the American Chemical Society

    doi: 10.1021/jacs.5b10983

    The effects of both sodium chloride (blue) and magnesium chloride (red) on the packing density of double stranded and single stranded DNA is probed by comparing their relative mobilities in the same 1.6 μm diameter capillary. (a) HindIII digested
    Figure Legend Snippet: The effects of both sodium chloride (blue) and magnesium chloride (red) on the packing density of double stranded and single stranded DNA is probed by comparing their relative mobilities in the same 1.6 μm diameter capillary. (a) HindIII digested

    Techniques Used:

    16) Product Images from "Is the abundance of Faecalibacterium prausnitzii relevant to Crohn's disease?"

    Article Title: Is the abundance of Faecalibacterium prausnitzii relevant to Crohn's disease?

    Journal: Fems Microbiology Letters

    doi: 10.1111/j.1574-6968.2010.02057.x

    Relative quantity of  Faecalibacterium prausnitzii  in faecal DNA determined by PCR. Agarose gel showing bands of the  F. prausnitzii  amplicon from 22 faecal samples. The upper band of 778 bp corresponds to the M21/2 subgroup; the lower 650 bp band corresponds to the A2-165 subgroup. The same amount of template DNA was added to each PCR reaction, and so these differences indicate the relative amount of  F. prausnitzii  in each patient. Where a PCR product was present, the brightness of the band was measured using the software  quantity one  (Bio-Rad) and converted to DNA amount by reference to a 1 kb ladder (New England Biolabs: right-hand lane).
    Figure Legend Snippet: Relative quantity of Faecalibacterium prausnitzii in faecal DNA determined by PCR. Agarose gel showing bands of the F. prausnitzii amplicon from 22 faecal samples. The upper band of 778 bp corresponds to the M21/2 subgroup; the lower 650 bp band corresponds to the A2-165 subgroup. The same amount of template DNA was added to each PCR reaction, and so these differences indicate the relative amount of F. prausnitzii in each patient. Where a PCR product was present, the brightness of the band was measured using the software quantity one (Bio-Rad) and converted to DNA amount by reference to a 1 kb ladder (New England Biolabs: right-hand lane).

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

    17) Product Images from "Cell Engineering and Cultivation of Chinese Hamster Ovary Cells for the Development of Orthogonal Eukaryotic Cell-free Translation Systems"

    Article Title: Cell Engineering and Cultivation of Chinese Hamster Ovary Cells for the Development of Orthogonal Eukaryotic Cell-free Translation Systems

    Journal: Frontiers in Molecular Biosciences

    doi: 10.3389/fmolb.2022.832379

    Evaluation of clonal cell lines expressing the eAzFRS. (A) Genotyping PCR of clonal cell lines isolated from clone pool gC12-T2-CPB. The expected outcome is indicated by visualize primer binding (arrows) on wilde type (WT) and modified cells. A Quick-Load 2-Log DNA Ladder 0.1–10.0 kb (New England Biolabs) was used. (B) Semi-quantitative western blot of cell clones. eAzFRS band intensities were normalized to the internal β-Actin control. The indicated fold change is expressed as ratio of band intensity of the samples compared to clone pool gC12-T2-CPB. (C) Exemplary fermentation process of clone RS7. Cell harvesting was performed three times at highest peaks (blue line). (D) Luciferase assay of cell-free synthesized A2aR and A2aRamb constructs based on cell lysates prepared from three harvest points of a cultivation process using CHO clone RS7. Experiments were performed in technical triplicates and bars represent the standard deviation.
    Figure Legend Snippet: Evaluation of clonal cell lines expressing the eAzFRS. (A) Genotyping PCR of clonal cell lines isolated from clone pool gC12-T2-CPB. The expected outcome is indicated by visualize primer binding (arrows) on wilde type (WT) and modified cells. A Quick-Load 2-Log DNA Ladder 0.1–10.0 kb (New England Biolabs) was used. (B) Semi-quantitative western blot of cell clones. eAzFRS band intensities were normalized to the internal β-Actin control. The indicated fold change is expressed as ratio of band intensity of the samples compared to clone pool gC12-T2-CPB. (C) Exemplary fermentation process of clone RS7. Cell harvesting was performed three times at highest peaks (blue line). (D) Luciferase assay of cell-free synthesized A2aR and A2aRamb constructs based on cell lysates prepared from three harvest points of a cultivation process using CHO clone RS7. Experiments were performed in technical triplicates and bars represent the standard deviation.

    Techniques Used: Expressing, Genotyping Assay, Polymerase Chain Reaction, Isolation, Binding Assay, Modification, Western Blot, Clone Assay, Cell Harvesting, Luciferase, Synthesized, Construct, Standard Deviation

    18) Product Images from "Ability of Polyphosphate and Nucleic Acids to Trigger Blood Clotting: Some Observations and Caveats"

    Article Title: Ability of Polyphosphate and Nucleic Acids to Trigger Blood Clotting: Some Observations and Caveats

    Journal: Frontiers in Medicine

    doi: 10.3389/fmed.2018.00107

    Traces of polyphosphate (polyP) in cell-derived DNA. DNA isolated from HEK 293 cells using the DNeasy Blood Tissue kit was extensively digested with benzonase to hydrolyze the DNA, concentrated, and then resolved by electrophoresis on a 4–20% polyacrylamide gel. Samples were: a locally prepared polyP ladder (lengths indicated in phosphate units); DNA purified from HEK 293 cells and digested with benzonase (“Pre”); the same material following digestion with calf intestinal alkaline phosphatase (CIAP); and 50 bp DNA ladder. The same gel was stained sequentially, using: (A) DAPI with extended photobleaching to detect polyP ( 27 ) and (B) SYBR Green I to detect DNA (after removing DAPI by repeated rinsing). The material in the lane marked “Pre” is clearly polyP as it photobleached rapidly (A) , was digested by CIAP (A) , and did not stain with SYBR Green 1 (B) .
    Figure Legend Snippet: Traces of polyphosphate (polyP) in cell-derived DNA. DNA isolated from HEK 293 cells using the DNeasy Blood Tissue kit was extensively digested with benzonase to hydrolyze the DNA, concentrated, and then resolved by electrophoresis on a 4–20% polyacrylamide gel. Samples were: a locally prepared polyP ladder (lengths indicated in phosphate units); DNA purified from HEK 293 cells and digested with benzonase (“Pre”); the same material following digestion with calf intestinal alkaline phosphatase (CIAP); and 50 bp DNA ladder. The same gel was stained sequentially, using: (A) DAPI with extended photobleaching to detect polyP ( 27 ) and (B) SYBR Green I to detect DNA (after removing DAPI by repeated rinsing). The material in the lane marked “Pre” is clearly polyP as it photobleached rapidly (A) , was digested by CIAP (A) , and did not stain with SYBR Green 1 (B) .

    Techniques Used: Derivative Assay, Isolation, Electrophoresis, Purification, Staining, SYBR Green Assay

    19) Product Images from "A Lamin-Binding Ligand Inhibits Homologous Recombination Repair of DNA Double-Strand Breaks"

    Article Title: A Lamin-Binding Ligand Inhibits Homologous Recombination Repair of DNA Double-Strand Breaks

    Journal: ACS Central Science

    doi: 10.1021/acscentsci.8b00379

    LBL1 induced DSBs in cancer cells. (A) LBL1 arrested the cells at G2/M phase. The cell cycle distribution of MDA-MB-231 cells treated with different concentrations of LBL1 for 48 h. Then the cell cycle profile was analyzed by flow cytometry after the cells were fixed and stained with PI. (B) LBL1 induced G2/M arrest and G1 peak broadening in MDA-MB-231 cells. The cells were treated with LBL1 for 48 h. The different cell cycle stages (G1, S, G2/M) are indicated. (C) LBL1 did not induce phosphorylation of H2AX in normal primary HFF. The cells were treated with indicated drugs for 24 h. Then the cells were collected, and the lysates were prepared for Western blot analysis with indicated antibodies. CPT was used as a positive control. (D, E) Quantification of γ-H2AX-foci-positive MDA-MB-231 cells. Data are presented as mean ± SD ( n = 3, ∼100 cells were analyzed for each experimental condition). Representative fluorescence micrographs are shown in part D, and quantification is shown in part E. (F) Quantification of tail DNA from the neutral COMET assay in MDA-MB-231 cells treated with LBL1 . Around 200 cells were analyzed for each condition ( n = 193 for DMSO and n = 203 for LBL1 -treated cells). The representative micrographs are shown in Figure S3B .
    Figure Legend Snippet: LBL1 induced DSBs in cancer cells. (A) LBL1 arrested the cells at G2/M phase. The cell cycle distribution of MDA-MB-231 cells treated with different concentrations of LBL1 for 48 h. Then the cell cycle profile was analyzed by flow cytometry after the cells were fixed and stained with PI. (B) LBL1 induced G2/M arrest and G1 peak broadening in MDA-MB-231 cells. The cells were treated with LBL1 for 48 h. The different cell cycle stages (G1, S, G2/M) are indicated. (C) LBL1 did not induce phosphorylation of H2AX in normal primary HFF. The cells were treated with indicated drugs for 24 h. Then the cells were collected, and the lysates were prepared for Western blot analysis with indicated antibodies. CPT was used as a positive control. (D, E) Quantification of γ-H2AX-foci-positive MDA-MB-231 cells. Data are presented as mean ± SD ( n = 3, ∼100 cells were analyzed for each experimental condition). Representative fluorescence micrographs are shown in part D, and quantification is shown in part E. (F) Quantification of tail DNA from the neutral COMET assay in MDA-MB-231 cells treated with LBL1 . Around 200 cells were analyzed for each condition ( n = 193 for DMSO and n = 203 for LBL1 -treated cells). The representative micrographs are shown in Figure S3B .

