kb plus dna ladder  (Thermo Fisher)


Bioz Verified Symbol Thermo Fisher is a verified supplier
Bioz Manufacturer Symbol Thermo Fisher manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 86

    Structured Review

    Thermo Fisher kb plus dna ladder
    EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid <t>DNA)</t> of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).
    Kb Plus Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/kb plus dna ladder/product/Thermo Fisher
    Average 86 stars, based on 40 article reviews
    Price from $9.99 to $1999.99
    kb plus dna ladder - by Bioz Stars, 2022-11
    86/100 stars

    Images

    1) Product Images from "Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering"

    Article Title: Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering

    Journal: bioRxiv

    doi: 10.1101/2022.10.31.514646

    EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid DNA) of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).
    Figure Legend Snippet: EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid DNA) of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).

    Techniques Used: Sequencing, In Vivo, In Vitro, Transformation Assay, Plasmid Preparation, Expressing, Standard Deviation

    EH sgRNA design. ( A ) RNA sequence alignments of the EH repeat, the predicted EH tracrRNA gene region and the designed EH sgRNA with the S. donghicola (Sdo) repeat, tracrRNA coding sequence and sgRNA, correspondingly. Matching positions are marked with asterisks. Promoter and terminator regions predicted for the EH tracrRNA gene are grey shaded. The constant region of the EH sgRNA sequence was conceived by joining the EH repeat sequence in orange and the EH tracrRNA sequence in blue. ( B ) Scheme of the EH sgRNA including a generic 23-nt spacer base-paired to the target strand in a DNA substrate containing a spacer-matching sequence and a compatible PAM (underlined). The EH sgRNA anti-repeat and tracrRNA sequences comprising the linker (tetraloop 5’-GAAA-3’), the anti-repeat and the two stem-loop forming segments, are coloured as in panel A.
    Figure Legend Snippet: EH sgRNA design. ( A ) RNA sequence alignments of the EH repeat, the predicted EH tracrRNA gene region and the designed EH sgRNA with the S. donghicola (Sdo) repeat, tracrRNA coding sequence and sgRNA, correspondingly. Matching positions are marked with asterisks. Promoter and terminator regions predicted for the EH tracrRNA gene are grey shaded. The constant region of the EH sgRNA sequence was conceived by joining the EH repeat sequence in orange and the EH tracrRNA sequence in blue. ( B ) Scheme of the EH sgRNA including a generic 23-nt spacer base-paired to the target strand in a DNA substrate containing a spacer-matching sequence and a compatible PAM (underlined). The EH sgRNA anti-repeat and tracrRNA sequences comprising the linker (tetraloop 5’-GAAA-3’), the anti-repeat and the two stem-loop forming segments, are coloured as in panel A.

    Techniques Used: Sequencing

    Representative agarose gel electrophoreses of in vitro EHCas9-mediated DNA cleavage reactions. Except indicated otherwise, experiments were performed under the following standard conditions: 30 min reaction time at 37°C, 20 mM MgCl 2 , 25 nM of an 840 bp linear DNA containing a target sequence and a compatible PAM, preincubated (15 min at 37°C) EHCas9:EH sgRNA mixtures (0.5 mM EHCas9 and 0.5 mM EH sgRNA concentration in the digestion reaction). The length of relevant bands (in kb) of a linear dsDNA molecular weight marker (M) and the position of bands corresponding to expected cut and uncut DNA substrates are indicated. (A) Samples from standard digestion reactions, mixed either after protein:guide preincubation (lane 2) or without preincubation (lane 7), and from reactions with a missing component (MgCl 2 , lane 3; a compatible PAM next to the target, lane 4; a guide, lane 5; the protein, lane 6) are included. (B) Samples from digestion reactions under standard conditions but for the protein concentration (up to 500 nM). (C) Samples from standard reactions incubated for up to 40 min. (D) Samples of digestions carried out under standard conditions except by the incubation temperature (from 20°C to 45 °C).
    Figure Legend Snippet: Representative agarose gel electrophoreses of in vitro EHCas9-mediated DNA cleavage reactions. Except indicated otherwise, experiments were performed under the following standard conditions: 30 min reaction time at 37°C, 20 mM MgCl 2 , 25 nM of an 840 bp linear DNA containing a target sequence and a compatible PAM, preincubated (15 min at 37°C) EHCas9:EH sgRNA mixtures (0.5 mM EHCas9 and 0.5 mM EH sgRNA concentration in the digestion reaction). The length of relevant bands (in kb) of a linear dsDNA molecular weight marker (M) and the position of bands corresponding to expected cut and uncut DNA substrates are indicated. (A) Samples from standard digestion reactions, mixed either after protein:guide preincubation (lane 2) or without preincubation (lane 7), and from reactions with a missing component (MgCl 2 , lane 3; a compatible PAM next to the target, lane 4; a guide, lane 5; the protein, lane 6) are included. (B) Samples from digestion reactions under standard conditions but for the protein concentration (up to 500 nM). (C) Samples from standard reactions incubated for up to 40 min. (D) Samples of digestions carried out under standard conditions except by the incubation temperature (from 20°C to 45 °C).

    Techniques Used: Agarose Gel Electrophoresis, In Vitro, Sequencing, Concentration Assay, Molecular Weight, Marker, Protein Concentration, Incubation

    Prokaryotic genome editing with EHCas9. (A) Overview of the single-step general procedure for positive selection of genome-edited E. coli. E. coli cells harbouring a plasmid ( e.g ., pKD46; ampicillin resistance, Amp R ) encoding Lambda Red recombination proteins (Gam, Beta, Exo) are co-transformed with an antibiotic resistance (Ab R ) selectable plasmid carrying inducible ehcas9 gene and a sgRNA targeting a sequence within the gene of interest (GOI) and a linear dsDNA template matching both sides of the target (flanking sites, FS). Recombination between the template and the flanking sites in the gene mediated by the Lambda Red recombination machinery (RM) will result in the deletion of the target sequence. The Cas9:sgRNA ribonucleoprotein complex will produce double-strand breaks in the non-edited target, often leading to cell death. Colonies grown at 37°C expressing Cas9 are selected on plates ( i.e ., arabinose and antibiotic-containing medium) and screened through PCR amplification and agarose gel electrophoresis to confirm the deletion. (B) An agarose gel electrophoresis of PCR products from the region surrounding pyrF (the gene of interest) in E. coli cells expressing the Lambda Red system from pKD46. DNA used for amplification was purified from chloramphenicol-resistant colonies grown in the presence of arabinose after co-transformation with a recombination template matching the flanks of pyrF (recombination would lead to a ca. 0.6 kb deletion), and a pBAD33-derivative plasmid (providing chloramphenicol resistance) encoding either both EHCas9 and an EH sgRNA that targets the pyrF gene (+ EHCas9) or only the EH sgRNA (-EHCas9). Each lane corresponds to a transformant clone. Bands running as linear DNA fragments with the length of the original (ca. 1 kb; WT) and the recombinant (ca. 0.5 kb; Mutant) pyrF region are indicated. The length of relevant bands of a linear dsDNA molecular weight marker is indicated.
    Figure Legend Snippet: Prokaryotic genome editing with EHCas9. (A) Overview of the single-step general procedure for positive selection of genome-edited E. coli. E. coli cells harbouring a plasmid ( e.g ., pKD46; ampicillin resistance, Amp R ) encoding Lambda Red recombination proteins (Gam, Beta, Exo) are co-transformed with an antibiotic resistance (Ab R ) selectable plasmid carrying inducible ehcas9 gene and a sgRNA targeting a sequence within the gene of interest (GOI) and a linear dsDNA template matching both sides of the target (flanking sites, FS). Recombination between the template and the flanking sites in the gene mediated by the Lambda Red recombination machinery (RM) will result in the deletion of the target sequence. The Cas9:sgRNA ribonucleoprotein complex will produce double-strand breaks in the non-edited target, often leading to cell death. Colonies grown at 37°C expressing Cas9 are selected on plates ( i.e ., arabinose and antibiotic-containing medium) and screened through PCR amplification and agarose gel electrophoresis to confirm the deletion. (B) An agarose gel electrophoresis of PCR products from the region surrounding pyrF (the gene of interest) in E. coli cells expressing the Lambda Red system from pKD46. DNA used for amplification was purified from chloramphenicol-resistant colonies grown in the presence of arabinose after co-transformation with a recombination template matching the flanks of pyrF (recombination would lead to a ca. 0.6 kb deletion), and a pBAD33-derivative plasmid (providing chloramphenicol resistance) encoding either both EHCas9 and an EH sgRNA that targets the pyrF gene (+ EHCas9) or only the EH sgRNA (-EHCas9). Each lane corresponds to a transformant clone. Bands running as linear DNA fragments with the length of the original (ca. 1 kb; WT) and the recombinant (ca. 0.5 kb; Mutant) pyrF region are indicated. The length of relevant bands of a linear dsDNA molecular weight marker is indicated.

