bamhi New England Biolabs Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    New England Biolabs pvuii new england biolabs
    TMV-CP DNA fragments (1% agarose gel). ( A ) The whole TMV-CP fragments with <t>BamH</t> I and Xho I restriction enzyme cutting sites which have been cloned in <t>PGEX-6P-1.</t> As shown in lane 1, amplified PCR product ran at approximately 500 bp compared with the DNA marker (lane M). Lane 2 is a positive control with DNA template. Lane 3 is a negative control without DNA template. ( B ) The whole TMV-CP fragments with Nde I and Xho I restriction enzyme cutting sites that have been cloned in pET28a. As shown in lane 1, amplified PCR product ran at approximately 500 bp compared with the DNA marker (lane M). Lane 2 is a negative control without DNA template. Lane 3 is a positive control with DNA template. ( C ) The truncation of four amino acids from the C-terminus of TMV-CP fragments with Nde I and Xho I restriction enzyme cutting sites that have been cloned in pET28a. Lane 1 is a negative control without DNA template, whereas lane 2 is a positive control with DNA template. Lane 3 is the amplified PCR product that ran at approximately 500 bp compared with the DNA marker (lane M).
    Pvuii New England Biolabs, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 376 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pvuii new england biolabs/product/New England Biolabs
    Average 99 stars, based on 376 article reviews
    Price from $9.99 to $1999.99
    pvuii new england biolabs - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs hf bamhi new england biolabs
    TMV-CP DNA fragments (1% agarose gel). ( A ) The whole TMV-CP fragments with <t>BamH</t> I and Xho I restriction enzyme cutting sites which have been cloned in <t>PGEX-6P-1.</t> As shown in lane 1, amplified PCR product ran at approximately 500 bp compared with the DNA marker (lane M). Lane 2 is a positive control with DNA template. Lane 3 is a negative control without DNA template. ( B ) The whole TMV-CP fragments with Nde I and Xho I restriction enzyme cutting sites that have been cloned in pET28a. As shown in lane 1, amplified PCR product ran at approximately 500 bp compared with the DNA marker (lane M). Lane 2 is a negative control without DNA template. Lane 3 is a positive control with DNA template. ( C ) The truncation of four amino acids from the C-terminus of TMV-CP fragments with Nde I and Xho I restriction enzyme cutting sites that have been cloned in pET28a. Lane 1 is a negative control without DNA template, whereas lane 2 is a positive control with DNA template. Lane 3 is the amplified PCR product that ran at approximately 500 bp compared with the DNA marker (lane M).
    Hf Bamhi New England Biolabs, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hf bamhi new england biolabs/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    hf bamhi new england biolabs - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs kpn hf restriction enzyme new england biolabs
    Generation of vPK transgenic mice. FLAG-tagged vPK was cloned, using HinDIII-HF and <t>BamHI-HF,</t> into a plasmid containing a Ub- and hGH-stabilization element. The linearized transgene fragment was microinjected into the embryos of C57BL/6 mice and implanted into pseudopregnant female mice. Each vPK line was developed from breeding a vPK founder to a C57BL/6 mouse. ( A ) Schematic of the linearized construct used to generate the vPK transgenic mice, as well as the cut sites and probe for the Southern blot in D . ( B ) <t>DNA</t> from the tails of 2 WT (wA and wB) and 2 vPK transgenic mice (vA and vB) for lines 1 and 2 was isolated and evaluated by PCR for the vPK transgene. ( C ) Expression of vPK protein in lysates from spleens of the mice in B as determined by SDS-PAGE and Western blot. Lysate from HEK-293 cells that transiently express vPK was used as a positive control for vPK expression. ( D ) Southern blot of WT, vPK1, and vPK2. DNA was isolated from the spleens of WT and vPK lines 1 and 2. D, double digest with HinDIII-HF and BamHI-HF; S, single digestion with AFlII; p-vPK, plasmid Ub.vPK.hGH.
    Kpn Hf Restriction Enzyme New England Biolabs, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 99 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/kpn hf restriction enzyme new england biolabs/product/New England Biolabs
    Average 99 stars, based on 99 article reviews
    Price from $9.99 to $1999.99
    kpn hf restriction enzyme new england biolabs - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs ecori bamhi
    Generation of vPK transgenic mice. FLAG-tagged vPK was cloned, using HinDIII-HF and <t>BamHI-HF,</t> into a plasmid containing a Ub- and hGH-stabilization element. The linearized transgene fragment was microinjected into the embryos of C57BL/6 mice and implanted into pseudopregnant female mice. Each vPK line was developed from breeding a vPK founder to a C57BL/6 mouse. ( A ) Schematic of the linearized construct used to generate the vPK transgenic mice, as well as the cut sites and probe for the Southern blot in D . ( B ) <t>DNA</t> from the tails of 2 WT (wA and wB) and 2 vPK transgenic mice (vA and vB) for lines 1 and 2 was isolated and evaluated by PCR for the vPK transgene. ( C ) Expression of vPK protein in lysates from spleens of the mice in B as determined by SDS-PAGE and Western blot. Lysate from HEK-293 cells that transiently express vPK was used as a positive control for vPK expression. ( D ) Southern blot of WT, vPK1, and vPK2. DNA was isolated from the spleens of WT and vPK lines 1 and 2. D, double digest with HinDIII-HF and BamHI-HF; S, single digestion with AFlII; p-vPK, plasmid Ub.vPK.hGH.
    Ecori Bamhi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ecori bamhi/product/New England Biolabs
    Average 99 stars, based on 50 article reviews
    Price from $9.99 to $1999.99
    ecori bamhi - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    Image Search Results