    Techniques Used: Multiple Displacement Amplification, Flow Cytometry, Staining, Western Blot, Positive Control, Fluorescence, Neutral Comet Assay

    20) Product Images from "Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes"

    Article Title: Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes

    Journal: mSphere

    doi: 10.1128/mSphere.00521-17

    Subcellular localization of PRP1 through endogenous tagging. (A) Schematic representation of generating C-terminal endogenously YFP-tagged gPRP1-YFP parasites by single homologous recombination into the RHΔ ku80 parent line. (B) PCR validation of the gPRP1-YFP genotype using the primer pair shown in panel A. Lane M contains 1-kb DNA ladder (New England Biolabs). (C) Live imaging of gPRP1-YFP parasites under intracellular and extracellular conditions as indicated. PC, phase contrast. (D) Live imaging of gPRP1-YFP parasites cotransfected with markers for the IMC (IMC1-mCherry), rhoptries (TLN1-mCherry), and micronemes (MIC8-mCherry). (E) Representative images of intracellular gPRP1-YFP parasites fixed using either 100% methanol (MetOH) or 4% paraformaldehyde (PFA) stained with anti-PRP1 (αPRP1) and anti-GFP (αGFP) antisera as indicated. Note that PFA fixation destroys the costaining of GFP and PRP1 and thus destroys the PRP1 epitope(s) recognized by the specific antiserum.
    Figure Legend Snippet: Subcellular localization of PRP1 through endogenous tagging. (A) Schematic representation of generating C-terminal endogenously YFP-tagged gPRP1-YFP parasites by single homologous recombination into the RHΔ ku80 parent line. (B) PCR validation of the gPRP1-YFP genotype using the primer pair shown in panel A. Lane M contains 1-kb DNA ladder (New England Biolabs). (C) Live imaging of gPRP1-YFP parasites under intracellular and extracellular conditions as indicated. PC, phase contrast. (D) Live imaging of gPRP1-YFP parasites cotransfected with markers for the IMC (IMC1-mCherry), rhoptries (TLN1-mCherry), and micronemes (MIC8-mCherry). (E) Representative images of intracellular gPRP1-YFP parasites fixed using either 100% methanol (MetOH) or 4% paraformaldehyde (PFA) stained with anti-PRP1 (αPRP1) and anti-GFP (αGFP) antisera as indicated. Note that PFA fixation destroys the costaining of GFP and PRP1 and thus destroys the PRP1 epitope(s) recognized by the specific antiserum.

    Techniques Used: Homologous Recombination, Polymerase Chain Reaction, Imaging, Staining

    21) Product Images from "BRD4 inhibitors block telomere elongation"

    Article Title: BRD4 inhibitors block telomere elongation

    Journal: bioRxiv

    doi: 10.1101/112169

    BRD4 inhibition causes telomere shortening in human and mouse cells in culture (A) Southern blot of telomeric DNA from HeLa cells treated with DMSO (lane 2-5), or 2.5 μ M OTX015 (lane 6-9) for 6 weeks, with samples taken at 2, 4 and 6 weeks of treatment. (B) Southern blot of telomeric DNA from mouse fibroblast cells, which were treated with DMSO (lane 2-5), or 0.5 μ M OTX015 (lane 6-9) for 6 weeks, with samples taken at 2, 4 and 6 weeks of treatment.
    Figure Legend Snippet: BRD4 inhibition causes telomere shortening in human and mouse cells in culture (A) Southern blot of telomeric DNA from HeLa cells treated with DMSO (lane 2-5), or 2.5 μ M OTX015 (lane 6-9) for 6 weeks, with samples taken at 2, 4 and 6 weeks of treatment. (B) Southern blot of telomeric DNA from mouse fibroblast cells, which were treated with DMSO (lane 2-5), or 0.5 μ M OTX015 (lane 6-9) for 6 weeks, with samples taken at 2, 4 and 6 weeks of treatment.

    Techniques Used: Inhibition, Southern Blot

    JQ1 blocks telomere elongation in a dose dependent manner Mouse fibroblasts were transduced with SVA lentivirus, encoding for mTERT and mTR and cultured for six days. (A) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, grown in the presence of DMSO (lane 2-3), 10 μM KU-55933 (lane 4-5) or 0.1 μ M JQ1 (lane 6-7). Lane 1 shows the 2-log ladder marker (NEB) sizes marked are in in kilobases. (B) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, in the presence of DMSO (lane 2-3), 10 μ M KU-55933 (lane 4-5), or decreasing concentrations of 33 nM JQ1 (lane 6-7), 11 nM JQ1 (lane 8-9) or 3.3 nM JQ1 (lane 10-11). Lane 1 shows the 2-log ladder marker (NEB) sizes marked are in in kilobases.
    Figure Legend Snippet: JQ1 blocks telomere elongation in a dose dependent manner Mouse fibroblasts were transduced with SVA lentivirus, encoding for mTERT and mTR and cultured for six days. (A) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, grown in the presence of DMSO (lane 2-3), 10 μM KU-55933 (lane 4-5) or 0.1 μ M JQ1 (lane 6-7). Lane 1 shows the 2-log ladder marker (NEB) sizes marked are in in kilobases. (B) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, in the presence of DMSO (lane 2-3), 10 μ M KU-55933 (lane 4-5), or decreasing concentrations of 33 nM JQ1 (lane 6-7), 11 nM JQ1 (lane 8-9) or 3.3 nM JQ1 (lane 10-11). Lane 1 shows the 2-log ladder marker (NEB) sizes marked are in in kilobases.

    Techniques Used: Transduction, Cell Culture, Southern Blot, Marker

    Three additional BRD4 inhibitors block telomere inhibition in a dose dependent manner Mouse fibroblasts transduced with SVA lentivirus were treated with four different BRD4 inhibitors: JQ1, IBET151, MS436 OTX015. (A) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, grown in the presence of DMSO (lane 2-3), 10 μ M KU-55933 (lane 4-5), 0.1 μ M JQ1 (lane 6-7), 5 μ M MS436 (lane 8-9), 0.5 μ M OTX015 (lane 10-11), or 1 μM IBET151 (lane 12-13). (B) Dose dependence of IBET151. Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, in the presence of 1 μM (lane 2-3), 0.5 μM (lane 4-5), 0.25 (lane 6-7), or 0.125 μ M (lane 8-9) IBET151. (C) Dose dependence of OTX015 and MS436. Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, in the presence of DMSO (lane 2-3), 10 μM KU-55933(lane 4-5), 250 nM (lane 6-7), 125 nM (lane 8-9) or 62.5 nM OTX015 (lane 10-11), 5 μM (lane 12-13), 2.5 μ M (lane 14-15), 1.25 μ M (lane 16-17) or 0.625 μ M (lane 18-19) MS436. Lane 1 in all panels shows the 2-log ladder marker (NEB), sizes marked are in in kilobases. In Panel B, other lanes between the marker and IBET treated lanes were removed.
    Figure Legend Snippet: Three additional BRD4 inhibitors block telomere inhibition in a dose dependent manner Mouse fibroblasts transduced with SVA lentivirus were treated with four different BRD4 inhibitors: JQ1, IBET151, MS436 OTX015. (A) Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, grown in the presence of DMSO (lane 2-3), 10 μ M KU-55933 (lane 4-5), 0.1 μ M JQ1 (lane 6-7), 5 μ M MS436 (lane 8-9), 0.5 μ M OTX015 (lane 10-11), or 1 μM IBET151 (lane 12-13). (B) Dose dependence of IBET151. Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, in the presence of 1 μM (lane 2-3), 0.5 μM (lane 4-5), 0.25 (lane 6-7), or 0.125 μ M (lane 8-9) IBET151. (C) Dose dependence of OTX015 and MS436. Southern blot of mouse fibroblast telomeric DNA, at days 2 and 6 post SVA transduction, in the presence of DMSO (lane 2-3), 10 μM KU-55933(lane 4-5), 250 nM (lane 6-7), 125 nM (lane 8-9) or 62.5 nM OTX015 (lane 10-11), 5 μM (lane 12-13), 2.5 μ M (lane 14-15), 1.25 μ M (lane 16-17) or 0.625 μ M (lane 18-19) MS436. Lane 1 in all panels shows the 2-log ladder marker (NEB), sizes marked are in in kilobases. In Panel B, other lanes between the marker and IBET treated lanes were removed.

