Structured Review

MACHEREY NAGEL pcr cleanup kit
Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the <t>PCR</t> verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic <t>DNA</t> of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).
Pcr Cleanup Kit, supplied by MACHEREY NAGEL, used in various techniques. Bioz Stars score: 92/100, based on 98 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/pcr cleanup kit/product/MACHEREY NAGEL
Average 92 stars, based on 98 article reviews
Price from $9.99 to $1999.99
pcr cleanup kit - by Bioz Stars, 2020-07
92/100 stars

Images

1) Product Images from "Modular and Integrative Vectors for Synthetic Biology Applications in Streptomyces spp."

Article Title: Modular and Integrative Vectors for Synthetic Biology Applications in Streptomyces spp.

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.00485-19

Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the PCR verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic DNA of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).
Figure Legend Snippet: Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the PCR verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic DNA of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).

Techniques Used: Polymerase Chain Reaction, Amplification, Molecular Weight

2) Product Images from "Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper. Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper"

Article Title: Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper. Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper

Journal: Ecology and Evolution

doi: 10.1002/ece3.3745

Expression of opsin genes in eyes of adult flounders. (a) RT ‐ PCR analysis of the opsin genes in ocular RNA from the three flounder species, including V. variegatus (Vva), M. achne (Mac), and P. olivaceus (Pol). Nucleotide sequences for rh2‐b and rh2‐c were detected in rh2‐b/c of Vva and Pol. RT ‐ PCR amplicons are indicated by arrows. RT (+): RT ‐ PCR , RT (−): Non‐reverse‐transcribed PCR was the negative control. (b) Genomic PCR analysis of the rh2‐a (Mac rh2‐a and Pol rh2‐a2 : white arrowhead, Pol rh2‐a1 : double arrowhead), rh2‐b and rh2‐c (arrow) for the flounder genomic DNA . Asterisk is nonspecific amplification. DNA size standards are indicated in kilobases (kb)
Figure Legend Snippet: Expression of opsin genes in eyes of adult flounders. (a) RT ‐ PCR analysis of the opsin genes in ocular RNA from the three flounder species, including V. variegatus (Vva), M. achne (Mac), and P. olivaceus (Pol). Nucleotide sequences for rh2‐b and rh2‐c were detected in rh2‐b/c of Vva and Pol. RT ‐ PCR amplicons are indicated by arrows. RT (+): RT ‐ PCR , RT (−): Non‐reverse‐transcribed PCR was the negative control. (b) Genomic PCR analysis of the rh2‐a (Mac rh2‐a and Pol rh2‐a2 : white arrowhead, Pol rh2‐a1 : double arrowhead), rh2‐b and rh2‐c (arrow) for the flounder genomic DNA . Asterisk is nonspecific amplification. DNA size standards are indicated in kilobases (kb)

Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Negative Control, Amplification

3) Product Images from "ARID3B: a Novel Regulator of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle"

Article Title: ARID3B: a Novel Regulator of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle

Journal: Journal of Virology

doi: 10.1128/JVI.03262-15

ARID3B interacts with the KSHV genome in a lytic reactivation-dependent manner. (A) DNA affinity assays performed according to the method in reference 25 ; biotinylated PCR products spanning oriLyt left of KSHV (GenBank accession number NC_009333.1 ) and control DNA amplified from the RTA coding region were bound to streptavidin-Dynabeads and incubated with lysates from reactivated 293T rKSHV.219 cells expressing FLAG-ARID3B. This suggested that ARID3B bound these sequences with preference for the A/T-rich region. IB, immunoblotting. (B) TREx-BCBL1-RTA cells were treated with doxycycline for 18 h (w/Dox) to reactivate the lytic cycle or were left untreated (w/o Dox). Samples were subjected to ChIP with an antibody to ARID3B or normal rabbit IgG and primers specific for sequences in the A/T-rich region of oriLyt or the RTA coding region. The percentage of output versus input DNA was calculated and is presented relative to normal rabbit IgG values from unreactivated (w/o Dox) cells (set to 1). Data represent two biological replicates (i.e., independent ChIPs) and two technical replicates per ChIP from a single experiment, and values are given as the mean ± standard deviation. Student t tests were used to determine statistical significance.
Figure Legend Snippet: ARID3B interacts with the KSHV genome in a lytic reactivation-dependent manner. (A) DNA affinity assays performed according to the method in reference 25 ; biotinylated PCR products spanning oriLyt left of KSHV (GenBank accession number NC_009333.1 ) and control DNA amplified from the RTA coding region were bound to streptavidin-Dynabeads and incubated with lysates from reactivated 293T rKSHV.219 cells expressing FLAG-ARID3B. This suggested that ARID3B bound these sequences with preference for the A/T-rich region. IB, immunoblotting. (B) TREx-BCBL1-RTA cells were treated with doxycycline for 18 h (w/Dox) to reactivate the lytic cycle or were left untreated (w/o Dox). Samples were subjected to ChIP with an antibody to ARID3B or normal rabbit IgG and primers specific for sequences in the A/T-rich region of oriLyt or the RTA coding region. The percentage of output versus input DNA was calculated and is presented relative to normal rabbit IgG values from unreactivated (w/o Dox) cells (set to 1). Data represent two biological replicates (i.e., independent ChIPs) and two technical replicates per ChIP from a single experiment, and values are given as the mean ± standard deviation. Student t tests were used to determine statistical significance.