    TMV-CP DNA fragments (1% agarose gel). ( A ) The whole TMV-CP fragments with BamH I and Xho I restriction enzyme cutting sites which have been cloned in PGEX-6P-1. As shown in lane 1, amplified PCR product ran at approximately 500 bp compared with the DNA marker (lane M). Lane 2 is a positive control with DNA template. Lane 3 is a negative control without DNA template. ( B ) The whole TMV-CP fragments with Nde I and Xho I restriction enzyme cutting sites that have been cloned in pET28a. As shown in lane 1, amplified PCR product ran at approximately 500 bp compared with the DNA marker (lane M). Lane 2 is a negative control without DNA template. Lane 3 is a positive control with DNA template. ( C ) The truncation of four amino acids from the C-terminus of TMV-CP fragments with Nde I and Xho I restriction enzyme cutting sites that have been cloned in pET28a. Lane 1 is a negative control without DNA template, whereas lane 2 is a positive control with DNA template. Lane 3 is the amplified PCR product that ran at approximately 500 bp compared with the DNA marker (lane M).

    Journal: Virology Journal

    Article Title: The development and application of new crystallization method for tobacco mosaic virus coat protein

    doi: 10.1186/1743-422X-9-279

    Figure Lengend Snippet: TMV-CP DNA fragments (1% agarose gel). ( A ) The whole TMV-CP fragments with BamH I and Xho I restriction enzyme cutting sites which have been cloned in PGEX-6P-1. As shown in lane 1, amplified PCR product ran at approximately 500 bp compared with the DNA marker (lane M). Lane 2 is a positive control with DNA template. Lane 3 is a negative control without DNA template. ( B ) The whole TMV-CP fragments with Nde I and Xho I restriction enzyme cutting sites that have been cloned in pET28a. As shown in lane 1, amplified PCR product ran at approximately 500 bp compared with the DNA marker (lane M). Lane 2 is a negative control without DNA template. Lane 3 is a positive control with DNA template. ( C ) The truncation of four amino acids from the C-terminus of TMV-CP fragments with Nde I and Xho I restriction enzyme cutting sites that have been cloned in pET28a. Lane 1 is a negative control without DNA template, whereas lane 2 is a positive control with DNA template. Lane 3 is the amplified PCR product that ran at approximately 500 bp compared with the DNA marker (lane M).