    Techniques Used: Blocking Assay, Inhibition, Transduction, Southern Blot, Marker

    22) Product Images from "Cryo-electron tomography reveals the multiplex anatomy of condensed native chromatin and its unfolding by histone citrullination"

    Article Title: Cryo-electron tomography reveals the multiplex anatomy of condensed native chromatin and its unfolding by histone citrullination

    Journal: bioRxiv

    doi: 10.1101/2022.07.11.499179

    Biochemical and TEM characterization of Mg 2+ -dependent secondary and tertiary structures in native human chromatin. (A) Agarose gel shows DNA of native chromatin isolated from K562 cells and fractionated by ultracentrifugation of sucrose gradients (lanes 1-13), DNA size markers (lane 14 (M)), and total soluble chromatin (lane S2). White arrow indicates the chromatin fraction #10 selected for TEM and Cryo-ET imaging. (B) Mg 2+ -induced 50% precipitation points determined for chromatin fractions #10 isolated from two independent batches of K562 cells. (C) DNP agarose gel showing native electrophoresis of the K562 chromatin crosslinked by glutaraldehyde at the indicated concentration of Mg 2+ (lanes 2 – 8). Lane 1 (M): DNA size markers. (D) TEM of the K562 chromatin crosslinked by glutaraldehyde at the indicated concentration of Mg 2+ shows compaction of individual particles at 0.75 mM Mg 2+ and formation of bulky self-associates at 1.25 and 2.0 mM Mg 2+ . Scale bar: 100 nm.
    Figure Legend Snippet: Biochemical and TEM characterization of Mg 2+ -dependent secondary and tertiary structures in native human chromatin. (A) Agarose gel shows DNA of native chromatin isolated from K562 cells and fractionated by ultracentrifugation of sucrose gradients (lanes 1-13), DNA size markers (lane 14 (M)), and total soluble chromatin (lane S2). White arrow indicates the chromatin fraction #10 selected for TEM and Cryo-ET imaging. (B) Mg 2+ -induced 50% precipitation points determined for chromatin fractions #10 isolated from two independent batches of K562 cells. (C) DNP agarose gel showing native electrophoresis of the K562 chromatin crosslinked by glutaraldehyde at the indicated concentration of Mg 2+ (lanes 2 – 8). Lane 1 (M): DNA size markers. (D) TEM of the K562 chromatin crosslinked by glutaraldehyde at the indicated concentration of Mg 2+ shows compaction of individual particles at 0.75 mM Mg 2+ and formation of bulky self-associates at 1.25 and 2.0 mM Mg 2+ . Scale bar: 100 nm.

    Techniques Used: Transmission Electron Microscopy, Agarose Gel Electrophoresis, Isolation, Tomography, Imaging, Electrophoresis, Concentration Assay

    23) Product Images from "Molecular and Phylogenetic analysis revealed new genotypes of Theileria annulata parasites from India"

    Article Title: Molecular and Phylogenetic analysis revealed new genotypes of Theileria annulata parasites from India

    Journal: Parasites & Vectors

    doi: 10.1186/s13071-015-1075-z

    PCR amplification in cattle DNA samples. Agarose gel electrophoresis of amplified DNA from different cattle blood DNA samples by using 18S rRNA. Lanes: 1-Negative control distill water: Lane 2- T. orientalis positive DNA sample; Lane 3 to Lane 8 positive blood DNA samples from cattle; Lane 9–100 base pairs DNA ladder
    Figure Legend Snippet: PCR amplification in cattle DNA samples. Agarose gel electrophoresis of amplified DNA from different cattle blood DNA samples by using 18S rRNA. Lanes: 1-Negative control distill water: Lane 2- T. orientalis positive DNA sample; Lane 3 to Lane 8 positive blood DNA samples from cattle; Lane 9–100 base pairs DNA ladder

    Techniques Used: Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Negative Control

    24) Product Images from "Molecular interactions underlying the phase separation of HP1α: Role of phosphorylation, ligand and nucleic acid binding"

    Article Title: Molecular interactions underlying the phase separation of HP1α: Role of phosphorylation, ligand and nucleic acid binding

    Journal: bioRxiv

    doi: 10.1101/2022.06.20.496886

    LLPS of HP1α with DNA. (a) Density profiles, saturation concentrations (inset) and snapshots of HP1α condensates as a function of the added DNA fraction, as determined in the CG coexistence simulations. (b) Intermolecular contacts between HP1α and DNA within the condensed phase. Preferential interactions between HP1α and DNA are shown in red. (c) Radius of gyration distribution of DNA within HP1α condensates. (d) Fluorescence microscopy images of LLPS of HP1α using 1.5 μM of 205 bp DNA, with and without 75 μM peptide as indicated on top of each column. Imaging was performed with 0.1 μM YOYO-1 dye which binds DNA. The white scale bar at the bottom right of each image represents 50 μm. (e) HP1α concentration in the supernatant after LLPS using a range of starting HP1α concentrations and 1.5 μM of DNA with and without 75 μM of peptide. (f) HP1α concentration in the supernatant after LLPS using 100 μM of HP1α and a range of DNA concentrations, with and without 75 μM peptide. (g) The A260/A280 ratio of the supernatant after LLPS using 100 μM of HP1α and a range of DNA concentrations, with and without 75 μM peptide. (h) HP1α-W174A concentration in the supernatant after LLPS using 100 μM of HP1α-W174A and a range of DNA concentrations, with and without 75 μM peptide. (i) The A260/A280 ratio of the supernatant after LLPS using 100 μM of HP1α-W174A and a range of DNA concentrations, with and without 75 μM peptide.
    Figure Legend Snippet: LLPS of HP1α with DNA. (a) Density profiles, saturation concentrations (inset) and snapshots of HP1α condensates as a function of the added DNA fraction, as determined in the CG coexistence simulations. (b) Intermolecular contacts between HP1α and DNA within the condensed phase. Preferential interactions between HP1α and DNA are shown in red. (c) Radius of gyration distribution of DNA within HP1α condensates. (d) Fluorescence microscopy images of LLPS of HP1α using 1.5 μM of 205 bp DNA, with and without 75 μM peptide as indicated on top of each column. Imaging was performed with 0.1 μM YOYO-1 dye which binds DNA. The white scale bar at the bottom right of each image represents 50 μm. (e) HP1α concentration in the supernatant after LLPS using a range of starting HP1α concentrations and 1.5 μM of DNA with and without 75 μM of peptide. (f) HP1α concentration in the supernatant after LLPS using 100 μM of HP1α and a range of DNA concentrations, with and without 75 μM peptide. (g) The A260/A280 ratio of the supernatant after LLPS using 100 μM of HP1α and a range of DNA concentrations, with and without 75 μM peptide. (h) HP1α-W174A concentration in the supernatant after LLPS using 100 μM of HP1α-W174A and a range of DNA concentrations, with and without 75 μM peptide. (i) The A260/A280 ratio of the supernatant after LLPS using 100 μM of HP1α-W174A and a range of DNA concentrations, with and without 75 μM peptide.

    Techniques Used: Fluorescence, Microscopy, Imaging, Concentration Assay

    A complex network of specific and non-specific interactions controls HP1α LLPS. (a) NTE phosphorylation leads to a compact HP1α conformation under dilute conditions and an extended conformation during LLPS. In both cases, interactions are driven by the phosphorylated NTE and the hinge regions of the protein. (b) The effect of peptides during phosphorylation-driven LLPS of HP1α. Positively charged peptides can promote pHP1α LLPS by neutralizing the negative charge of the droplets (and increasing their density), by non-specific interactions that cross-link pHP1α dimers, and by specific interactions that redistribute the charge patterns on pHP1α. Peptides with low charge, on the other hand, disrupt pHP1α LLPS by adding negative charge to the pHP1α dimer and/or by screening phosphorylated NTE-hinge interactions. (c) The effect of peptides during DNA-driven LLPS of HP1α. Positively charged peptides may disrupt LLPS at low HP1α concentrations by competing for binding sites with DNA. Negatively charged or neutral peptides can disrupt LLPS by screening hinge-DNA interactions.
    Figure Legend Snippet: A complex network of specific and non-specific interactions controls HP1α LLPS. (a) NTE phosphorylation leads to a compact HP1α conformation under dilute conditions and an extended conformation during LLPS. In both cases, interactions are driven by the phosphorylated NTE and the hinge regions of the protein. (b) The effect of peptides during phosphorylation-driven LLPS of HP1α. Positively charged peptides can promote pHP1α LLPS by neutralizing the negative charge of the droplets (and increasing their density), by non-specific interactions that cross-link pHP1α dimers, and by specific interactions that redistribute the charge patterns on pHP1α. Peptides with low charge, on the other hand, disrupt pHP1α LLPS by adding negative charge to the pHP1α dimer and/or by screening phosphorylated NTE-hinge interactions. (c) The effect of peptides during DNA-driven LLPS of HP1α. Positively charged peptides may disrupt LLPS at low HP1α concentrations by competing for binding sites with DNA. Negatively charged or neutral peptides can disrupt LLPS by screening hinge-DNA interactions.