    Techniques Used: Selection, Plasmid Preparation, Transformation Assay, Sequencing, Expressing, Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Purification, Recombinant, Mutagenesis, Molecular Weight, Marker

    2) Product Images from "Single nucleotide polymorphism analysis of pvmdr-1 in Plasmodium vivax isolated from military personnel of Republic of Korea in 2016 and 2017"

    Article Title: Single nucleotide polymorphism analysis of pvmdr-1 in Plasmodium vivax isolated from military personnel of Republic of Korea in 2016 and 2017

    Journal: Malaria Journal

    doi: 10.1186/s12936-022-04214-6

    Gel electrophoresis of P. vivax 18S rRNA and pvmdr-1 nested PCR. a 18S rRNA nested PCR. Blood samples were collected from malaria patients who agreed to the study. All blood samples collected in three hospitals (Yangju, Koyang and Ildong), during 2016 and 2017, were screened using 18S rRNA nested PCR. Based on the screened result, 73 samples were identified as positive samples. 1100 bp or 120 bp was detected by 2nd PCR of 18S rRNA . b Nested PCR targeting pvmdr-1 amplicons ranged from 104 bp to 4,254 bp were observed in 73 P. vivax positive samples using pvmdr-1 nested PCR. M: 1 Kb Plus DNA Ladder
    Figure Legend Snippet: Gel electrophoresis of P. vivax 18S rRNA and pvmdr-1 nested PCR. a 18S rRNA nested PCR. Blood samples were collected from malaria patients who agreed to the study. All blood samples collected in three hospitals (Yangju, Koyang and Ildong), during 2016 and 2017, were screened using 18S rRNA nested PCR. Based on the screened result, 73 samples were identified as positive samples. 1100 bp or 120 bp was detected by 2nd PCR of 18S rRNA . b Nested PCR targeting pvmdr-1 amplicons ranged from 104 bp to 4,254 bp were observed in 73 P. vivax positive samples using pvmdr-1 nested PCR. M: 1 Kb Plus DNA Ladder

    Techniques Used: Nucleic Acid Electrophoresis, Nested PCR, Polymerase Chain Reaction

    3) Product Images from "Topical application of Porphyromonas gingivalis into the gingival pocket in mice leads to chronic-active infection, periodontitis and systemic inflammation"

    Article Title: Topical application of Porphyromonas gingivalis into the gingival pocket in mice leads to chronic-active infection, periodontitis and systemic inflammation

    Journal: International Journal of Molecular Medicine

    doi: 10.3892/ijmm.2022.5159

    Research design and electrophoretic images of amplified Pg DNA from the gingival pocket swabs of mice collected at 4 and 8 weeks after the final PBS or Pg inoculation for 5 weeks. (A) Schematic diagram of the research design. (B) Electrophoretic image of amplified Pg DNA from mice sacrificed 4 weeks after completing the last inoculation (inoculation duration, 5 weeks). (C) Electrophoretic image of amplified Pg DNA from mice sacrificed 8 weeks after completing the last inoculation (inoculation duration, 5 weeks). The lanes indicate the following: +, positive control (1,000 CFU of purified Pg DNA); -, negative control; 1–10, samples taken from the gingival pocket. Pg, Porphyromonas gingivalis.
    Figure Legend Snippet: Research design and electrophoretic images of amplified Pg DNA from the gingival pocket swabs of mice collected at 4 and 8 weeks after the final PBS or Pg inoculation for 5 weeks. (A) Schematic diagram of the research design. (B) Electrophoretic image of amplified Pg DNA from mice sacrificed 4 weeks after completing the last inoculation (inoculation duration, 5 weeks). (C) Electrophoretic image of amplified Pg DNA from mice sacrificed 8 weeks after completing the last inoculation (inoculation duration, 5 weeks). The lanes indicate the following: +, positive control (1,000 CFU of purified Pg DNA); -, negative control; 1–10, samples taken from the gingival pocket. Pg, Porphyromonas gingivalis.

    Techniques Used: Amplification, Mouse Assay, Positive Control, Purification, Negative Control

    4) Product Images from "Pore-Forming Cardiotoxin VVA2 (Volvatoxin A2) Variant I82E/L86K Is an Atypical Duplex-Specific Nuclease"

    Article Title: Pore-Forming Cardiotoxin VVA2 (Volvatoxin A2) Variant I82E/L86K Is an Atypical Duplex-Specific Nuclease

    Journal: Toxins

    doi: 10.3390/toxins14060392

    Structure–function relationship and metal ion interaction studies of VVA2 variants. ( A – D ) Nuclease activities of VVA2 variants at 0–120 min were studied as stated in the Materials and Methods. Related gel profiles are shown in ( A ) and ( C ), while calculated nicking rates are shown in ( B ) and ( D ). Image J and GraphPad Prism were used to quantify figures and analysis the results. RF I–III: replicative form I–III (supercoiled form, nicked form, and linear form DNA); L (in the column header): linearized pUC19 by BamH1. N ≥ 3. Related data points are shown as average ± SD (standard deviation). ( E ) Nicking rates of VVA2 variants at 30 min. Related mean, SD, and comparison to Re-VVA2 I82E/L86K are shown in the table. ( F , G ) Metal ion binding of Re-VVA2 I82E/L86K and its variants. F: Mg 2+ binding; G: Mn 2+ binding. Excitation was monitored at 290 nm. Re-V: Re-VVA2 I82E/L86K; Re-V-E111A: Re-VVA2-E111A/I82E/L86K. Data were calculated and analyzed by GraphPad Prism. N ≥ 3.
    Figure Legend Snippet: Structure–function relationship and metal ion interaction studies of VVA2 variants. ( A – D ) Nuclease activities of VVA2 variants at 0–120 min were studied as stated in the Materials and Methods. Related gel profiles are shown in ( A ) and ( C ), while calculated nicking rates are shown in ( B ) and ( D ). Image J and GraphPad Prism were used to quantify figures and analysis the results. RF I–III: replicative form I–III (supercoiled form, nicked form, and linear form DNA); L (in the column header): linearized pUC19 by BamH1. N ≥ 3. Related data points are shown as average ± SD (standard deviation). ( E ) Nicking rates of VVA2 variants at 30 min. Related mean, SD, and comparison to Re-VVA2 I82E/L86K are shown in the table. ( F , G ) Metal ion binding of Re-VVA2 I82E/L86K and its variants. F: Mg 2+ binding; G: Mn 2+ binding. Excitation was monitored at 290 nm. Re-V: Re-VVA2 I82E/L86K; Re-V-E111A: Re-VVA2-E111A/I82E/L86K. Data were calculated and analyzed by GraphPad Prism. N ≥ 3.

    Techniques Used: Standard Deviation, Binding Assay

    Proposed mechanism of Re-VVA2 I82E/L86K as a duplex-specific nuclease (DSN). Re-VVA2 I82E/L86K interacts with DNA with the mediation of Mg 2+ or Mn 2+ . E111 plays an important role in the interaction. The “double-hit” mechanism may be used in the cleavage reaction on plasmid DNA and linearized DNA, such as genomic DNA, finally resulting in fragmented DNA.
    Figure Legend Snippet: Proposed mechanism of Re-VVA2 I82E/L86K as a duplex-specific nuclease (DSN). Re-VVA2 I82E/L86K interacts with DNA with the mediation of Mg 2+ or Mn 2+ . E111 plays an important role in the interaction. The “double-hit” mechanism may be used in the cleavage reaction on plasmid DNA and linearized DNA, such as genomic DNA, finally resulting in fragmented DNA.