    Article Snippet: Both plasmid PGEX-6P-1 (Novagen) and CP were digested with BamH I (NEB, 10 units/μL)/Xho I (NEB, 10 units/μL) and cloned into the same sites in PGEX-6P-1 (PGEX-6P-1-WT-GST-TMV-CP32 ).

    Techniques: Agarose Gel Electrophoresis, Clone Assay, Amplification, Polymerase Chain Reaction, Marker, Positive Control, Negative Control

    Distinct Influences of the Ku80 C-terminus on DNA-PK Activation with Linearized Plasmid DNA. a) DNA-PK kinase stimulation with plasmid DNA linearized with EcoRV generating blunt-ended termini and with KpnI generating 4 base 3’ single stranded overhangs. b) DNA-PK kinase stimulation with plasmid DNA linearized with XhoI and BamHI generating 4 base 5’ single stranded overhangs. DNA substrates are depicted pictorially. DNA termini generated by digestion are depicted below each graph indicating locations of pyrimidines (Py) and purines (Pu). Kinase activity is reported as the mean and SD of pmol of phosphate transferred. Asterisks indicate statistically significant differences compared to wild type (p

    Journal: PLoS ONE

    Article Title: Recognition of DNA Termini by the C-Terminal Region of the Ku80 and the DNA-Dependent Protein Kinase Catalytic Subunit

    doi: 10.1371/journal.pone.0127321

    Figure Lengend Snippet: Distinct Influences of the Ku80 C-terminus on DNA-PK Activation with Linearized Plasmid DNA. a) DNA-PK kinase stimulation with plasmid DNA linearized with EcoRV generating blunt-ended termini and with KpnI generating 4 base 3’ single stranded overhangs. b) DNA-PK kinase stimulation with plasmid DNA linearized with XhoI and BamHI generating 4 base 5’ single stranded overhangs. DNA substrates are depicted pictorially. DNA termini generated by digestion are depicted below each graph indicating locations of pyrimidines (Py) and purines (Pu). Kinase activity is reported as the mean and SD of pmol of phosphate transferred. Asterisks indicate statistically significant differences compared to wild type (p

    Article Snippet: Kinase assays using plasmid DNA substrates were performed with pcDNA3.1 digested with either XhoI, BamHI, EcoRV, and KpnI or pCAG-GFP digested with XbaI or EcoRI (New England Biolabs).

    Techniques: Activation Assay, Plasmid Preparation, Generated, Activity Assay

    Sperm transfected with E6/E7 plasmid penetrate oocytes. a . Scheme of the recombinant plasmid pIRES2-AcGFP1-E6E7. E6/E7 genes have been amplified (1032 bp) from plasmid p1321 HPV-16 E6/E7 by PCR and subcloned to plasmid pIRES2-AcGFP1 between SalI and BamHI restriction sites. b . PCR for HPV E6/E7 genes from transfected sperm. Lane M: DNA marker (100 bp); 1: sperm transfected with recombinant E6/E7 plasmid; 2: negative control (no template); 3: sperm transfected only with Lipofectamine 2000; 4: positive control (pIRES2-AcGFP1-E6E7 plasmid). c . Mean number of human sperm penetrated per hamster oocyte in control and sperm transfected with HPV-16 E6/E7 plasmid. d . Hamster oocytes penetrated by control sperm and sperm transfected with HPV16 E6/E7 plasmid in bright field (BF, upper panel) and fluorescence (FL, lower panel) using SYBR green DNA stain.

    Journal: PLoS ONE

    Article Title: Mechanism of Human Papillomavirus Binding to Human Spermatozoa and Fertilizing Ability of Infected Spermatozoa