    Techniques Used: Binding Assay

    25) Product Images from "Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase"

    Article Title: Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.00873-15

    Evaluation of editing efficacy and cargo capacity. (A and B) Effect of arm size on editing efficacy. (A) Design of donor templates with various arm sizes (0.1 to 1 kb), in which the target site (red) is modified to contain an EcoRV site (yellow). The all-in-one vectors with these templates introduce EcoRV into the β- gal gene via SNHR. (B) Editing efficacy evaluation by EcoRV digestion of p3/p4 PCR product. The percentage of edited genome in the whole population of control with donor-free vector (CK), recovered cells (T0), and TMP-resistant cells from three serial transfers (T1 to T3) is calculated by densitometry analysis. (C to F) Genetic cargo capacity evaluation by delivering foreign DNA fragments with various sizes into the genome. (C) Design of four donor templates with 0.71-kb Fd:: afp , 1.72-kb promoterless alsS , and 3-kb and 6-kb λ DNA (blue) between 1-kb arms. Using SNHR, the alsS fragment and the remainder are inserted into two different sites, 3198D and pyrF , respectively. (D) PCR identification of Δ pyrF/afp + and alsS + mutants generated by the insertion of Fd:: afp and alsS fragments, using wild type (CK) as a control. Primer pairs are indicated and drawn in panel C. (E) Enrichment of Δ pyrF/afp + mutant in the population during serial transfer (T0 to T3) using wild type (CK) as control. (F) Fluorescence microscopy of plasmid-cured Δ pyrF/afp + mutant.
    Figure Legend Snippet: Evaluation of editing efficacy and cargo capacity. (A and B) Effect of arm size on editing efficacy. (A) Design of donor templates with various arm sizes (0.1 to 1 kb), in which the target site (red) is modified to contain an EcoRV site (yellow). The all-in-one vectors with these templates introduce EcoRV into the β- gal gene via SNHR. (B) Editing efficacy evaluation by EcoRV digestion of p3/p4 PCR product. The percentage of edited genome in the whole population of control with donor-free vector (CK), recovered cells (T0), and TMP-resistant cells from three serial transfers (T1 to T3) is calculated by densitometry analysis. (C to F) Genetic cargo capacity evaluation by delivering foreign DNA fragments with various sizes into the genome. (C) Design of four donor templates with 0.71-kb Fd:: afp , 1.72-kb promoterless alsS , and 3-kb and 6-kb λ DNA (blue) between 1-kb arms. Using SNHR, the alsS fragment and the remainder are inserted into two different sites, 3198D and pyrF , respectively. (D) PCR identification of Δ pyrF/afp + and alsS + mutants generated by the insertion of Fd:: afp and alsS fragments, using wild type (CK) as a control. Primer pairs are indicated and drawn in panel C. (E) Enrichment of Δ pyrF/afp + mutant in the population during serial transfer (T0 to T3) using wild type (CK) as control. (F) Fluorescence microscopy of plasmid-cured Δ pyrF/afp + mutant.

    Techniques Used: Modification, Introduce, Polymerase Chain Reaction, Plasmid Preparation, Generated, Mutagenesis, Fluorescence, Microscopy

    26) Product Images from "Point mutation of the xylose reductase (XR) gene reduces xylitol accumulation and increases citric acid production in Aspergillus carbonarius"

    Article Title: Point mutation of the xylose reductase (XR) gene reduces xylitol accumulation and increases citric acid production in Aspergillus carbonarius

    Journal: Journal of Industrial Microbiology & Biotechnology

    doi: 10.1007/s10295-014-1415-6

    Gel electrophoresis of SQ-PCR reactions. Bands i1 , i2 , i3 represent 6, 2, and 0.2 % of total reaction volume loaded for insert. Bands g1 , g2 , and g3 represent 6, 2 and 0.2 %, respectively, of total reaction volume loaded for genomic fragment. M 1-kb DNA ladder
    Figure Legend Snippet: Gel electrophoresis of SQ-PCR reactions. Bands i1 , i2 , i3 represent 6, 2, and 0.2 % of total reaction volume loaded for insert. Bands g1 , g2 , and g3 represent 6, 2 and 0.2 %, respectively, of total reaction volume loaded for genomic fragment. M 1-kb DNA ladder

    Techniques Used: Nucleic Acid Electrophoresis, Polymerase Chain Reaction

    27) Product Images from "Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA"

    Article Title: Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkv415

    Plasmid cleavage by Pf Ago. ( A ) pWUR790 expression plasmid. ( B ) Pf Ago expressed at 20°C and purified in absence of Mn 2+ cleaves expression plasmid pWUR790. Agarose gels with plasmid targets incubated without protein (lane 1), with Pf AgoDM (lane 2) and with Pf Ago (lane 3). M1: 1-kb DNA ladder (New England Biolabs). M2: pWUR790 marker with open circular (OC), linearized (LIN) and supercoiled (SC) pWUR790. ( C ) pWUR704 target plasmid, target site indicated in gray. ( D ) Target region (gray) and FW and RV siDNA guides (black). Predicted cleavage sites are indicated with a black triangle. ( E ) Agarose gels with plasmid targets incubated with Pf AgoDM (lane 1), with guide free Pf Ago (lane 2) and with Pf Ago loaded with FW siDNA, RV siDNA, or both (lane 3–5) in reaction buffer with 250 mM NaCl (left panel) or 500 mM NaCl (right panel). M1: 1 kb GeneRuler marker (Thermo Scientific). M2: pWUR704 marker with open circular (OC), linearized (LIN) and supercoiled (SC) pWUR704.
    Figure Legend Snippet: Plasmid cleavage by Pf Ago. ( A ) pWUR790 expression plasmid. ( B ) Pf Ago expressed at 20°C and purified in absence of Mn 2+ cleaves expression plasmid pWUR790. Agarose gels with plasmid targets incubated without protein (lane 1), with Pf AgoDM (lane 2) and with Pf Ago (lane 3). M1: 1-kb DNA ladder (New England Biolabs). M2: pWUR790 marker with open circular (OC), linearized (LIN) and supercoiled (SC) pWUR790. ( C ) pWUR704 target plasmid, target site indicated in gray. ( D ) Target region (gray) and FW and RV siDNA guides (black). Predicted cleavage sites are indicated with a black triangle. ( E ) Agarose gels with plasmid targets incubated with Pf AgoDM (lane 1), with guide free Pf Ago (lane 2) and with Pf Ago loaded with FW siDNA, RV siDNA, or both (lane 3–5) in reaction buffer with 250 mM NaCl (left panel) or 500 mM NaCl (right panel). M1: 1 kb GeneRuler marker (Thermo Scientific). M2: pWUR704 marker with open circular (OC), linearized (LIN) and supercoiled (SC) pWUR704.

    Techniques Used: Plasmid Preparation, Expressing, Purification, Incubation, Marker

    28) Product Images from "Generating Transgenic Mice from Bacterial Artificial Chromosomes: Transgenesis Efficiency, Integration and Expression Outcomes"

    Article Title: Generating Transgenic Mice from Bacterial Artificial Chromosomes: Transgenesis Efficiency, Integration and Expression Outcomes