Techniques Used: Polymerase Chain Reaction, Amplification, Incubation, Expressing, Chromatin Immunoprecipitation, Standard Deviation

Related Articles

Nucleic Acid Electrophoresis:

Article Title: Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota
Article Snippet: .. PCR products were validated for correct size and absence of contamination by gel electrophoresis, followed by gel purification with the NucleoSpin Gel and PCR cleanup kit (Macherey–Nagel, Germany) and DNA quantification. .. Gel purification is required to remove the plastid derived PCR product (light gel band at approx.

Amplification:

Article Title: Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper. Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper
Article Snippet: .. Amplified DNA fragments were purifi ed using the Nucleospin gel and PCR cleanup kit (Macherey‐Nagel, Düren, Germany) after agarose gel electrophoresis. .. Custom oligonucleotides designed for PCR (Table ) were synthesized at Life Technologies (Carlsbad, CA, USA).

Agarose Gel Electrophoresis:

Article Title: Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper. Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper
Article Snippet: .. Amplified DNA fragments were purifi ed using the Nucleospin gel and PCR cleanup kit (Macherey‐Nagel, Düren, Germany) after agarose gel electrophoresis. .. Custom oligonucleotides designed for PCR (Table ) were synthesized at Life Technologies (Carlsbad, CA, USA).

Article Title: Ablation of Programmed −1 Ribosomal Frameshifting in Venezuelan Equine Encephalitis Virus Results in Attenuated Neuropathogenicity
Article Snippet: .. The restriction digestion products were separated via 1% agarose gel electrophoresis, visualized by ethidium bromide staining and UV detection, and isolated by use of a NucleoSpin gel and PCR cleanup kit (Macherey-Nagel). .. Experimental plasmid inserts containing putative frameshift signals were generated as gBlocks (IDT) using complementary oligonucleotides and cloned into the linearized plasmid backbone by use of an in-fusion HD cloning kit (Clontech Laboratories).

Isolation:

Article Title: Ablation of Programmed −1 Ribosomal Frameshifting in Venezuelan Equine Encephalitis Virus Results in Attenuated Neuropathogenicity
Article Snippet: .. The restriction digestion products were separated via 1% agarose gel electrophoresis, visualized by ethidium bromide staining and UV detection, and isolated by use of a NucleoSpin gel and PCR cleanup kit (Macherey-Nagel). .. Experimental plasmid inserts containing putative frameshift signals were generated as gBlocks (IDT) using complementary oligonucleotides and cloned into the linearized plasmid backbone by use of an in-fusion HD cloning kit (Clontech Laboratories).

Purification:

Article Title: Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes
Article Snippet: .. The obtained amplicons were purified with Qiagen PCR CleanUp kit (Macherey-Nagel, Hoerdt, France) and normalized after quantification with the Qubit dsDNA HS Assay Kit (Life Technologies, United States). .. The equimolar pool of uniquely barcoded amplicons was paired-end sequenced (2 × 300 bp) on an Illumina MiSeq platform at the Institute for Integrative Genome Biology, University of California, Riverside.

Article Title: TCR Fingerprinting and Off-Target Peptide Identification
Article Snippet: .. Initial denaturation step was performed at 98°C for 1 min followed by 40 PCR cycles, consisting of a denaturation step at 98°C for 10 s, an annealing step at 65°C for 3 s, an extension step at 72°C for 10 s and a final extension step at 72°C for 5 min. PCR reactions were purified using the NucleoSpinGel and PCR Cleanup Kit from Macherey-Nagel. .. In vitro transcription was performed using HiScribe™ T7 ARCA mRNA Kit (with tailing; NEB) following the manufacturer's protocol for mRNA Synthesis with Modified Nucleotides.