    doi: 10.1371/journal.pone.0015036

    Figure Lengend Snippet: Sperm transfected with E6/E7 plasmid penetrate oocytes. a . Scheme of the recombinant plasmid pIRES2-AcGFP1-E6E7. E6/E7 genes have been amplified (1032 bp) from plasmid p1321 HPV-16 E6/E7 by PCR and subcloned to plasmid pIRES2-AcGFP1 between SalI and BamHI restriction sites. b . PCR for HPV E6/E7 genes from transfected sperm. Lane M: DNA marker (100 bp); 1: sperm transfected with recombinant E6/E7 plasmid; 2: negative control (no template); 3: sperm transfected only with Lipofectamine 2000; 4: positive control (pIRES2-AcGFP1-E6E7 plasmid). c . Mean number of human sperm penetrated per hamster oocyte in control and sperm transfected with HPV-16 E6/E7 plasmid. d . Hamster oocytes penetrated by control sperm and sperm transfected with HPV16 E6/E7 plasmid in bright field (BF, upper panel) and fluorescence (FL, lower panel) using SYBR green DNA stain.

    Article Snippet: The PCR mixture consisted of 5 µL Expand high fidelity buffer with MgCl2 , 1 µL of PCR grade nucleotide mix (10×), 20 pmol of each primer with SalI and BamHI restriction sites (New England Biolabs, Ipswich, MA) including forward: 5′-GTGCGCGTCGACGTGATGCACCAAAAGAGAACTG-3′ and reverse: 5′-GTGCGCGGATCCGTGTGGTTTCTGAGAACAGATG-3′ , 0,75 µL Expand high fidelity enzyme mix (Expand High Fidelity PCR System dNTPack, Roche Applied Science, Mannheim, Germany) and sterile H2 O in a final volume of 50 μL.

    Techniques: Transfection, Plasmid Preparation, Recombinant, Amplification, Polymerase Chain Reaction, Marker, Negative Control, Positive Control, Fluorescence, SYBR Green Assay, Staining

    Replication fork leading strands progress up to the psoralen crosslink. (A) Sequence of the plasmid around the psoralen ICL with restriction sites used in B and C. Double arrows indicate the size of the replicated strands (lagging or leading) spanning the ICL site for the control or repaired plasmid. Single arrows indicate the progression of the leading strand to the ICL for the crosslinked plasmid. The strand size is shown above each product. (B) Mapping of leading strand progression for pTUC and pTUC-PSO after 65 min of incubation in Xenopus egg extracts in the continuous presence of [α- 32 P]-dATP. Plasmids were digested by the indicated enzymes and analyzed on 10% polyacrylamide denaturing gel. Faint bands visible in lanes 3 and 4 likely result from a star activity of Sac II. The two 28 nt size indicators are at two different positions due to gel smiling. (C) Mapping of leading strand progression for pTUC and pTUC-PSO at 25, 35, 50, 65, 85, 95, 120 and 180 min. Plasmids were digested with EcoRI and BamHI and subjected to migration on a 10% polyacrylamide denaturing gel. 28 nt and 46 nt fragments correspond to the DNA size expected for the leading strand arriving at the psoralen from the EcoRI side or BamHI side, respectively.

    Journal: PLoS ONE

    Article Title: Replication-Fork Stalling and Processing at a Single Psoralen Interstrand Crosslink in Xenopus Egg Extracts

    doi: 10.1371/journal.pone.0018554

    Figure Lengend Snippet: Replication fork leading strands progress up to the psoralen crosslink. (A) Sequence of the plasmid around the psoralen ICL with restriction sites used in B and C. Double arrows indicate the size of the replicated strands (lagging or leading) spanning the ICL site for the control or repaired plasmid. Single arrows indicate the progression of the leading strand to the ICL for the crosslinked plasmid. The strand size is shown above each product. (B) Mapping of leading strand progression for pTUC and pTUC-PSO after 65 min of incubation in Xenopus egg extracts in the continuous presence of [α- 32 P]-dATP. Plasmids were digested by the indicated enzymes and analyzed on 10% polyacrylamide denaturing gel. Faint bands visible in lanes 3 and 4 likely result from a star activity of Sac II. The two 28 nt size indicators are at two different positions due to gel smiling. (C) Mapping of leading strand progression for pTUC and pTUC-PSO at 25, 35, 50, 65, 85, 95, 120 and 180 min. Plasmids were digested with EcoRI and BamHI and subjected to migration on a 10% polyacrylamide denaturing gel. 28 nt and 46 nt fragments correspond to the DNA size expected for the leading strand arriving at the psoralen from the EcoRI side or BamHI side, respectively.