    Journal: Transgenic research

    doi: 10.1007/s11248-009-9271-2

    Pulsed-Field Gel Analysis of BAC DNA. 1a. Analysis of intact circular BAC DNA and sheared BAC DNA. Lane 1: Midrange PFG Marker II (New England Biolabs). Lanes 2, 3, and 4: BAC 2039 (expected size 182kb). Lane 2: Circular BAC DNA: 0.34 ug. Lane 3: Circular BAC DNA: 3.4 ug. Lane 4: Not I cut BAC DNA. Lane 5: deliberately empty. Lanes 6, 7, and 8 contain three fractions from a size exclusion column for BAC 2053. The expected size fragment is 140 kb. All three fractions contain sheared DNA smaller than 97 kb instead of intact linearized BAC DNA. 1b. Comparative analysis of sheared BAC DNA with conventional gel electrophoresis and pulsed-field gel electrophoresis. Lane 1: 2-Log DNA Ladder (New England Biolabs) separation on a conventional 0.8% agarose gel. Lane 2. Sheared BAC DNA runs as a sharp band on a conventional gel. Lane 3. Midrange PFG Marker II (New England Biolabs) separation on a pulsed-field gel. Lane 4. The same sheared BAC DNA that resolves as a sharp band on a conventional gel (Lane 2) appears as a smear upon pulsed-field gel electrophoresis. Arrow indicates expected size of BAC in Lane 4.
    Figure Legend Snippet: Pulsed-Field Gel Analysis of BAC DNA. 1a. Analysis of intact circular BAC DNA and sheared BAC DNA. Lane 1: Midrange PFG Marker II (New England Biolabs). Lanes 2, 3, and 4: BAC 2039 (expected size 182kb). Lane 2: Circular BAC DNA: 0.34 ug. Lane 3: Circular BAC DNA: 3.4 ug. Lane 4: Not I cut BAC DNA. Lane 5: deliberately empty. Lanes 6, 7, and 8 contain three fractions from a size exclusion column for BAC 2053. The expected size fragment is 140 kb. All three fractions contain sheared DNA smaller than 97 kb instead of intact linearized BAC DNA. 1b. Comparative analysis of sheared BAC DNA with conventional gel electrophoresis and pulsed-field gel electrophoresis. Lane 1: 2-Log DNA Ladder (New England Biolabs) separation on a conventional 0.8% agarose gel. Lane 2. Sheared BAC DNA runs as a sharp band on a conventional gel. Lane 3. Midrange PFG Marker II (New England Biolabs) separation on a pulsed-field gel. Lane 4. The same sheared BAC DNA that resolves as a sharp band on a conventional gel (Lane 2) appears as a smear upon pulsed-field gel electrophoresis. Arrow indicates expected size of BAC in Lane 4.

    Techniques Used: Pulsed-Field Gel, BAC Assay, Marker, Nucleic Acid Electrophoresis, Electrophoresis, Agarose Gel Electrophoresis

    29) Product Images from "Isolation of a Novel Bacteriophage Specific for the Periodontal Pathogen Fusobacterium nucleatum ▿"

    Article Title: Isolation of a Novel Bacteriophage Specific for the Periodontal Pathogen Fusobacterium nucleatum ▿

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.01135-10

    Restriction digest patterns electrophoresed on a 1.5% agarose gel and stained with ethidium bromide. (A) FnpΦ02 genomic DNA digested with restriction enzymes. Lanes: L1, 100-bp DNA ladder marker (Fermentas Inc., Canada); L2, 1-kb ladder marker (Fermentas Inc., Canada); L3, undigested DNA; L4, DNA/HindIII; L5, DNA/DraI; L6, DNA/XbaI; and L7, lambda DNA/HindIII. (B) Higher magnification of the bands of the digestion of FnpΦ02 with HindIII used for genome size determination. Selected sizes of the marker are indicated in panel A.
    Figure Legend Snippet: Restriction digest patterns electrophoresed on a 1.5% agarose gel and stained with ethidium bromide. (A) FnpΦ02 genomic DNA digested with restriction enzymes. Lanes: L1, 100-bp DNA ladder marker (Fermentas Inc., Canada); L2, 1-kb ladder marker (Fermentas Inc., Canada); L3, undigested DNA; L4, DNA/HindIII; L5, DNA/DraI; L6, DNA/XbaI; and L7, lambda DNA/HindIII. (B) Higher magnification of the bands of the digestion of FnpΦ02 with HindIII used for genome size determination. Selected sizes of the marker are indicated in panel A.

    Techniques Used: Agarose Gel Electrophoresis, Staining, Marker, Lambda DNA Preparation

    30) Product Images from "Using weapons instead of perfume – chemical association strategies of the myrmecophilous bug Scolopostethus pacificus (Rhyparochromidae)"

    Article Title: Using weapons instead of perfume – chemical association strategies of the myrmecophilous bug Scolopostethus pacificus (Rhyparochromidae)

    Journal: bioRxiv

    doi: 10.1101/2020.12.08.412577

    (A) Molecular gut content analysis of Scolopostethus pacificus . Standard ITS2 primers (CAS5ps+CAS28s) amplified the 563bp long bug ITS2, but no ITS amplification was detected with ant-specific Loc1 and Loc2 primers. (B) As a positive control the ant-specific primers Loc1 (167 bp) and Loc2 (228 bp) were amplified with ant DNA. To demonstrate that Loc1 and Loc2 can amplify ant DNA from a predator which recently consumed ants, I dissected guts of Platyusa sonomea rove beetles, that had preyed on ants. For all give rove beetle samples, Loc1 and Loc2 amplified and their identities were confirmed with Sanger sequencing. The ladder shown on the left (A+B) is the 1 kb DNA Ladder from New England Biolabs.
    Figure Legend Snippet: (A) Molecular gut content analysis of Scolopostethus pacificus . Standard ITS2 primers (CAS5ps+CAS28s) amplified the 563bp long bug ITS2, but no ITS amplification was detected with ant-specific Loc1 and Loc2 primers. (B) As a positive control the ant-specific primers Loc1 (167 bp) and Loc2 (228 bp) were amplified with ant DNA. To demonstrate that Loc1 and Loc2 can amplify ant DNA from a predator which recently consumed ants, I dissected guts of Platyusa sonomea rove beetles, that had preyed on ants. For all give rove beetle samples, Loc1 and Loc2 amplified and their identities were confirmed with Sanger sequencing. The ladder shown on the left (A+B) is the 1 kb DNA Ladder from New England Biolabs.

    Techniques Used: Amplification, Positive Control, Sequencing

    31) Product Images from "Escalating Association of Vibrio cholerae O139 with Cholera Outbreaks in India"

    Article Title: Escalating Association of Vibrio cholerae O139 with Cholera Outbreaks in India

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.40.7.2635-2637.2002

    RAPD profiles of outbreak strains using primer 1281. (a) Lanes 1 and 11, 1-kb ladder; lanes 2 and 3, Orissa, 1999; lanes 4 and 5, Ahmedabad, 2000; lanes 6 and 7, Karnataka, 2000; lanes 8, 9, and 10, Hyderabad, 2000. (b) Lanes 1 and 11, 1-kb ladder; lane 2, O139 reference strain ATCC 51394 (originally designated MO45); lanes 3, 4, 5, and 6, Orissa, 2000; lanes 7, 8, 9, and 10, Calcutta, 2000.
    Figure Legend Snippet: RAPD profiles of outbreak strains using primer 1281. (a) Lanes 1 and 11, 1-kb ladder; lanes 2 and 3, Orissa, 1999; lanes 4 and 5, Ahmedabad, 2000; lanes 6 and 7, Karnataka, 2000; lanes 8, 9, and 10, Hyderabad, 2000. (b) Lanes 1 and 11, 1-kb ladder; lane 2, O139 reference strain ATCC 51394 (originally designated MO45); lanes 3, 4, 5, and 6, Orissa, 2000; lanes 7, 8, 9, and 10, Calcutta, 2000.

    Techniques Used:

    32) Product Images from "Engineering BioBrick vectors from BioBrick parts"

    Article Title: Engineering BioBrick vectors from BioBrick parts

    Journal: Journal of Biological Engineering

    doi: 10.1186/1754-1611-2-5

    Using the new BioBrick vectors . To verify the function of the new BioBrick vectors, we performed a colony PCR using primers that anneal to the verification primer binding sites. To check the length of the resulting PCR products, we electrophoresed the reactions through an 0.8% agarose gel. Lanes 1–8 are the PCR products resulting from the amplification of the following BioBrick parts cloned into new BioBrick vectors. The desired PCR product lengths are in parentheses. Lane 1 is pSB4A5-I52001 (1370 bp), lane 2 is pSB4K5-T9003 (1883 bp), lane 3 is pSB4C5-E0435 (814 bp), lane 4 is pSB4T5-P20061 (2988 bp), lane 5 is pSB3K5-I52002 (1370 bp), lane 6 is pSB3C5-I52001 (1370 bp), lane 7 is pSB3T5-I6413 (867 bp), and lane 8 is BBa_I51020 (1370 bp). Lane 9 is 1 μ g of 2-log DNA ladder (New England Biolabs, Inc.). The 0.5 kb, 1 kb, and 3 kb DNA fragments in the DNA ladder are annotated.
    Figure Legend Snippet: Using the new BioBrick vectors . To verify the function of the new BioBrick vectors, we performed a colony PCR using primers that anneal to the verification primer binding sites. To check the length of the resulting PCR products, we electrophoresed the reactions through an 0.8% agarose gel. Lanes 1–8 are the PCR products resulting from the amplification of the following BioBrick parts cloned into new BioBrick vectors. The desired PCR product lengths are in parentheses. Lane 1 is pSB4A5-I52001 (1370 bp), lane 2 is pSB4K5-T9003 (1883 bp), lane 3 is pSB4C5-E0435 (814 bp), lane 4 is pSB4T5-P20061 (2988 bp), lane 5 is pSB3K5-I52002 (1370 bp), lane 6 is pSB3C5-I52001 (1370 bp), lane 7 is pSB3T5-I6413 (867 bp), and lane 8 is BBa_I51020 (1370 bp). Lane 9 is 1 μ g of 2-log DNA ladder (New England Biolabs, Inc.). The 0.5 kb, 1 kb, and 3 kb DNA fragments in the DNA ladder are annotated.