    Techniques Used: Plasmid Preparation

    Kinetic characters and optimal conditions (pH/temperature) of Re-VVA2 I82E/L86K as a nuclease. ( A ) The nicking rate of Re-VVA2 I82E/L86K on pUC19 calculated from Figure 2 D; 167.87 nM Re-VVA2 I82E/L86K was used. The nicking rates ([RF II]/[RF II + RF I) were calculated and analyzed by ImageJ and GraphPad Prism. N ≥ 3. ( B ) Nuclease activity of Re-VVA2 I82E/L86K at different pH. ( C ) Nuclease activity of Re-VVA2 I82E/L86K at different temperatures. 1% agarose gel and Midori green were used to separate and detect products. Re-VVA2 I82E/L86K concentration: 167.87 nM; RF I–III: replicative form I–III (supercoiled form, nicked form, and linear form DNA); L (in the column header): linearized pUC19 by BamH1; CON: control group, pUC19 incubated with other reagents except for VVA2 variant; M: GeneRuler 1 kb DNA Ladder. Related nicking rates were calculated and analyzed by ImageJ and GraphPad Prism. N ≥ 3. Related data points are shown as average ± SD (standard deviation).
    Figure Legend Snippet: Kinetic characters and optimal conditions (pH/temperature) of Re-VVA2 I82E/L86K as a nuclease. ( A ) The nicking rate of Re-VVA2 I82E/L86K on pUC19 calculated from Figure 2 D; 167.87 nM Re-VVA2 I82E/L86K was used. The nicking rates ([RF II]/[RF II + RF I) were calculated and analyzed by ImageJ and GraphPad Prism. N ≥ 3. ( B ) Nuclease activity of Re-VVA2 I82E/L86K at different pH. ( C ) Nuclease activity of Re-VVA2 I82E/L86K at different temperatures. 1% agarose gel and Midori green were used to separate and detect products. Re-VVA2 I82E/L86K concentration: 167.87 nM; RF I–III: replicative form I–III (supercoiled form, nicked form, and linear form DNA); L (in the column header): linearized pUC19 by BamH1; CON: control group, pUC19 incubated with other reagents except for VVA2 variant; M: GeneRuler 1 kb DNA Ladder. Related nicking rates were calculated and analyzed by ImageJ and GraphPad Prism. N ≥ 3. Related data points are shown as average ± SD (standard deviation).

    Techniques Used: Activity Assay, Agarose Gel Electrophoresis, Concentration Assay, Incubation, Variant Assay, Standard Deviation

    Assay on the endonuclease activity of mushroom VVA2 and recombinant VVA2 I82E/L86K. ( A ) Endonuclease activity of mushroom VVA2 and recombinant VVA2 variant I82E/L86K (Re-VVA2 I82E/L86K). Various amounts of corresponding proteins were incubated with pUC19 (22.26 nM) with 10 mM Mg 2+ as stated in the Material and Methods. pUC19 treated by Nb. BsrDI and BamH1 were used to indicate nicked and linear DNA (marked as L in the column head). ( B–D ) Endonuclease activity of Re-VVA2 I82E/L86K (( B ) 1.68 µM, ( C ) 839.35 nM, ( D ) 167.87 nM) on RF I pUC19. Reactions were set as stated in Material and Methods. RF I: replicative form I, supercoiled form; RF II: replicative form II, nicked form; RF III: replicative form III, linear form. M: DNA marker (GeneRuler 1 kb DNA Ladder, Thermo Fisher). CON: control group, pUC19 was incubated without VVA2; L (in the column header): linearized pUC19 by BamH1; reaction products were analyzed on 1% agarose gel.
    Figure Legend Snippet: Assay on the endonuclease activity of mushroom VVA2 and recombinant VVA2 I82E/L86K. ( A ) Endonuclease activity of mushroom VVA2 and recombinant VVA2 variant I82E/L86K (Re-VVA2 I82E/L86K). Various amounts of corresponding proteins were incubated with pUC19 (22.26 nM) with 10 mM Mg 2+ as stated in the Material and Methods. pUC19 treated by Nb. BsrDI and BamH1 were used to indicate nicked and linear DNA (marked as L in the column head). ( B–D ) Endonuclease activity of Re-VVA2 I82E/L86K (( B ) 1.68 µM, ( C ) 839.35 nM, ( D ) 167.87 nM) on RF I pUC19. Reactions were set as stated in Material and Methods. RF I: replicative form I, supercoiled form; RF II: replicative form II, nicked form; RF III: replicative form III, linear form. M: DNA marker (GeneRuler 1 kb DNA Ladder, Thermo Fisher). CON: control group, pUC19 was incubated without VVA2; L (in the column header): linearized pUC19 by BamH1; reaction products were analyzed on 1% agarose gel.

    Techniques Used: Activity Assay, Recombinant, Variant Assay, Incubation, Marker, Agarose Gel Electrophoresis

    Assay on the nuclease activity of Re-VVA2 I82E/L86K on various nucleic acids. ( A ) Re-VVA2 I82E/L86K on E. coli genomic DNA. Re-VVA2 I82E/L86K was used at 833 nM, 83.3 nM, and 8.3 nM for the reaction. CON: control group, E. coli genomic DNA incubated with reaction buffer without VVA2. M: DNA marker (GeneRuler 1 kb DNA Ladder, Thermo Fisher, Waltham, NJ, USA). ( B ) Nuclease activity of Re-VVA2 I82E/L86K on E. coli RNA and yeast rRNA. Re-VVA2 I82E/L86K at 833 nM, 83.3 nM, and 8.3 nM for E. coli RNA was used for the reactions. CON: control group, RNA was incubated with buffer without VVA2. ( C ) Nuclease activity of Re-VVA2 I82E/L86K on 60-mer ssDNA; 200 nM to 20 µM ssDNA and 3.3 nM-330 nM Re-VVA2 I82E/L86K under 20 mM Mg 2+ were used to assay its nuclease activity. CON: control group, a 60-mer ssDNA incubated with other reagents except for VVA2. M: DNA marker (100 bp DNA Ladder Dye Plus, Takara).
    Figure Legend Snippet: Assay on the nuclease activity of Re-VVA2 I82E/L86K on various nucleic acids. ( A ) Re-VVA2 I82E/L86K on E. coli genomic DNA. Re-VVA2 I82E/L86K was used at 833 nM, 83.3 nM, and 8.3 nM for the reaction. CON: control group, E. coli genomic DNA incubated with reaction buffer without VVA2. M: DNA marker (GeneRuler 1 kb DNA Ladder, Thermo Fisher, Waltham, NJ, USA). ( B ) Nuclease activity of Re-VVA2 I82E/L86K on E. coli RNA and yeast rRNA. Re-VVA2 I82E/L86K at 833 nM, 83.3 nM, and 8.3 nM for E. coli RNA was used for the reactions. CON: control group, RNA was incubated with buffer without VVA2. ( C ) Nuclease activity of Re-VVA2 I82E/L86K on 60-mer ssDNA; 200 nM to 20 µM ssDNA and 3.3 nM-330 nM Re-VVA2 I82E/L86K under 20 mM Mg 2+ were used to assay its nuclease activity. CON: control group, a 60-mer ssDNA incubated with other reagents except for VVA2. M: DNA marker (100 bp DNA Ladder Dye Plus, Takara).