    Article Snippet: Denaturing gel electrophoretic analysis of crosslinked products Crosslinked samples were digested with BamHI + EcoRI (New England Biolabs), filled with [α-32 P]-dATP using AMV reverse transcriptase as described by the manufacturer (Finnzyme).

    Techniques: Sequencing, Plasmid Preparation, Incubation, Activity Assay, Migration

    TFO and purification of monomodified plasmid. (A) Structure of the TFO linked in 3′ to 4, 5′, 8-trimethylpsoralen and in 5′ to biotin. (B) Localization of the TFO binding site and position of the psoralen ICL on pTUC plasmid. P and A are schematic representations of primers for q-PCR used in (D). P primers surround the psoralen ICL site and amplify a region of 113 nt, the A primers amplify an undamaged regions of 129 nt. (C) Analysis of the crosslinked plasmid after UV irradiation and before (input) or after (purified) DTT elution from a strepatvidin column. DNA was digested with BamHI + EcoRI and radioactively labelled before electrophoresis on a 10% polyacrylamide denaturing gel. Interpretative diagrams of the relevant molecular species are shown on lane sides. (D) Input and purified plasmids were subjected to q-PCR with primers P and A. Mean values of 3 q-PCRs for the input and 12 q-PCRs for the purified plasmid are presented. For calculation details see Material and Methods . (E) After purification pTUC-PSO was analyzed on a 0.8% agarose gel TBE 1x alongside with control plasmid and a molecular weight ladder.

    Journal: PLoS ONE

    Article Title: Replication-Fork Stalling and Processing at a Single Psoralen Interstrand Crosslink in Xenopus Egg Extracts

    doi: 10.1371/journal.pone.0018554

    Figure Lengend Snippet: TFO and purification of monomodified plasmid. (A) Structure of the TFO linked in 3′ to 4, 5′, 8-trimethylpsoralen and in 5′ to biotin. (B) Localization of the TFO binding site and position of the psoralen ICL on pTUC plasmid. P and A are schematic representations of primers for q-PCR used in (D). P primers surround the psoralen ICL site and amplify a region of 113 nt, the A primers amplify an undamaged regions of 129 nt. (C) Analysis of the crosslinked plasmid after UV irradiation and before (input) or after (purified) DTT elution from a strepatvidin column. DNA was digested with BamHI + EcoRI and radioactively labelled before electrophoresis on a 10% polyacrylamide denaturing gel. Interpretative diagrams of the relevant molecular species are shown on lane sides. (D) Input and purified plasmids were subjected to q-PCR with primers P and A. Mean values of 3 q-PCRs for the input and 12 q-PCRs for the purified plasmid are presented. For calculation details see Material and Methods . (E) After purification pTUC-PSO was analyzed on a 0.8% agarose gel TBE 1x alongside with control plasmid and a molecular weight ladder.

    Article Snippet: Denaturing gel electrophoretic analysis of crosslinked products Crosslinked samples were digested with BamHI + EcoRI (New England Biolabs), filled with [α-32 P]-dATP using AMV reverse transcriptase as described by the manufacturer (Finnzyme).

    Techniques: Purification, Plasmid Preparation, Binding Assay, Polymerase Chain Reaction, Irradiation, Electrophoresis, Agarose Gel Electrophoresis, Molecular Weight

    Figure 4. In vivo assembly of synthetic genes by IVOE. Each overlapping region allowed crossover events to occur between fragments giving rise to an autonomously repaired vector containing single and double expression cassettes in the correct orientation. ( A ) and ( B ) Single expression cassettes are constructed in pESC by engineering specific primers containing overhangs to foster in vivo cloning with the linearized plasmid in yeast (pJRoC30 was used as template for Vp or Lac amplifications). ( C ) and ( D ) The pESC constructs obtained in ( A ) and ( B ) were used as scaffolds to assemble Lac and Vp genes under the control of different promoter/terminator pairs. Primers used: (1)-MCS1- Vp / Lac -α-BamHI, (2)-MCS2- Vp -ter-NheI, (3)-MCS2- Lac -ter-NheI, (4)-MCS1- Vp / Lac -α-SpeI, (5)-MCS1- Lac -ter-SacI and (6)-MCS1- Vp -ter-SacI. Black arrows indicate the direction of the transcription process.