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

    33) Product Images from "Pharmacological Activation of cGAS for Cancer Immunotherapy"

    Article Title: Pharmacological Activation of cGAS for Cancer Immunotherapy

    Journal: Frontiers in Immunology

    doi: 10.3389/fimmu.2021.753472

    Engineering DNA/Polymer Nanoparticles for Intracellular Activation of cGAS. (A) Agarose gel image. DNA Ladder refers to the TrackIt™ 1 Kb Plus DNA Ladder, and Free DNA refers to uncomplexed phosphorothioate-capped 95-BP dsDNA. Lanes comprise 1 µg DNA mixed with the indicated amount of D-PDB. (B) DLS analysis of phosphorothioate-capped 95-BP dsDNA/D-PDB complexes at varying N/P charge ratios. Frequency indicates the number-based particle size distribution. Hydrodynamic size indicates the particle diameter in nm. (C) RAW-Dual reporter cell assay of phosphorothioate-capped 95-BP dsDNA/D-PDB complexes at varying N/P charge ratios. (D) RAW-Dual reporter cell assay of synthetic, variable-length ISD library complexed to D-PDB at an N/P charge ratio of 4, and indicated experimental controls were used. (E) THP1-Dual reporter cell assay of synthetic, variable-length ISD library complexed to D-PDB at an N/P charge ratio of 4, and indicated experimental controls were used. (F) A549-Dual reporter cell assay of synthetic, variable-length ISD library complexed to D-PDB at an N/P charge ratio of 4, and indicated experimental controls were used. (G) Dose response of the cGAS inhibitor, RU.521 in RAW-Dual reporter cells. After a 4 hour incubation with RU.521, cells were treated with 25 nM phosphorothioate-capped 95-BP dsDNA complexed to D-PDB at an N/P charge ratio of 4. (H) RAW-Lucia ISG-KO-cGAS reporter cell assay of synthetic, variable-length ISD library complexed to D-PDB at an N/P charge ratio of 4, and indicated experimental controls were used. The dose response curves for free D-PDB are positioned along the x-axis in terms of the molar amount of polymer chains rather than molar amount of loaded dsDNA, and each dose response that utilized the polymer was administered using equivalent D-PDB concentrations.
    Figure Legend Snippet: Engineering DNA/Polymer Nanoparticles for Intracellular Activation of cGAS. (A) Agarose gel image. DNA Ladder refers to the TrackIt™ 1 Kb Plus DNA Ladder, and Free DNA refers to uncomplexed phosphorothioate-capped 95-BP dsDNA. Lanes comprise 1 µg DNA mixed with the indicated amount of D-PDB. (B) DLS analysis of phosphorothioate-capped 95-BP dsDNA/D-PDB complexes at varying N/P charge ratios. Frequency indicates the number-based particle size distribution. Hydrodynamic size indicates the particle diameter in nm. (C) RAW-Dual reporter cell assay of phosphorothioate-capped 95-BP dsDNA/D-PDB complexes at varying N/P charge ratios. (D) RAW-Dual reporter cell assay of synthetic, variable-length ISD library complexed to D-PDB at an N/P charge ratio of 4, and indicated experimental controls were used. (E) THP1-Dual reporter cell assay of synthetic, variable-length ISD library complexed to D-PDB at an N/P charge ratio of 4, and indicated experimental controls were used. (F) A549-Dual reporter cell assay of synthetic, variable-length ISD library complexed to D-PDB at an N/P charge ratio of 4, and indicated experimental controls were used. (G) Dose response of the cGAS inhibitor, RU.521 in RAW-Dual reporter cells. After a 4 hour incubation with RU.521, cells were treated with 25 nM phosphorothioate-capped 95-BP dsDNA complexed to D-PDB at an N/P charge ratio of 4. (H) RAW-Lucia ISG-KO-cGAS reporter cell assay of synthetic, variable-length ISD library complexed to D-PDB at an N/P charge ratio of 4, and indicated experimental controls were used. The dose response curves for free D-PDB are positioned along the x-axis in terms of the molar amount of polymer chains rather than molar amount of loaded dsDNA, and each dose response that utilized the polymer was administered using equivalent D-PDB concentrations.

    Techniques Used: Activation Assay, Agarose Gel Electrophoresis, Incubation

    34) Product Images from "Reconstituting the 4-Strand DNA Strand Exchange"

    Article Title: Reconstituting the 4-Strand DNA Strand Exchange

    Journal: Methods in enzymology

    doi: 10.1016/bs.mie.2017.11.013

    Analysis of the DNA substrates, intermediates, and gapped DNA product by electrophoresis in a 1.4% agarose gel. Lane 1: 1-kb DNA ladder. Lane 2, 3, and 5: purified circular ssDNA pBS II SK (+) (100 ng), 2065 bp dsDNA (125 ng), and gapped DNA (125 ng), respectively. Lane 4: DNA products of the annealing reaction (415 ng).
    Figure Legend Snippet: Analysis of the DNA substrates, intermediates, and gapped DNA product by electrophoresis in a 1.4% agarose gel. Lane 1: 1-kb DNA ladder. Lane 2, 3, and 5: purified circular ssDNA pBS II SK (+) (100 ng), 2065 bp dsDNA (125 ng), and gapped DNA (125 ng), respectively. Lane 4: DNA products of the annealing reaction (415 ng).

    Techniques Used: Electrophoresis, Agarose Gel Electrophoresis, Purification

    35) Product Images from "Immortalization of Salivary Gland Epithelial Cells of Xerostomic Patients: Establishment and Characterization of Novel Cell Lines"

    Article Title: Immortalization of Salivary Gland Epithelial Cells of Xerostomic Patients: Establishment and Characterization of Novel Cell Lines

    Journal: Journal of Clinical Medicine

    doi: 10.3390/jcm9123820

    Immunofluorescence detection of salivary epithelium markers in matrigel cultured iSGEC-nSS2 cells. Legend. Detection of salivary epithelium markers ( red ) by immunofluorescence in matrigel cultures of iSGEC-nSS2 p-80 after 7 days. Spheroids expressed acinar cell markers (AQP5, AMY1A), tight-junction protein (ZO-1), and had clearly defined myoepithelial cells (α-SMA). Cells growing on the surface of the matrigel and spheroids expressed salivary epithelial markers KRT8, KRT18, and KRT19 proteins. Vimentin was expressed low and sparsely among cells and did not indicate regular staining patters. Scale bar represents 50 µm. DNA ( blue ) is highlighted with DAPI.
    Figure Legend Snippet: Immunofluorescence detection of salivary epithelium markers in matrigel cultured iSGEC-nSS2 cells. Legend. Detection of salivary epithelium markers ( red ) by immunofluorescence in matrigel cultures of iSGEC-nSS2 p-80 after 7 days. Spheroids expressed acinar cell markers (AQP5, AMY1A), tight-junction protein (ZO-1), and had clearly defined myoepithelial cells (α-SMA). Cells growing on the surface of the matrigel and spheroids expressed salivary epithelial markers KRT8, KRT18, and KRT19 proteins. Vimentin was expressed low and sparsely among cells and did not indicate regular staining patters. Scale bar represents 50 µm. DNA ( blue ) is highlighted with DAPI.

    Techniques Used: Immunofluorescence, Cell Culture, Staining

    36) Product Images from "High throughput single cell sequencing of both T-cell-receptor-beta alleles"

    Article Title: High throughput single cell sequencing of both T-cell-receptor-beta alleles

    Journal: bioRxiv

    doi: 10.1101/320614

    ( a ) Full list of cluster tags (PCR products). PCR fragments amplified using Dβ forward (D1 or D2) and Jβ reverse (J1 or J2) nested primers include both germline configuration (germ) and rearranged DNA (x). PCR fragments amplified using Vβ forward (V) and Jβ reverse (J1 or J2) nested primers encode either productive (p, green) or unproductive (u, red) TCRβ protein. ( b ) Full list of Trb gene status and patterns. Status of an allele are shown with possible combination of 1-2 PCR fragments. GL: germline configuration (patter g). DJ: D-to-J rearranged (pattern d). uVDJ: V-to-DJ rearranged DNA encoding unproductive TCRβ (pattern u). pVDJ: V-to-DJ rearranged DNA encoding productive TCRβ (pattern p). Rearrangement with Trbv31 region (V31) increases the complexity. Full list of possible combination of PCR fragment tags per cell is found in tag_status.csv file in code.zip file. Combination of 2-4 tags used to identify allele status of each cell.
    Figure Legend Snippet: ( a ) Full list of cluster tags (PCR products). PCR fragments amplified using Dβ forward (D1 or D2) and Jβ reverse (J1 or J2) nested primers include both germline configuration (germ) and rearranged DNA (x). PCR fragments amplified using Vβ forward (V) and Jβ reverse (J1 or J2) nested primers encode either productive (p, green) or unproductive (u, red) TCRβ protein. ( b ) Full list of Trb gene status and patterns. Status of an allele are shown with possible combination of 1-2 PCR fragments. GL: germline configuration (patter g). DJ: D-to-J rearranged (pattern d). uVDJ: V-to-DJ rearranged DNA encoding unproductive TCRβ (pattern u). pVDJ: V-to-DJ rearranged DNA encoding productive TCRβ (pattern p). Rearrangement with Trbv31 region (V31) increases the complexity. Full list of possible combination of PCR fragment tags per cell is found in tag_status.csv file in code.zip file. Combination of 2-4 tags used to identify allele status of each cell.