    Techniques Used: Activity Assay, Incubation, Marker

    5) Product Images from "Low-cost sample preservation methods for high-throughput processing of rumen microbiomes"

    Article Title: Low-cost sample preservation methods for high-throughput processing of rumen microbiomes

    Journal: Animal Microbiome

    doi: 10.1186/s42523-022-00190-z

    Electrophoresis gel of 12 sheep samples to show DNA integrity from four sample preservation methods. a GHx2 b EtOH c GRC d TNx2
    Figure Legend Snippet: Electrophoresis gel of 12 sheep samples to show DNA integrity from four sample preservation methods. a GHx2 b EtOH c GRC d TNx2

    Techniques Used: Electrophoresis, Preserving

    6) Product Images from "Beyond Domestic Cats: Environmental Detection of Sporothrix brasiliensis DNA in a Hyperendemic Area of Sporotrichosis in Rio de Janeiro State, Brazil"

    Article Title: Beyond Domestic Cats: Environmental Detection of Sporothrix brasiliensis DNA in a Hyperendemic Area of Sporotrichosis in Rio de Janeiro State, Brazil

    Journal: Journal of Fungi

    doi: 10.3390/jof8060604

    Soil samples with Sporothrix brasiliensis DNA detection. ( A ) Soil around an acerola fruit tree ( Malpighia emarginata ). ( B ) Soil around a coconut tree ( Cocos nucifera ) enriched with cow dung. ( C ) Soil around an artificial lake. ( D ) Soil from the bottom of a stream. Sites A to C are located in Seropédica. Site D is located in Nova Iguaçú.
    Figure Legend Snippet: Soil samples with Sporothrix brasiliensis DNA detection. ( A ) Soil around an acerola fruit tree ( Malpighia emarginata ). ( B ) Soil around a coconut tree ( Cocos nucifera ) enriched with cow dung. ( C ) Soil around an artificial lake. ( D ) Soil from the bottom of a stream. Sites A to C are located in Seropédica. Site D is located in Nova Iguaçú.

    Techniques Used:

    Representative nested-PCR agarose gel of the DNA extracted from soil samples, demonstrating 16 amplified fragments with the amplification of 152 bp fragments. 1 and 24 = Molecular Weight (1 kb Plus–Invitrogen), 2 to 10 = samples from Seropédica, and 11 to 19 = samples from Nova Iguaçu, 20 = Positive control S. brasiliensis (IPEC 16490) and 21, 22 and 23 = Negative control.
    Figure Legend Snippet: Representative nested-PCR agarose gel of the DNA extracted from soil samples, demonstrating 16 amplified fragments with the amplification of 152 bp fragments. 1 and 24 = Molecular Weight (1 kb Plus–Invitrogen), 2 to 10 = samples from Seropédica, and 11 to 19 = samples from Nova Iguaçu, 20 = Positive control S. brasiliensis (IPEC 16490) and 21, 22 and 23 = Negative control.

    Techniques Used: Nested PCR, Agarose Gel Electrophoresis, Amplification, Molecular Weight, Positive Control, Negative Control

    7) Product Images from "A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development"

    Article Title: A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development

    Journal: Frontiers in Plant Science

    doi: 10.3389/fpls.2022.906603

    Loss of lncCOBRA1 results in delayed germination and smaller plants. (A) Diagram of lncCOBRA1 ( AT1G05913 ) locus. Gray arrows represent the two snoRNAs annotated within lncCOBRA1 . Triangles represent the location of the T-DNA insertion in SALK_086689 and location of the two guide RNAs used to generate a CRISPR deletion. (B) Relative abundance of lncCOBRA1 in Col-0, lnccobra1-1 , and lnccobra1-1/lncCOBRA1pro:lncCOBRA1 . Abundance is normalized by the geomean of UBC9 and UBC10 and relative to Col-0. *** Denotes p -value
    Figure Legend Snippet: Loss of lncCOBRA1 results in delayed germination and smaller plants. (A) Diagram of lncCOBRA1 ( AT1G05913 ) locus. Gray arrows represent the two snoRNAs annotated within lncCOBRA1 . Triangles represent the location of the T-DNA insertion in SALK_086689 and location of the two guide RNAs used to generate a CRISPR deletion. (B) Relative abundance of lncCOBRA1 in Col-0, lnccobra1-1 , and lnccobra1-1/lncCOBRA1pro:lncCOBRA1 . Abundance is normalized by the geomean of UBC9 and UBC10 and relative to Col-0. *** Denotes p -value

    Techniques Used: CRISPR

    8) Product Images from "A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development"

    Article Title: A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development

    Journal: Frontiers in Plant Science

    doi: 10.3389/fpls.2022.906603

    Loss of lncCOBRA1 results in delayed germination and smaller plants. (A) Diagram of lncCOBRA1 ( AT1G05913 ) locus. Gray arrows represent the two snoRNAs annotated within lncCOBRA1 . Triangles represent the location of the T-DNA insertion in SALK_086689 and location of the two guide RNAs used to generate a CRISPR deletion. (B) Relative abundance of lncCOBRA1 in Col-0, lnccobra1-1 , and lnccobra1-1/lncCOBRA1pro:lncCOBRA1 . Abundance is normalized by the geomean of UBC9 and UBC10 and relative to Col-0. *** Denotes p -value
    Figure Legend Snippet: Loss of lncCOBRA1 results in delayed germination and smaller plants. (A) Diagram of lncCOBRA1 ( AT1G05913 ) locus. Gray arrows represent the two snoRNAs annotated within lncCOBRA1 . Triangles represent the location of the T-DNA insertion in SALK_086689 and location of the two guide RNAs used to generate a CRISPR deletion. (B) Relative abundance of lncCOBRA1 in Col-0, lnccobra1-1 , and lnccobra1-1/lncCOBRA1pro:lncCOBRA1 . Abundance is normalized by the geomean of UBC9 and UBC10 and relative to Col-0. *** Denotes p -value

    Techniques Used: CRISPR

    9) Product Images from "Molecular Characterization of ESBLs and QnrS Producers From Selected Enterobacteriaceae Strains Isolated From Commercial Poultry Production Systems in Kiambu County, Kenya"

    Article Title: Molecular Characterization of ESBLs and QnrS Producers From Selected Enterobacteriaceae Strains Isolated From Commercial Poultry Production Systems in Kiambu County, Kenya

    Journal: Microbiology Insights

    doi: 10.1177/11786361211063619

    LM-DNA ladder for electrophoretic reaction with positive isolates for Peer Review bla TEM genes. Abbreviations: E, Escherichia coli isolate; M, molecular weight markers (gene ruler 100-5000 bp DNA ladder); NC, negative control; PC, positive control; S, Salmonella spp. isolate; Shig, Shigella species.
    Figure Legend Snippet: LM-DNA ladder for electrophoretic reaction with positive isolates for Peer Review bla TEM genes. Abbreviations: E, Escherichia coli isolate; M, molecular weight markers (gene ruler 100-5000 bp DNA ladder); NC, negative control; PC, positive control; S, Salmonella spp. isolate; Shig, Shigella species.

    Techniques Used: Transmission Electron Microscopy, Molecular Weight, Negative Control, Positive Control

    LM-DNA ladder, for electrophoretic reaction with positive isolates for QnrS genes among the isolates. Abbreviations: E, Escherichia coli isolate; M, molecular weight markers (gene ruler 100-5000 bp DNA ladder); PC, positive control; S, Salmonella spp. isolate.
    Figure Legend Snippet: LM-DNA ladder, for electrophoretic reaction with positive isolates for QnrS genes among the isolates. Abbreviations: E, Escherichia coli isolate; M, molecular weight markers (gene ruler 100-5000 bp DNA ladder); PC, positive control; S, Salmonella spp. isolate.

    Techniques Used: Molecular Weight, Positive Control

    LM-DNA ladder, for electrophoretic reaction with positive isolates for bla SHV genes among the isolates. Abbreviations: E, Escherichia coli isolate; K, Klebsiella spp.; M, molecular weight markers (gene ruler 100-5000 bp DNA ladder); NC, negative control; PC, positive control; S, Salmonella spp. isolates.
    Figure Legend Snippet: LM-DNA ladder, for electrophoretic reaction with positive isolates for bla SHV genes among the isolates. Abbreviations: E, Escherichia coli isolate; K, Klebsiella spp.; M, molecular weight markers (gene ruler 100-5000 bp DNA ladder); NC, negative control; PC, positive control; S, Salmonella spp. isolates.