Article Title: Isolation and Characterization of an Anti-listerial Bacteriocin fromLeuconostoc lactis SD501
Article Snippet: .. Then, the PCR products were purified using a commercial PCR cleanup kit for the purification of sequencing fragments (MACHEREY-NAGEL GmbH, Germany). .. The sequencing of the 16S rDNA fragment was performed by Cosmogenetech Co., Ltd. (Korea).

Article Title: Modular and Integrative Vectors for Synthetic Biology Applications in Streptomyces spp.
Article Snippet: .. DNA fragments were purified from agarose gels using the NucleoSpin gel and PCR cleanup kit from Macherey-Nagel. ..

Article Title: ARID3B: a Novel Regulator of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle
Article Snippet: .. DNA was purified using the NucleoSpin gel and PCR cleanup kit from Macherey-Nagel (catalog no. 740609) according to their DNA cleanup protocol for samples containing SDS. .. DNA was eluted with 90 μl buffer NE, and 5 μl of the DNA solution was used as the template DNA for qPCR using primers specific for the A/T-rich region of oriLyt left (forward primer, 5′-CCCTCCTTTGTTTTCCGGAAG-3′; reverse primer, 5′CTCATCGGGCCCTATTATAAAG-3′) and the RTA coding region (forward primer, 5′-GTCTACCTTCCGAGGATTATGG-3′; reverse primer, 5′-GATTCTGGCATGAGACCGCTTC-3′).

Polymerase Chain Reaction:

Article Title: Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes
Article Snippet: .. The obtained amplicons were purified with Qiagen PCR CleanUp kit (Macherey-Nagel, Hoerdt, France) and normalized after quantification with the Qubit dsDNA HS Assay Kit (Life Technologies, United States). .. The equimolar pool of uniquely barcoded amplicons was paired-end sequenced (2 × 300 bp) on an Illumina MiSeq platform at the Institute for Integrative Genome Biology, University of California, Riverside.

Article Title: TCR Fingerprinting and Off-Target Peptide Identification
Article Snippet: .. Initial denaturation step was performed at 98°C for 1 min followed by 40 PCR cycles, consisting of a denaturation step at 98°C for 10 s, an annealing step at 65°C for 3 s, an extension step at 72°C for 10 s and a final extension step at 72°C for 5 min. PCR reactions were purified using the NucleoSpinGel and PCR Cleanup Kit from Macherey-Nagel. .. In vitro transcription was performed using HiScribe™ T7 ARCA mRNA Kit (with tailing; NEB) following the manufacturer's protocol for mRNA Synthesis with Modified Nucleotides.

Article Title: Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper. Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper
Article Snippet: .. Amplified DNA fragments were purifi ed using the Nucleospin gel and PCR cleanup kit (Macherey‐Nagel, Düren, Germany) after agarose gel electrophoresis. .. Custom oligonucleotides designed for PCR (Table ) were synthesized at Life Technologies (Carlsbad, CA, USA).

Article Title: Ablation of Programmed −1 Ribosomal Frameshifting in Venezuelan Equine Encephalitis Virus Results in Attenuated Neuropathogenicity
Article Snippet: .. The restriction digestion products were separated via 1% agarose gel electrophoresis, visualized by ethidium bromide staining and UV detection, and isolated by use of a NucleoSpin gel and PCR cleanup kit (Macherey-Nagel). .. Experimental plasmid inserts containing putative frameshift signals were generated as gBlocks (IDT) using complementary oligonucleotides and cloned into the linearized plasmid backbone by use of an in-fusion HD cloning kit (Clontech Laboratories).

Article Title: Isolation and Characterization of an Anti-listerial Bacteriocin fromLeuconostoc lactis SD501
Article Snippet: .. Then, the PCR products were purified using a commercial PCR cleanup kit for the purification of sequencing fragments (MACHEREY-NAGEL GmbH, Germany). .. The sequencing of the 16S rDNA fragment was performed by Cosmogenetech Co., Ltd. (Korea).

Article Title: Modular and Integrative Vectors for Synthetic Biology Applications in Streptomyces spp.
Article Snippet: .. DNA fragments were purified from agarose gels using the NucleoSpin gel and PCR cleanup kit from Macherey-Nagel. ..

Article Title: Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota
Article Snippet: .. PCR products were validated for correct size and absence of contamination by gel electrophoresis, followed by gel purification with the NucleoSpin Gel and PCR cleanup kit (Macherey–Nagel, Germany) and DNA quantification. .. Gel purification is required to remove the plastid derived PCR product (light gel band at approx.