    Techniques Used: Polymerase Chain Reaction, Amplification

    High-throughput Trb genomic DNA sequencing from single-cells. ( a ) Strategy for multiplex PCR amplification of genomic DNA sequences at the Trb gene VDJ loci from single cells. Final PCR products were mixed and then sequenced by PacBio RS II sequencer. V β n: V region primers. D β n: D region primers. J β n: J region primers. AF: adapter forward. AR: adapter reverse. BC: barcode. Details are described in Methods. ( b ) Schematic presentation of VDJ rearrangement at the Trb locus with simplified illustration of multiplex primer location. Genomic DNA recombination events are initiated by recombining D β (diversity) and J β (joining) segments on both chromosomes. Subsequently, on only one chromosome, one of the V β (variable) segments is joined to the previously rearranged DJ recombinant. Not only the selection of each VDJ segment, but also multiple lengths of spacer sequence between V, D and J, generates an incalculable number of VDJ sequence possibilities. mRNA splicing joins C β (constant) segments to the rearranged VDJ DNA recombinants to generate a final TCR β protein. VDJ rearrangement that generates a stop codon or elongated transcript results in a predictedly unproductive TCR β . ( c ) Successful amplification of rearranged VDJ, DJ and germline D-to-J regions were confirmed by agarose gel electrophoresis with NEB 2-log DNA ladder in the last (left panel) and first (right panel) lanes.
    Figure Legend Snippet: High-throughput Trb genomic DNA sequencing from single-cells. ( a ) Strategy for multiplex PCR amplification of genomic DNA sequences at the Trb gene VDJ loci from single cells. Final PCR products were mixed and then sequenced by PacBio RS II sequencer. V β n: V region primers. D β n: D region primers. J β n: J region primers. AF: adapter forward. AR: adapter reverse. BC: barcode. Details are described in Methods. ( b ) Schematic presentation of VDJ rearrangement at the Trb locus with simplified illustration of multiplex primer location. Genomic DNA recombination events are initiated by recombining D β (diversity) and J β (joining) segments on both chromosomes. Subsequently, on only one chromosome, one of the V β (variable) segments is joined to the previously rearranged DJ recombinant. Not only the selection of each VDJ segment, but also multiple lengths of spacer sequence between V, D and J, generates an incalculable number of VDJ sequence possibilities. mRNA splicing joins C β (constant) segments to the rearranged VDJ DNA recombinants to generate a final TCR β protein. VDJ rearrangement that generates a stop codon or elongated transcript results in a predictedly unproductive TCR β . ( c ) Successful amplification of rearranged VDJ, DJ and germline D-to-J regions were confirmed by agarose gel electrophoresis with NEB 2-log DNA ladder in the last (left panel) and first (right panel) lanes.

    Techniques Used: High Throughput Screening Assay, DNA Sequencing, Multiplex Assay, Polymerase Chain Reaction, Amplification, Recombinant, Selection, Sequencing, Agarose Gel Electrophoresis

    37) Product Images from "Genotoxicity Evaluation of Metformin in Freshwater Planarian Dugesia japonica by the Comet Assay and RAPD Analysis"

    Article Title: Genotoxicity Evaluation of Metformin in Freshwater Planarian Dugesia japonica by the Comet Assay and RAPD Analysis

    Journal: BioMed Research International

    doi: 10.1155/2022/2822605

    Genomic DNAs and RAPD profiles of planarian D. japonica . (a, b) The quality of genomic DNAs isolated from D. japonica treated with 10 mmol/L (a) and 50 mmol/L (b) metformin for 1, 3, and 5 days. M is the 1 kb DNA ladder (10,000, 8000, 6000, 5000, 4000, 3000, 2000, 1500, 1000, and 500 bp from top to bottom). CK is control. (c) Reproducibility of RAPD profiles generated from planarian genomic DNA by primer S75. M is the DL2000 DNA marker (2000, 1000, 750, 500, 250, and 100 bp from top to bottom). (d–f) RAPD profiles of genomic DNAs from D. japonica treated with metformin using primers S64, S84, and S5. 0 is control; 1 and 2 represent 10 mmol/L and 50 mmol/L; a, b, and c represent 1, 3, and 5 days, respectively; M is the DL2000 DNA marker.
    Figure Legend Snippet: Genomic DNAs and RAPD profiles of planarian D. japonica . (a, b) The quality of genomic DNAs isolated from D. japonica treated with 10 mmol/L (a) and 50 mmol/L (b) metformin for 1, 3, and 5 days. M is the 1 kb DNA ladder (10,000, 8000, 6000, 5000, 4000, 3000, 2000, 1500, 1000, and 500 bp from top to bottom). CK is control. (c) Reproducibility of RAPD profiles generated from planarian genomic DNA by primer S75. M is the DL2000 DNA marker (2000, 1000, 750, 500, 250, and 100 bp from top to bottom). (d–f) RAPD profiles of genomic DNAs from D. japonica treated with metformin using primers S64, S84, and S5. 0 is control; 1 and 2 represent 10 mmol/L and 50 mmol/L; a, b, and c represent 1, 3, and 5 days, respectively; M is the DL2000 DNA marker.

    Techniques Used: Isolation, Generated, Marker

    38) Product Images from "An Optimized Protocol for ChIP-Seq from Human Embryonic Stem Cell Cultures"

    Article Title: An Optimized Protocol for ChIP-Seq from Human Embryonic Stem Cell Cultures

    Journal: Star Protocols

    doi: 10.1016/j.xpro.2020.100062

    An Example of a Sonication Optimization Experiment, Where Fixed H1 hESCs Were Sheared Using a Bioruptor Plus Sonication System for the Indicated Number of Cycles of 30 s ON/30 s OFF Sheared DNA was then purified and separated on a 1.8% Agarose Gel. 10 was determined to be the minimum number of cycles required to shear the majority of chromatin into the 100 bp to 500 bp range.
    Figure Legend Snippet: An Example of a Sonication Optimization Experiment, Where Fixed H1 hESCs Were Sheared Using a Bioruptor Plus Sonication System for the Indicated Number of Cycles of 30 s ON/30 s OFF Sheared DNA was then purified and separated on a 1.8% Agarose Gel. 10 was determined to be the minimum number of cycles required to shear the majority of chromatin into the 100 bp to 500 bp range.

    Techniques Used: Sonication, Purification, Agarose Gel Electrophoresis

    Example Sonicated Chromatin (Input Samples) from H1 hESC Cultured in mTeSR1 on Matrigel, Separated on an Agilent Tapestation System with a High Sensitivity D1000 ScreenTape Both the pseudo-gel image (A) and the plot of signal intensity vs predicted fragment size (B) show that the majority of the DNA lies in the 100 bp to 500 bp range, with an intensity peak at 260 bp and an average size of 352 bp for signal over the 50–1,000 bp range. Upper (1,500 bp) and Lower (25 bp) size markers are indicated.
    Figure Legend Snippet: Example Sonicated Chromatin (Input Samples) from H1 hESC Cultured in mTeSR1 on Matrigel, Separated on an Agilent Tapestation System with a High Sensitivity D1000 ScreenTape Both the pseudo-gel image (A) and the plot of signal intensity vs predicted fragment size (B) show that the majority of the DNA lies in the 100 bp to 500 bp range, with an intensity peak at 260 bp and an average size of 352 bp for signal over the 50–1,000 bp range. Upper (1,500 bp) and Lower (25 bp) size markers are indicated.