    Journal: Bioengineered

    Article Title: Assembly of evolved ligninolytic genes in Saccharomyces cerevisiae

    doi: 10.4161/bioe.29167

    Figure Lengend Snippet: Figure 4. In vivo assembly of synthetic genes by IVOE. Each overlapping region allowed crossover events to occur between fragments giving rise to an autonomously repaired vector containing single and double expression cassettes in the correct orientation. ( A ) and ( B ) Single expression cassettes are constructed in pESC by engineering specific primers containing overhangs to foster in vivo cloning with the linearized plasmid in yeast (pJRoC30 was used as template for Vp or Lac amplifications). ( C ) and ( D ) The pESC constructs obtained in ( A ) and ( B ) were used as scaffolds to assemble Lac and Vp genes under the control of different promoter/terminator pairs. Primers used: (1)-MCS1- Vp / Lac -α-BamHI, (2)-MCS2- Vp -ter-NheI, (3)-MCS2- Lac -ter-NheI, (4)-MCS1- Vp / Lac -α-SpeI, (5)-MCS1- Lac -ter-SacI and (6)-MCS1- Vp -ter-SacI. Black arrows indicate the direction of the transcription process.

    Article Snippet: The ura3 -deficient S. cerevisiae strain BJ5465 ( α ura3–52 trp1 leu2Δ1 his3Δ200 pep4::HIS2 prb1Δ1.6R can1 GAL1 ) was obtained from LGCPromochem, the NucleoSpin Plasmid kit was purchased from Macherey-Nagel, and the restriction enzymes BamHI, NheI, SpeI, SacI, and NotI from New England Biolabs.

    Techniques: In Vivo, Plasmid Preparation, Expressing, Construct, Clone Assay

    ZEBRA mutants defective in lytic replication and late gene expression. (A) Z(R187K) and Z(K188A) fail to activate two late proteins, FR3 and LR2. Immunoblot analysis of extracts prepared from BZKO cells transfected with expression vectors encoding wt ZEBRA (Z) and the following ZEBRA mutants: Z(K188A), Z(F193E), and Z(R187K). The membrane was probed for the EBV gene products, Rta, EA-D (early antigen-diffuse, the DNA polymerase processivity factor or BMRF1), ZEBRA, LR2 and FR3. NS, non specific. B) Z(Y180E), but not its revertant, specifically fails to activate EBV late gene expression. An immunoblot of transfected BZKO cells was probed with antibodies as described in panel A. C) and D) Southern blots assessing lytic viral DNA replication. Total DNA was extracted 48 hrs after transfection of the expression vectors. The DNA was digested with BamH1. The blots were probed with either a 0.3 kb subfragment of the Xho 1.9 fragment (Fig. 1C) or the BamH1 W fragment (Fig. 1D). FT, fused termini of the endogenous viral genome (v); Z(p), plasmid encoding ZEBRA; CMV, (p) empty plasmid; W(v), the BamW fragment of the endogenous virus (v).

    Journal: PLoS Pathogens

    Article Title: A Subset of Replication Proteins Enhances Origin Recognition and Lytic Replication by the Epstein-Barr Virus ZEBRA Protein