Article Title: ARID3B: a Novel Regulator of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle
Article Snippet: .. DNA was purified using the NucleoSpin gel and PCR cleanup kit from Macherey-Nagel (catalog no. 740609) according to their DNA cleanup protocol for samples containing SDS. .. DNA was eluted with 90 μl buffer NE, and 5 μl of the DNA solution was used as the template DNA for qPCR using primers specific for the A/T-rich region of oriLyt left (forward primer, 5′-CCCTCCTTTGTTTTCCGGAAG-3′; reverse primer, 5′CTCATCGGGCCCTATTATAAAG-3′) and the RTA coding region (forward primer, 5′-GTCTACCTTCCGAGGATTATGG-3′; reverse primer, 5′-GATTCTGGCATGAGACCGCTTC-3′).

Sequencing:

Article Title: Isolation and Characterization of an Anti-listerial Bacteriocin fromLeuconostoc lactis SD501
Article Snippet: .. Then, the PCR products were purified using a commercial PCR cleanup kit for the purification of sequencing fragments (MACHEREY-NAGEL GmbH, Germany). .. The sequencing of the 16S rDNA fragment was performed by Cosmogenetech Co., Ltd. (Korea).

Staining:

Article Title: Ablation of Programmed −1 Ribosomal Frameshifting in Venezuelan Equine Encephalitis Virus Results in Attenuated Neuropathogenicity
Article Snippet: .. The restriction digestion products were separated via 1% agarose gel electrophoresis, visualized by ethidium bromide staining and UV detection, and isolated by use of a NucleoSpin gel and PCR cleanup kit (Macherey-Nagel). .. Experimental plasmid inserts containing putative frameshift signals were generated as gBlocks (IDT) using complementary oligonucleotides and cloned into the linearized plasmid backbone by use of an in-fusion HD cloning kit (Clontech Laboratories).

Gel Purification:

Article Title: Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota
Article Snippet: .. PCR products were validated for correct size and absence of contamination by gel electrophoresis, followed by gel purification with the NucleoSpin Gel and PCR cleanup kit (Macherey–Nagel, Germany) and DNA quantification. .. Gel purification is required to remove the plastid derived PCR product (light gel band at approx.

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    MACHEREY NAGEL pcr cleanup kit
    Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the <t>PCR</t> verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic <t>DNA</t> of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).
    Pcr Cleanup Kit, supplied by MACHEREY NAGEL, used in various techniques. Bioz Stars score: 92/100, based on 98 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr cleanup kit/product/MACHEREY NAGEL
    Average 92 stars, based on 98 article reviews
    Price from $9.99 to $1999.99
    pcr cleanup kit - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

    88
    MACHEREY NAGEL nucleospin extract ii pcr cleanup kit
    Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the <t>PCR</t> verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic <t>DNA</t> of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).
    Nucleospin Extract Ii Pcr Cleanup Kit, supplied by MACHEREY NAGEL, 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/nucleospin extract ii pcr cleanup kit/product/MACHEREY NAGEL
    Average 88 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nucleospin extract ii pcr cleanup kit - by Bioz Stars, 2020-07
    88/100 stars
      Buy from Supplier

    Image Search Results


    Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the PCR verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic DNA of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).

    Journal: Applied and Environmental Microbiology

    Article Title: Modular and Integrative Vectors for Synthetic Biology Applications in Streptomyces spp.

    doi: 10.1128/AEM.00485-19

    Figure Lengend Snippet: Verification of the integration of pOSV802 in S. coelicolor M145, S. lividans TK23, and S. albus J1074 chromosomes. (A) Principle of the PCR verification of the integration of the pOSV801 to pOSV812 vectors in the Streptomyces chromosomes (PCR 1 and PCR 2) (PCR 3, PCR verification before excision of modules 1 to 3). (B) PCR fragments obtained by PCR 1 ( attL region; expected sizes, 913 bp for M145 and TK23, 888 bp for J1074) and by PCR 2 ( attR region; expected sizes, 911 bp for M145 and TK23, 907 bp for J1074) on the three Streptomyces strains bearing pOSV802. No PCR amplification is expected when the genomic DNA of the wild-type Streptomyces strains is used as the matrix. MW corresponds to the molecular weight ladder (Thermo Scientific GeneRuler DNA ladder mix).

    Article Snippet: DNA fragments were purified from agarose gels using the NucleoSpin gel and PCR cleanup kit from Macherey-Nagel.