    Techniques Used: Sonication, Cell Culture

    39) Product Images from "The Myb/SANT domain of the telomere-binding protein TRF2 alters chromatin structure"

    Article Title: The Myb/SANT domain of the telomere-binding protein TRF2 alters chromatin structure

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp515

    Analysis of nucleosomal array fibers. The pRST5 plasmid and expected fragments created by PvuII or SfaNI digestion ( A ). Micrococcal nuclease digestion at indicated time points of nucleosomal arrays reconstituted onto PvuII ( B ); SfaNI ( C ) digested pRST5 DNA. Multi-gels of telomeric nucleosomal array fibers (NA) and histone-free DNA (DNA) from pRST5 digested with PvuII ( D ); and SfaNI ( E ) prepared and subjected to electrophoresis according to ‘Materials and Methods’ section. Spheres refer to carboxylate-coated microsphere standards (35 nm radius). The ‘1 kb tel’ and ‘2 kb tel’ refer to the telomeric fragments liberated by PvuII and SfaNI digestion respectively. ‘N’ refers to the fragments without telomeric DNA. Logarithmic plot of pore sizes ( P e ) versus agarose% ( F ). Data was obtained from multi-gels run with bacteriophage T3 (Phage) in this laboratory or previous work [Phage, previous, (  24 )] and 35 nm carboxylate-coated microspheres (Microspheres).  P e  for each agarose concentration was calculated according to ‘Materials and Methods’. Symbols with error bars represent the mean ± 1 SD of four to eight determinations.
    Figure Legend Snippet: Analysis of nucleosomal array fibers. The pRST5 plasmid and expected fragments created by PvuII or SfaNI digestion ( A ). Micrococcal nuclease digestion at indicated time points of nucleosomal arrays reconstituted onto PvuII ( B ); SfaNI ( C ) digested pRST5 DNA. Multi-gels of telomeric nucleosomal array fibers (NA) and histone-free DNA (DNA) from pRST5 digested with PvuII ( D ); and SfaNI ( E ) prepared and subjected to electrophoresis according to ‘Materials and Methods’ section. Spheres refer to carboxylate-coated microsphere standards (35 nm radius). The ‘1 kb tel’ and ‘2 kb tel’ refer to the telomeric fragments liberated by PvuII and SfaNI digestion respectively. ‘N’ refers to the fragments without telomeric DNA. Logarithmic plot of pore sizes ( P e ) versus agarose% ( F ). Data was obtained from multi-gels run with bacteriophage T3 (Phage) in this laboratory or previous work [Phage, previous, ( 24 )] and 35 nm carboxylate-coated microspheres (Microspheres). P e for each agarose concentration was calculated according to ‘Materials and Methods’. Symbols with error bars represent the mean ± 1 SD of four to eight determinations.

    Techniques Used: Plasmid Preparation, Electrophoresis, Concentration Assay

    TRF2 DBD binds specifically to telomeric DNA and nucleosomal arrays. 0.6% agarose gels of TRF2 DBD binding to DNA (DNA) ( A ) and nucleosomal arrays (NA) ( B ) from the pRST5 fragment digested to obtain a 1-kb DNA fragment with 580-bp telomeric DNA (telo) and 2.5-kb non-telomeric DNA (N-telo). Gels similar to (A) and (B), respectively except the pRST5 was digested to obtain a 2-kb fragment containing the 580-bp telomeric DNA (telo) with a 1 kb and smaller fragments being non-telomeric (N-telo) ( C and D ).
    Figure Legend Snippet: TRF2 DBD binds specifically to telomeric DNA and nucleosomal arrays. 0.6% agarose gels of TRF2 DBD binding to DNA (DNA) ( A ) and nucleosomal arrays (NA) ( B ) from the pRST5 fragment digested to obtain a 1-kb DNA fragment with 580-bp telomeric DNA (telo) and 2.5-kb non-telomeric DNA (N-telo). Gels similar to (A) and (B), respectively except the pRST5 was digested to obtain a 2-kb fragment containing the 580-bp telomeric DNA (telo) with a 1 kb and smaller fragments being non-telomeric (N-telo) ( C and D ).

    Techniques Used: Binding Assay

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 97
    New England Biolabs 1 kb ladder
    Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a <t>1-kb</t> DNA
    1 Kb Ladder, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/1 kb ladder/product/New England Biolabs
    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    1 kb ladder - by Bioz Stars, 2022-09
    97/100 stars
      Buy from Supplier

    Image Search Results


    Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a 1-kb DNA

    Journal: Journal of aquatic animal health

    Article Title: Edwardsiellosis Caused by Edwardsiella ictaluri in Laboratory Populations of Zebrafish Danio rerio

    doi: 10.1080/08997659.2013.782226

    Figure Lengend Snippet: Linearized plasmid profiles of Edwardsiella ictaluri isolates. Plasmid DNA from E. ictaluri isolated from Channel Catfish or Zebrafish was digested with EcoRI or BstZ17I, respectively, and separated by 0.6% agarose gel electrophoresis using a 1-kb DNA

    Article Snippet: Plasmids were digested with either EcoRI or BstZ17I and were separated by 0.6% agarose gel electrophoresis with 1-kb ladder (New England Biolabs) as the size standard.

    Techniques: Plasmid Preparation, Isolation, Agarose Gel Electrophoresis

    1% agarose gel electrophoresis of PCR products . PCR products derived from 24 PLUG primer sets were separated using a 1% agarose gel in TAE buffer. Lane numbers correspond to marker numbers indicated in Table 1. M: 2-Log DNA Ladder (New England BioLabs Inc., Ipswich, MA, USA).

    Journal: BMC Genomics

    Article Title: PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes

    doi: 10.1186/1471-2164-8-135

    Figure Lengend Snippet: 1% agarose gel electrophoresis of PCR products . PCR products derived from 24 PLUG primer sets were separated using a 1% agarose gel in TAE buffer. Lane numbers correspond to marker numbers indicated in Table 1. M: 2-Log DNA Ladder (New England BioLabs Inc., Ipswich, MA, USA).

    Article Snippet: Band sizes were estimated against a '2-Log DNA Ladder' (New England BioLabs Inc., Ipswich, MA, USA).

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Derivative Assay, Marker

    Subcellular localization of PRP1 through endogenous tagging. (A) Schematic representation of generating C-terminal endogenously YFP-tagged gPRP1-YFP parasites by single homologous recombination into the RHΔ ku80 parent line. (B) PCR validation of the gPRP1-YFP genotype using the primer pair shown in panel A. Lane M contains 1-kb DNA ladder (New England Biolabs). (C) Live imaging of gPRP1-YFP parasites under intracellular and extracellular conditions as indicated. PC, phase contrast. (D) Live imaging of gPRP1-YFP parasites cotransfected with markers for the IMC (IMC1-mCherry), rhoptries (TLN1-mCherry), and micronemes (MIC8-mCherry). (E) Representative images of intracellular gPRP1-YFP parasites fixed using either 100% methanol (MetOH) or 4% paraformaldehyde (PFA) stained with anti-PRP1 (αPRP1) and anti-GFP (αGFP) antisera as indicated. Note that PFA fixation destroys the costaining of GFP and PRP1 and thus destroys the PRP1 epitope(s) recognized by the specific antiserum.

    Journal: mSphere

    Article Title: Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes

    doi: 10.1128/mSphere.00521-17

    Figure Lengend Snippet: Subcellular localization of PRP1 through endogenous tagging. (A) Schematic representation of generating C-terminal endogenously YFP-tagged gPRP1-YFP parasites by single homologous recombination into the RHΔ ku80 parent line. (B) PCR validation of the gPRP1-YFP genotype using the primer pair shown in panel A. Lane M contains 1-kb DNA ladder (New England Biolabs). (C) Live imaging of gPRP1-YFP parasites under intracellular and extracellular conditions as indicated. PC, phase contrast. (D) Live imaging of gPRP1-YFP parasites cotransfected with markers for the IMC (IMC1-mCherry), rhoptries (TLN1-mCherry), and micronemes (MIC8-mCherry). (E) Representative images of intracellular gPRP1-YFP parasites fixed using either 100% methanol (MetOH) or 4% paraformaldehyde (PFA) stained with anti-PRP1 (αPRP1) and anti-GFP (αGFP) antisera as indicated. Note that PFA fixation destroys the costaining of GFP and PRP1 and thus destroys the PRP1 epitope(s) recognized by the specific antiserum.

    Article Snippet: M represents 1-kb DNA ladder (NEB).

    Techniques: Homologous Recombination, Polymerase Chain Reaction, Imaging, Staining

    EMSA. The indicated proteins were incubated with a 1-kb DNA ladder, and the sample aliquots were then treated with proteinase K. All the samples were analyzed by agarose gel electrophoresis. Lanes: L : 1-kb DNA ladder; 1 : the tested proteins without the

    Journal: The Journal of Biological Chemistry

    Article Title: Functional and Structural Characterization of Novel Type of Linker Connecting Capsid and Nucleocapsid Protein Domains in Murine Leukemia Virus *

    doi: 10.1074/jbc.M116.746461

    Figure Lengend Snippet: EMSA. The indicated proteins were incubated with a 1-kb DNA ladder, and the sample aliquots were then treated with proteinase K. All the samples were analyzed by agarose gel electrophoresis. Lanes: L : 1-kb DNA ladder; 1 : the tested proteins without the

    Article Snippet: The studied proteins (58 pmol) were mixed with 165 ng of a 1-kb DNA ladder (New England Biolabs) in the total volume of 10 μl of buffer J (50 m m Tris, pH 7.0, 100 m m NaCl).

    Techniques: Incubation, Agarose Gel Electrophoresis