    Techniques Used: Molecular Weight, Negative Control, Positive Control

    LM-DNA ladder (100 bp for gene size determination), for electrophoretic reaction with positive isolates for bla CTX-M genes among the isolates. Abbreviations: E, Escherichia coli isolate; M, molecular weight markers (gene ruler 100-5000 bp DNA ladder); NC, negative control; PC, positive control; S, Salmonella spp. isolate; Shig, Shigella species.
    Figure Legend Snippet: LM-DNA ladder (100 bp for gene size determination), for electrophoretic reaction with positive isolates for bla CTX-M genes among the isolates. Abbreviations: E, Escherichia coli isolate; M, molecular weight markers (gene ruler 100-5000 bp DNA ladder); NC, negative control; PC, positive control; S, Salmonella spp. isolate; Shig, Shigella species.

    Techniques Used: Molecular Weight, Negative Control, Positive Control

    LM-DNA ladder, for electrophoretic reaction with positive isolates for bla OXA genes among the isolates. Abbreviations: E, Escherichia coli isolate; M, molecular weight markers (gene ruler 100-5000 bp DNA ladder); S, Salmonella spp. isolates; Shig, Shigella spp.
    Figure Legend Snippet: LM-DNA ladder, for electrophoretic reaction with positive isolates for bla OXA genes among the isolates. Abbreviations: E, Escherichia coli isolate; M, molecular weight markers (gene ruler 100-5000 bp DNA ladder); S, Salmonella spp. isolates; Shig, Shigella spp.

    Techniques Used: Molecular Weight

    10) Product Images from "Heterologous Expression, Purification, and Immunomodulatory Effects of Recombinant Lipoprotein GUDIV-103 Isolated from Ureaplasma diversum"

    Article Title: Heterologous Expression, Purification, and Immunomodulatory Effects of Recombinant Lipoprotein GUDIV-103 Isolated from Ureaplasma diversum

    Journal: Microorganisms

    doi: 10.3390/microorganisms10051032

    Cloning, heterologous expression, and purification of recombinant GUDIV-103 (rGUDIV-103). ( A ) Top, nucleotide sequence inserted into the pET28a(+) vector; bottom, translation of the inserted sequence. Green, red, grey, and purple nucleotides correspond to the GUDIV translation start codon, stop codon, N-terminal histidine tail, and the TGG codon encoding tryptophan, which replaces the TGA codon in Escherichia coli , respectively. The underlined sequences were used to build the forward and reverse primers for assessing gene insertion. ( B ) Agarose gel electrophoresis of plasmids isolated from two different One Shot TOP10 transformants (C1 and C2). ( C ) Agarose gel electrophoresis of PCR-amplified GUDIV-103 fragment using the primers stated in panel A and DNA extracted from E. coli BL21 (DE3) Star transformed with pET-28a(+) gudiv-103 vector. EBU: untransformed E. coli BL21 (DE3) Star; NC: negative control—all elements of the reaction except the target DNA. Ladder: Marker TrackIt 100 bp DNA ladder (Invitrogen, São Paulo, Brazil). ( D ) Assessing different expression temperatures on GUDIV_103 solubility by sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE) (left) and Western blotting (right). T-zero: total uninduced E. coli BL21 (DE3) Star extract; T over: rGUDIV-103 expression in E. coli BL21 (DE3) Star after overnight isopropyl β- d -1-thiogalactopyranoside (IPTG) induction. Bands at approximately 27 kDa correspond to GUDIV_103 expression. Insoluble: insoluble fraction of the total bacterial extract after induction; soluble: soluble fraction of the bacterial extract after induction. Ladder: Novex Sharp pre-Stained Protein Standard (Thermo Fisher Scientific). ( E ) Left, monitoring HisTrap purification of GUDIV_103 by spectrophotometry (280 nm) using 25 and 120 mM imidazole wash steps, followed by elution with 500 mM imidazole; right, SDS–PAGE. Flow: eluate before imidazole wash steps. ( F ) Purification and optimisation using 130–160 mM imidazole in the wash step, followed by elution with 500 mM imidazole; analysed by SDS–PAGE (left) and Western blotting (right). Ladder: Novex Sharp protein standard (Invitrogen).
    Figure Legend Snippet: Cloning, heterologous expression, and purification of recombinant GUDIV-103 (rGUDIV-103). ( A ) Top, nucleotide sequence inserted into the pET28a(+) vector; bottom, translation of the inserted sequence. Green, red, grey, and purple nucleotides correspond to the GUDIV translation start codon, stop codon, N-terminal histidine tail, and the TGG codon encoding tryptophan, which replaces the TGA codon in Escherichia coli , respectively. The underlined sequences were used to build the forward and reverse primers for assessing gene insertion. ( B ) Agarose gel electrophoresis of plasmids isolated from two different One Shot TOP10 transformants (C1 and C2). ( C ) Agarose gel electrophoresis of PCR-amplified GUDIV-103 fragment using the primers stated in panel A and DNA extracted from E. coli BL21 (DE3) Star transformed with pET-28a(+) gudiv-103 vector. EBU: untransformed E. coli BL21 (DE3) Star; NC: negative control—all elements of the reaction except the target DNA. Ladder: Marker TrackIt 100 bp DNA ladder (Invitrogen, São Paulo, Brazil). ( D ) Assessing different expression temperatures on GUDIV_103 solubility by sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE) (left) and Western blotting (right). T-zero: total uninduced E. coli BL21 (DE3) Star extract; T over: rGUDIV-103 expression in E. coli BL21 (DE3) Star after overnight isopropyl β- d -1-thiogalactopyranoside (IPTG) induction. Bands at approximately 27 kDa correspond to GUDIV_103 expression. Insoluble: insoluble fraction of the total bacterial extract after induction; soluble: soluble fraction of the bacterial extract after induction. Ladder: Novex Sharp pre-Stained Protein Standard (Thermo Fisher Scientific). ( E ) Left, monitoring HisTrap purification of GUDIV_103 by spectrophotometry (280 nm) using 25 and 120 mM imidazole wash steps, followed by elution with 500 mM imidazole; right, SDS–PAGE. Flow: eluate before imidazole wash steps. ( F ) Purification and optimisation using 130–160 mM imidazole in the wash step, followed by elution with 500 mM imidazole; analysed by SDS–PAGE (left) and Western blotting (right). Ladder: Novex Sharp protein standard (Invitrogen).

    Techniques Used: Clone Assay, Expressing, Purification, Recombinant, Sequencing, Plasmid Preparation, Agarose Gel Electrophoresis, Isolation, Polymerase Chain Reaction, Amplification, Transformation Assay, Positron Emission Tomography, Negative Control, Marker, Solubility, Polyacrylamide Gel Electrophoresis, SDS Page, Western Blot, Staining, Spectrophotometry

    Identification of GUDIV -103 from Ureaplasma diversum isolates and phylogenetic analysis. ( A ) Agarose gel electrophoresis of PCR-amplified GUDIV -103 fragment using DNA extracted from 46 U. diversum strains from different Brazilian states. MW: molecular weight marker TrackIt 100 bp ladder (Invitrogen, São Paulo, Brazil). NC (negative control): All elements of the reaction except the target DNA. ( B ) Phylogenetic tree generated using the neighbour-joining method with a Tajima–Nei distance matrix (MEGA-X version 4.1) following the alignment of GUDIV -103 sequences from U. diversum isolates and the reference strain, ATCC 49782. Strains from Mato Grosso do Sul, Bahia, and São Paulo are underlined in blue, green, and black, respectively.
    Figure Legend Snippet: Identification of GUDIV -103 from Ureaplasma diversum isolates and phylogenetic analysis. ( A ) Agarose gel electrophoresis of PCR-amplified GUDIV -103 fragment using DNA extracted from 46 U. diversum strains from different Brazilian states. MW: molecular weight marker TrackIt 100 bp ladder (Invitrogen, São Paulo, Brazil). NC (negative control): All elements of the reaction except the target DNA. ( B ) Phylogenetic tree generated using the neighbour-joining method with a Tajima–Nei distance matrix (MEGA-X version 4.1) following the alignment of GUDIV -103 sequences from U. diversum isolates and the reference strain, ATCC 49782. Strains from Mato Grosso do Sul, Bahia, and São Paulo are underlined in blue, green, and black, respectively.

    Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification, Molecular Weight, Marker, Negative Control, Generated

    11) Product Images from "Development of a Polymerase Spiral Reaction-Based Isothermal Assay for Rapid Identification of Thrips palmi"

    Article Title: Development of a Polymerase Spiral Reaction-Based Isothermal Assay for Rapid Identification of Thrips palmi

    Journal: Frontiers in Molecular Biosciences

    doi: 10.3389/fmolb.2022.853339

    Assessment of cross-reactivity of primer pair AG339F-AG340R in (A) . PCR and (B) . PSR. Lanes 1, 8, 15: 1 kb plus DNA ladder, lanes 2–6: PCR with DNA templates of T. palmi (2), S. dorsalis (3), T. tabaci (3), and F. schultzei (4), respectively. Lanes 9–13: PSR with DNA templates of T. palmi (9), S. dorsalis (10), T. tabaci (11), and F. schultzei (12), respectively. Lanes 16–19: Nco I-digested PSR amplicons from DNA templates of T. palmi (16), S. dorsalis (17), T. tabaci (18), and F. schultzei (19), respectively. Lanes 7, 14, 20: no-template water control.
    Figure Legend Snippet: Assessment of cross-reactivity of primer pair AG339F-AG340R in (A) . PCR and (B) . PSR. Lanes 1, 8, 15: 1 kb plus DNA ladder, lanes 2–6: PCR with DNA templates of T. palmi (2), S. dorsalis (3), T. tabaci (3), and F. schultzei (4), respectively. Lanes 9–13: PSR with DNA templates of T. palmi (9), S. dorsalis (10), T. tabaci (11), and F. schultzei (12), respectively. Lanes 16–19: Nco I-digested PSR amplicons from DNA templates of T. palmi (16), S. dorsalis (17), T. tabaci (18), and F. schultzei (19), respectively. Lanes 7, 14, 20: no-template water control.

    Techniques Used: Polymerase Chain Reaction

    PSR-amplified products using primer pair AG339F-AG340R resolved on 2% agarose gel. Lane 1: 1 kb plus DNA ladder, lanes 2–4: PSR amplicons with T. palmi DNA templates, lanes 5–7: Nco I-digested PSR amplicons, 8: no-template water control.
    Figure Legend Snippet: PSR-amplified products using primer pair AG339F-AG340R resolved on 2% agarose gel. Lane 1: 1 kb plus DNA ladder, lanes 2–4: PSR amplicons with T. palmi DNA templates, lanes 5–7: Nco I-digested PSR amplicons, 8: no-template water control.

    Techniques Used: Amplification, Agarose Gel Electrophoresis

    (A) Sensitivity of PSR assay using primer pair AG339F-AG340R. Ten-fold serially-diluted T. palmi DNA was used as a template and products resolved on 2% agarose gel. Lanes 1, 9, 17: 1 kb plus DNA ladder. Lanes 2–8, 10–15: PSR amplicons of serially-diluted T. palmi template of 5 ng × 10 ng (2), 5 ng (3), 5 ng × 10 −1 ng (4), 5 ng × 10 −2 ng (5), 5 ng × 10 −3 ng (6), 5 ng × 10 −4 ng (7), 5 ng × 10 −5 ng (8), 5 ng × 10 −6 ng (10), 5 ng × 10 −7 ng (11), 5 ng × 10 −8 ng (12), 5 ng × 10 −9 ng (13), 5 ng × 10 −10 ng (14), 5 ng × 10 −11 ng (15), lane 16: no-template water control. (B) . Sensitivity of PCR assessed using the same primer pair and template. Lane 17: 1 kb plus DNA ladder, lanes 18–23: PCR amplicons of serially diluted T. palmi template of 5 ng × 10 ng (18), 5 ng (19), 5 ng × 10 −1 ng (20), 5 ng × 10 −2 ng (21), 5 ng × 10 −3 ng (22), 5 ng × 10 −4 ng (23), lane 24: no-template water control.
    Figure Legend Snippet: (A) Sensitivity of PSR assay using primer pair AG339F-AG340R. Ten-fold serially-diluted T. palmi DNA was used as a template and products resolved on 2% agarose gel. Lanes 1, 9, 17: 1 kb plus DNA ladder. Lanes 2–8, 10–15: PSR amplicons of serially-diluted T. palmi template of 5 ng × 10 ng (2), 5 ng (3), 5 ng × 10 −1 ng (4), 5 ng × 10 −2 ng (5), 5 ng × 10 −3 ng (6), 5 ng × 10 −4 ng (7), 5 ng × 10 −5 ng (8), 5 ng × 10 −6 ng (10), 5 ng × 10 −7 ng (11), 5 ng × 10 −8 ng (12), 5 ng × 10 −9 ng (13), 5 ng × 10 −10 ng (14), 5 ng × 10 −11 ng (15), lane 16: no-template water control. (B) . Sensitivity of PCR assessed using the same primer pair and template. Lane 17: 1 kb plus DNA ladder, lanes 18–23: PCR amplicons of serially diluted T. palmi template of 5 ng × 10 ng (18), 5 ng (19), 5 ng × 10 −1 ng (20), 5 ng × 10 −2 ng (21), 5 ng × 10 −3 ng (22), 5 ng × 10 −4 ng (23), lane 24: no-template water control.

    Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction

    Schematic representation of PSR assay. FP and RP denote forward and reverse primers targeting the mtCOIII region of T. palmi . The 3′ sequence of forward primer is denoted as “F” and that of reverse primer is denoted as “R” and is complementary to the target mtCOIII sequence. An adapter sequence (A) was added at 5′ of revere primer. The adapter sequence of forward primer (Ar) is reverse to adapter sequence of reverse primer (A). At 65°C, the double-stranded template DNA unfolds in presence of Betaine. In the left panel, F segment of the forward primer (FP) anneals to the complementary single-strand of DNA (step 1) and extends (step 2). After the melting, the R segment of the reverse primer (RP) binds to it (step 3) and extends (step 4). Now, both the strands melt and form a single chain (step 5). As the sequences of A and Arc are reverse complementary to each other, it makes a circular structure in step 6. The 3′ end continues to extend and gives spiral amplification (step 7). Similarly, mechanism of amplification happens for another single-stranded chain in the right panel.
    Figure Legend Snippet: Schematic representation of PSR assay. FP and RP denote forward and reverse primers targeting the mtCOIII region of T. palmi . The 3′ sequence of forward primer is denoted as “F” and that of reverse primer is denoted as “R” and is complementary to the target mtCOIII sequence. An adapter sequence (A) was added at 5′ of revere primer. The adapter sequence of forward primer (Ar) is reverse to adapter sequence of reverse primer (A). At 65°C, the double-stranded template DNA unfolds in presence of Betaine. In the left panel, F segment of the forward primer (FP) anneals to the complementary single-strand of DNA (step 1) and extends (step 2). After the melting, the R segment of the reverse primer (RP) binds to it (step 3) and extends (step 4). Now, both the strands melt and form a single chain (step 5). As the sequences of A and Arc are reverse complementary to each other, it makes a circular structure in step 6. The 3′ end continues to extend and gives spiral amplification (step 7). Similarly, mechanism of amplification happens for another single-stranded chain in the right panel.