    Techniques: Polymerase Chain Reaction, Amplification, Molecular Weight

    Expression of opsin genes in eyes of adult flounders. (a) RT ‐ PCR analysis of the opsin genes in ocular RNA from the three flounder species, including V. variegatus (Vva), M. achne (Mac), and P. olivaceus (Pol). Nucleotide sequences for rh2‐b and rh2‐c were detected in rh2‐b/c of Vva and Pol. RT ‐ PCR amplicons are indicated by arrows. RT (+): RT ‐ PCR , RT (−): Non‐reverse‐transcribed PCR was the negative control. (b) Genomic PCR analysis of the rh2‐a (Mac rh2‐a and Pol rh2‐a2 : white arrowhead, Pol rh2‐a1 : double arrowhead), rh2‐b and rh2‐c (arrow) for the flounder genomic DNA . Asterisk is nonspecific amplification. DNA size standards are indicated in kilobases (kb)

    Journal: Ecology and Evolution

    Article Title: Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper. Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper

    doi: 10.1002/ece3.3745

    Figure Lengend Snippet: Expression of opsin genes in eyes of adult flounders. (a) RT ‐ PCR analysis of the opsin genes in ocular RNA from the three flounder species, including V. variegatus (Vva), M. achne (Mac), and P. olivaceus (Pol). Nucleotide sequences for rh2‐b and rh2‐c were detected in rh2‐b/c of Vva and Pol. RT ‐ PCR amplicons are indicated by arrows. RT (+): RT ‐ PCR , RT (−): Non‐reverse‐transcribed PCR was the negative control. (b) Genomic PCR analysis of the rh2‐a (Mac rh2‐a and Pol rh2‐a2 : white arrowhead, Pol rh2‐a1 : double arrowhead), rh2‐b and rh2‐c (arrow) for the flounder genomic DNA . Asterisk is nonspecific amplification. DNA size standards are indicated in kilobases (kb)

    Article Snippet: Amplified DNA fragments were purifi ed using the Nucleospin gel and PCR cleanup kit (Macherey‐Nagel, Düren, Germany) after agarose gel electrophoresis.

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Negative Control, Amplification

    ARID3B interacts with the KSHV genome in a lytic reactivation-dependent manner. (A) DNA affinity assays performed according to the method in reference 25 ; biotinylated PCR products spanning oriLyt left of KSHV (GenBank accession number NC_009333.1 ) and control DNA amplified from the RTA coding region were bound to streptavidin-Dynabeads and incubated with lysates from reactivated 293T rKSHV.219 cells expressing FLAG-ARID3B. This suggested that ARID3B bound these sequences with preference for the A/T-rich region. IB, immunoblotting. (B) TREx-BCBL1-RTA cells were treated with doxycycline for 18 h (w/Dox) to reactivate the lytic cycle or were left untreated (w/o Dox). Samples were subjected to ChIP with an antibody to ARID3B or normal rabbit IgG and primers specific for sequences in the A/T-rich region of oriLyt or the RTA coding region. The percentage of output versus input DNA was calculated and is presented relative to normal rabbit IgG values from unreactivated (w/o Dox) cells (set to 1). Data represent two biological replicates (i.e., independent ChIPs) and two technical replicates per ChIP from a single experiment, and values are given as the mean ± standard deviation. Student t tests were used to determine statistical significance.

    Journal: Journal of Virology

    Article Title: ARID3B: a Novel Regulator of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle

    doi: 10.1128/JVI.03262-15

    Figure Lengend Snippet: ARID3B interacts with the KSHV genome in a lytic reactivation-dependent manner. (A) DNA affinity assays performed according to the method in reference 25 ; biotinylated PCR products spanning oriLyt left of KSHV (GenBank accession number NC_009333.1 ) and control DNA amplified from the RTA coding region were bound to streptavidin-Dynabeads and incubated with lysates from reactivated 293T rKSHV.219 cells expressing FLAG-ARID3B. This suggested that ARID3B bound these sequences with preference for the A/T-rich region. IB, immunoblotting. (B) TREx-BCBL1-RTA cells were treated with doxycycline for 18 h (w/Dox) to reactivate the lytic cycle or were left untreated (w/o Dox). Samples were subjected to ChIP with an antibody to ARID3B or normal rabbit IgG and primers specific for sequences in the A/T-rich region of oriLyt or the RTA coding region. The percentage of output versus input DNA was calculated and is presented relative to normal rabbit IgG values from unreactivated (w/o Dox) cells (set to 1). Data represent two biological replicates (i.e., independent ChIPs) and two technical replicates per ChIP from a single experiment, and values are given as the mean ± standard deviation. Student t tests were used to determine statistical significance.

    Article Snippet: DNA was purified using the NucleoSpin gel and PCR cleanup kit from Macherey-Nagel (catalog no. 740609) according to their DNA cleanup protocol for samples containing SDS.

    Techniques: Polymerase Chain Reaction, Amplification, Incubation, Expressing, Chromatin Immunoprecipitation, Standard Deviation