    Techniques Used: Sequencing, Amplification

    12) Product Images from "Protease-activated receptor-2 activation enhances epithelial wound healing via epidermal growth factor receptor"

    Article Title: Protease-activated receptor-2 activation enhances epithelial wound healing via epidermal growth factor receptor

    Journal: Tissue Barriers

    doi: 10.1080/21688370.2021.1968763

    CMT-93 cells express protease-activated receptor 2 (PAR2). A: RT-PCR for PAR2 mRNA expression in CMT-93 cells. Reactions lacking reverse transcriptase enzyme (RT) and template control lacking cDNA were performed as controls. DNA ladder and the sizes (bp) are shown on the right of image, with expected product size being 167 bp (n = 3). B: Confocal immunocytochemistry for PAR2 in CMT-93 cell monolayers (n = 2). Green shows positive immunoreactivity for PAR2 and blue shows DAPI staining for nuclei. C: z stacks of optical sections through cell monolayers. Scale bar represents 10 μm.
    Figure Legend Snippet: CMT-93 cells express protease-activated receptor 2 (PAR2). A: RT-PCR for PAR2 mRNA expression in CMT-93 cells. Reactions lacking reverse transcriptase enzyme (RT) and template control lacking cDNA were performed as controls. DNA ladder and the sizes (bp) are shown on the right of image, with expected product size being 167 bp (n = 3). B: Confocal immunocytochemistry for PAR2 in CMT-93 cell monolayers (n = 2). Green shows positive immunoreactivity for PAR2 and blue shows DAPI staining for nuclei. C: z stacks of optical sections through cell monolayers. Scale bar represents 10 μm.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Expressing, Immunocytochemistry, Staining

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 96
    Thermo Fisher generuler 1 kb plus dna ladder
    Generuler 1 Kb Plus Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/generuler 1 kb plus dna ladder/product/Thermo Fisher
    Average 96 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    generuler 1 kb plus dna ladder - by Bioz Stars, 2022-11
    96/100 stars
      Buy from Supplier

    88
    Thermo Fisher trackit 1 kb plus dna ladder
    Quantification of the number of dodecamers by fragment length analysis. ( Left ) PCR amplification with 5′-FAM labelled primers of a portion of ~180 bp across the dodecamer repeats of the CSTB promoter, performed on genomic <t>DNA</t> extracted from CTRL and ULD iPSCs and visualization of the amplified fragments on agarose gel (100-bp <t>DNA</t> <t>ladder</t> was used as a size marker). The position of Fw and Rv primers (at −296 bp and −118 bp, respectively) is indicated. ( Right ) Fragment length analysis by capillary electrophoresis of PCR products. The sizes of the main fragments are indicated above the peaks in bp. At 180 bp is the peak for the CTRL (2 dodecamers); at 644 bp are the peaks for the first allele of ULD1 and ULD2 (41 dodecamers); at 921 bp is the peak for the second allele of ULD1 (64 dodecamers); at 909 bp is the peak for the second allele of ULD2 (63 dodecamers). GeneScan LIZ 1200 was used as marker size (orange peaks in CTRL electropherogram) and the data were analyzed by Eurofins with GeneMapper 6 software (Applied Biosystems). Representative images were created using Peak Scanner software (v. 2.0; Applied Biosystems).
    Trackit 1 Kb Plus Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/trackit 1 kb plus dna ladder/product/Thermo Fisher
    Average 88 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    trackit 1 kb plus dna ladder - by Bioz Stars, 2022-11
    88/100 stars
      Buy from Supplier

    90
    Thermo Fisher kb plus dna ladder
    EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid <t>DNA)</t> of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).
    Kb Plus Dna Ladder, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/kb plus dna ladder/product/Thermo Fisher
    Average 90 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    kb plus dna ladder - by Bioz Stars, 2022-11
    90/100 stars
      Buy from Supplier

    Image Search Results


    Quantification of the number of dodecamers by fragment length analysis. ( Left ) PCR amplification with 5′-FAM labelled primers of a portion of ~180 bp across the dodecamer repeats of the CSTB promoter, performed on genomic DNA extracted from CTRL and ULD iPSCs and visualization of the amplified fragments on agarose gel (100-bp DNA ladder was used as a size marker). The position of Fw and Rv primers (at −296 bp and −118 bp, respectively) is indicated. ( Right ) Fragment length analysis by capillary electrophoresis of PCR products. The sizes of the main fragments are indicated above the peaks in bp. At 180 bp is the peak for the CTRL (2 dodecamers); at 644 bp are the peaks for the first allele of ULD1 and ULD2 (41 dodecamers); at 921 bp is the peak for the second allele of ULD1 (64 dodecamers); at 909 bp is the peak for the second allele of ULD2 (63 dodecamers). GeneScan LIZ 1200 was used as marker size (orange peaks in CTRL electropherogram) and the data were analyzed by Eurofins with GeneMapper 6 software (Applied Biosystems). Representative images were created using Peak Scanner software (v. 2.0; Applied Biosystems).

    Journal: Cells

    Article Title: Insights into the Genetic Profile of Two Siblings Affected by Unverricht-Lundborg Disease Using Patient-Derived hiPSCs

    doi: 10.3390/cells11213491

    Figure Lengend Snippet: Quantification of the number of dodecamers by fragment length analysis. ( Left ) PCR amplification with 5′-FAM labelled primers of a portion of ~180 bp across the dodecamer repeats of the CSTB promoter, performed on genomic DNA extracted from CTRL and ULD iPSCs and visualization of the amplified fragments on agarose gel (100-bp DNA ladder was used as a size marker). The position of Fw and Rv primers (at −296 bp and −118 bp, respectively) is indicated. ( Right ) Fragment length analysis by capillary electrophoresis of PCR products. The sizes of the main fragments are indicated above the peaks in bp. At 180 bp is the peak for the CTRL (2 dodecamers); at 644 bp are the peaks for the first allele of ULD1 and ULD2 (41 dodecamers); at 921 bp is the peak for the second allele of ULD1 (64 dodecamers); at 909 bp is the peak for the second allele of ULD2 (63 dodecamers). GeneScan LIZ 1200 was used as marker size (orange peaks in CTRL electropherogram) and the data were analyzed by Eurofins with GeneMapper 6 software (Applied Biosystems). Representative images were created using Peak Scanner software (v. 2.0; Applied Biosystems).

    Article Snippet: PCR products were loaded on 1% agarose gel without loading dye using TrackIt 1 Kb Plus DNA Ladder (Invitrogen, Waltham, MA, USA).

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

    EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid DNA) of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).

    Journal: bioRxiv

    Article Title: Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering

    doi: 10.1101/2022.10.31.514646

    Figure Lengend Snippet: EHCas9 PAM screening and validation. ( A ) Sequence logo of the PAM region preferred by EHCas9 for target cleavage, as determined by in vivo screening of a PAM library. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 2nd to the 4th position were tested (the first position was kept invariable, corresponding to thymine). ( B ) Sequence logo of the consensus PAM preferred by EHCas9 for target cleavage as determined through in vitro screening. Nucleotide positions 3’ from the end of the spacer-matching strand of the target are indicated. Nucleotides from the 1st to the 7th position were tested. ( C ) In vivo PAM validation. The efficiency of transformation (number of colony-forming units – CFU - per mg of plasmid DNA) of E. coli cells expressing (+ EHCas9) or not (-EHCas9) EHCas9 in addition to a guide EH crRNA and the predicted EH tracrRNA, with plasmids carrying a target adjacent to sequences varying in the 2 nd , the 3 rd and the 4 th positions (ACC, GGA, GGC, GGG, GGT) of the PAM region, is represented. Data are the mean of three replicates (error bars correspond to the standard deviation).

    Article Snippet: The 1 Kb Plus DNA Ladder (Invitrogen) was included in the agarose gels as a DNA weight marker.

    Techniques: Sequencing, In Vivo, In Vitro, Transformation Assay, Plasmid Preparation, Expressing, Standard Deviation

    EH sgRNA design. ( A ) RNA sequence alignments of the EH repeat, the predicted EH tracrRNA gene region and the designed EH sgRNA with the S. donghicola (Sdo) repeat, tracrRNA coding sequence and sgRNA, correspondingly. Matching positions are marked with asterisks. Promoter and terminator regions predicted for the EH tracrRNA gene are grey shaded. The constant region of the EH sgRNA sequence was conceived by joining the EH repeat sequence in orange and the EH tracrRNA sequence in blue. ( B ) Scheme of the EH sgRNA including a generic 23-nt spacer base-paired to the target strand in a DNA substrate containing a spacer-matching sequence and a compatible PAM (underlined). The EH sgRNA anti-repeat and tracrRNA sequences comprising the linker (tetraloop 5’-GAAA-3’), the anti-repeat and the two stem-loop forming segments, are coloured as in panel A.

    Journal: bioRxiv

    Article Title: Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering

    doi: 10.1101/2022.10.31.514646

    Figure Lengend Snippet: EH sgRNA design. ( A ) RNA sequence alignments of the EH repeat, the predicted EH tracrRNA gene region and the designed EH sgRNA with the S. donghicola (Sdo) repeat, tracrRNA coding sequence and sgRNA, correspondingly. Matching positions are marked with asterisks. Promoter and terminator regions predicted for the EH tracrRNA gene are grey shaded. The constant region of the EH sgRNA sequence was conceived by joining the EH repeat sequence in orange and the EH tracrRNA sequence in blue. ( B ) Scheme of the EH sgRNA including a generic 23-nt spacer base-paired to the target strand in a DNA substrate containing a spacer-matching sequence and a compatible PAM (underlined). The EH sgRNA anti-repeat and tracrRNA sequences comprising the linker (tetraloop 5’-GAAA-3’), the anti-repeat and the two stem-loop forming segments, are coloured as in panel A.

    Article Snippet: The 1 Kb Plus DNA Ladder (Invitrogen) was included in the agarose gels as a DNA weight marker.

    Techniques: Sequencing

    Representative agarose gel electrophoreses of in vitro EHCas9-mediated DNA cleavage reactions. Except indicated otherwise, experiments were performed under the following standard conditions: 30 min reaction time at 37°C, 20 mM MgCl 2 , 25 nM of an 840 bp linear DNA containing a target sequence and a compatible PAM, preincubated (15 min at 37°C) EHCas9:EH sgRNA mixtures (0.5 mM EHCas9 and 0.5 mM EH sgRNA concentration in the digestion reaction). The length of relevant bands (in kb) of a linear dsDNA molecular weight marker (M) and the position of bands corresponding to expected cut and uncut DNA substrates are indicated. (A) Samples from standard digestion reactions, mixed either after protein:guide preincubation (lane 2) or without preincubation (lane 7), and from reactions with a missing component (MgCl 2 , lane 3; a compatible PAM next to the target, lane 4; a guide, lane 5; the protein, lane 6) are included. (B) Samples from digestion reactions under standard conditions but for the protein concentration (up to 500 nM). (C) Samples from standard reactions incubated for up to 40 min. (D) Samples of digestions carried out under standard conditions except by the incubation temperature (from 20°C to 45 °C).

    Journal: bioRxiv

    Article Title: Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering

    doi: 10.1101/2022.10.31.514646

    Figure Lengend Snippet: Representative agarose gel electrophoreses of in vitro EHCas9-mediated DNA cleavage reactions. Except indicated otherwise, experiments were performed under the following standard conditions: 30 min reaction time at 37°C, 20 mM MgCl 2 , 25 nM of an 840 bp linear DNA containing a target sequence and a compatible PAM, preincubated (15 min at 37°C) EHCas9:EH sgRNA mixtures (0.5 mM EHCas9 and 0.5 mM EH sgRNA concentration in the digestion reaction). The length of relevant bands (in kb) of a linear dsDNA molecular weight marker (M) and the position of bands corresponding to expected cut and uncut DNA substrates are indicated. (A) Samples from standard digestion reactions, mixed either after protein:guide preincubation (lane 2) or without preincubation (lane 7), and from reactions with a missing component (MgCl 2 , lane 3; a compatible PAM next to the target, lane 4; a guide, lane 5; the protein, lane 6) are included. (B) Samples from digestion reactions under standard conditions but for the protein concentration (up to 500 nM). (C) Samples from standard reactions incubated for up to 40 min. (D) Samples of digestions carried out under standard conditions except by the incubation temperature (from 20°C to 45 °C).

    Article Snippet: The 1 Kb Plus DNA Ladder (Invitrogen) was included in the agarose gels as a DNA weight marker.

    Techniques: Agarose Gel Electrophoresis, In Vitro, Sequencing, Concentration Assay, Molecular Weight, Marker, Protein Concentration, Incubation

    Prokaryotic genome editing with EHCas9. (A) Overview of the single-step general procedure for positive selection of genome-edited E. coli. E. coli cells harbouring a plasmid ( e.g ., pKD46; ampicillin resistance, Amp R ) encoding Lambda Red recombination proteins (Gam, Beta, Exo) are co-transformed with an antibiotic resistance (Ab R ) selectable plasmid carrying inducible ehcas9 gene and a sgRNA targeting a sequence within the gene of interest (GOI) and a linear dsDNA template matching both sides of the target (flanking sites, FS). Recombination between the template and the flanking sites in the gene mediated by the Lambda Red recombination machinery (RM) will result in the deletion of the target sequence. The Cas9:sgRNA ribonucleoprotein complex will produce double-strand breaks in the non-edited target, often leading to cell death. Colonies grown at 37°C expressing Cas9 are selected on plates ( i.e ., arabinose and antibiotic-containing medium) and screened through PCR amplification and agarose gel electrophoresis to confirm the deletion. (B) An agarose gel electrophoresis of PCR products from the region surrounding pyrF (the gene of interest) in E. coli cells expressing the Lambda Red system from pKD46. DNA used for amplification was purified from chloramphenicol-resistant colonies grown in the presence of arabinose after co-transformation with a recombination template matching the flanks of pyrF (recombination would lead to a ca. 0.6 kb deletion), and a pBAD33-derivative plasmid (providing chloramphenicol resistance) encoding either both EHCas9 and an EH sgRNA that targets the pyrF gene (+ EHCas9) or only the EH sgRNA (-EHCas9). Each lane corresponds to a transformant clone. Bands running as linear DNA fragments with the length of the original (ca. 1 kb; WT) and the recombinant (ca. 0.5 kb; Mutant) pyrF region are indicated. The length of relevant bands of a linear dsDNA molecular weight marker is indicated.

    Journal: bioRxiv

    Article Title: Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering

    doi: 10.1101/2022.10.31.514646

    Figure Lengend Snippet: Prokaryotic genome editing with EHCas9. (A) Overview of the single-step general procedure for positive selection of genome-edited E. coli. E. coli cells harbouring a plasmid ( e.g ., pKD46; ampicillin resistance, Amp R ) encoding Lambda Red recombination proteins (Gam, Beta, Exo) are co-transformed with an antibiotic resistance (Ab R ) selectable plasmid carrying inducible ehcas9 gene and a sgRNA targeting a sequence within the gene of interest (GOI) and a linear dsDNA template matching both sides of the target (flanking sites, FS). Recombination between the template and the flanking sites in the gene mediated by the Lambda Red recombination machinery (RM) will result in the deletion of the target sequence. The Cas9:sgRNA ribonucleoprotein complex will produce double-strand breaks in the non-edited target, often leading to cell death. Colonies grown at 37°C expressing Cas9 are selected on plates ( i.e ., arabinose and antibiotic-containing medium) and screened through PCR amplification and agarose gel electrophoresis to confirm the deletion. (B) An agarose gel electrophoresis of PCR products from the region surrounding pyrF (the gene of interest) in E. coli cells expressing the Lambda Red system from pKD46. DNA used for amplification was purified from chloramphenicol-resistant colonies grown in the presence of arabinose after co-transformation with a recombination template matching the flanks of pyrF (recombination would lead to a ca. 0.6 kb deletion), and a pBAD33-derivative plasmid (providing chloramphenicol resistance) encoding either both EHCas9 and an EH sgRNA that targets the pyrF gene (+ EHCas9) or only the EH sgRNA (-EHCas9). Each lane corresponds to a transformant clone. Bands running as linear DNA fragments with the length of the original (ca. 1 kb; WT) and the recombinant (ca. 0.5 kb; Mutant) pyrF region are indicated. The length of relevant bands of a linear dsDNA molecular weight marker is indicated.

    Article Snippet: The 1 Kb Plus DNA Ladder (Invitrogen) was included in the agarose gels as a DNA weight marker.

    Techniques: Selection, Plasmid Preparation, Transformation Assay, Sequencing, Expressing, Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Purification, Recombinant, Mutagenesis, Molecular Weight, Marker