    doi: 10.1371/journal.ppat.1001054

    Figure Lengend Snippet: ZEBRA mutants defective in lytic replication and late gene expression. (A) Z(R187K) and Z(K188A) fail to activate two late proteins, FR3 and LR2. Immunoblot analysis of extracts prepared from BZKO cells transfected with expression vectors encoding wt ZEBRA (Z) and the following ZEBRA mutants: Z(K188A), Z(F193E), and Z(R187K). The membrane was probed for the EBV gene products, Rta, EA-D (early antigen-diffuse, the DNA polymerase processivity factor or BMRF1), ZEBRA, LR2 and FR3. NS, non specific. B) Z(Y180E), but not its revertant, specifically fails to activate EBV late gene expression. An immunoblot of transfected BZKO cells was probed with antibodies as described in panel A. C) and D) Southern blots assessing lytic viral DNA replication. Total DNA was extracted 48 hrs after transfection of the expression vectors. The DNA was digested with BamH1. The blots were probed with either a 0.3 kb subfragment of the Xho 1.9 fragment (Fig. 1C) or the BamH1 W fragment (Fig. 1D). FT, fused termini of the endogenous viral genome (v); Z(p), plasmid encoding ZEBRA; CMV, (p) empty plasmid; W(v), the BamW fragment of the endogenous virus (v).

    Article Snippet: Ten micrograms of DNA was digested with 40 units BamH1 (New England Biolabs) for 3 h at 37°C.

    Techniques: Expressing, Transfection, Plasmid Preparation

    Generation of vPK transgenic mice. FLAG-tagged vPK was cloned, using HinDIII-HF and BamHI-HF, into a plasmid containing a Ub- and hGH-stabilization element. The linearized transgene fragment was microinjected into the embryos of C57BL/6 mice and implanted into pseudopregnant female mice. Each vPK line was developed from breeding a vPK founder to a C57BL/6 mouse. ( A ) Schematic of the linearized construct used to generate the vPK transgenic mice, as well as the cut sites and probe for the Southern blot in D . ( B ) DNA from the tails of 2 WT (wA and wB) and 2 vPK transgenic mice (vA and vB) for lines 1 and 2 was isolated and evaluated by PCR for the vPK transgene. ( C ) Expression of vPK protein in lysates from spleens of the mice in B as determined by SDS-PAGE and Western blot. Lysate from HEK-293 cells that transiently express vPK was used as a positive control for vPK expression. ( D ) Southern blot of WT, vPK1, and vPK2. DNA was isolated from the spleens of WT and vPK lines 1 and 2. D, double digest with HinDIII-HF and BamHI-HF; S, single digestion with AFlII; p-vPK, plasmid Ub.vPK.hGH.

    Journal: The Journal of Clinical Investigation

    Article Title: Human herpesvirus–encoded kinase induces B cell lymphomas in vivo

    doi: 10.1172/JCI97053

    Figure Lengend Snippet: Generation of vPK transgenic mice. FLAG-tagged vPK was cloned, using HinDIII-HF and BamHI-HF, into a plasmid containing a Ub- and hGH-stabilization element. The linearized transgene fragment was microinjected into the embryos of C57BL/6 mice and implanted into pseudopregnant female mice. Each vPK line was developed from breeding a vPK founder to a C57BL/6 mouse. ( A ) Schematic of the linearized construct used to generate the vPK transgenic mice, as well as the cut sites and probe for the Southern blot in D . ( B ) DNA from the tails of 2 WT (wA and wB) and 2 vPK transgenic mice (vA and vB) for lines 1 and 2 was isolated and evaluated by PCR for the vPK transgene. ( C ) Expression of vPK protein in lysates from spleens of the mice in B as determined by SDS-PAGE and Western blot. Lysate from HEK-293 cells that transiently express vPK was used as a positive control for vPK expression. ( D ) Southern blot of WT, vPK1, and vPK2. DNA was isolated from the spleens of WT and vPK lines 1 and 2. D, double digest with HinDIII-HF and BamHI-HF; S, single digestion with AFlII; p-vPK, plasmid Ub.vPK.hGH.

    Article Snippet: Fifteen micrograms of DNA from each mouse was double digested with BamHI-HF and HindIII-HF (New England BioLabs) and single digested using AflII (New England BioLabs) in a total volume of 100 μl at 37°C overnight.

    Techniques: Transgenic Assay, Mouse Assay, Clone Assay, Plasmid Preparation, Construct, Southern Blot, Western Blot, Isolation, Polymerase Chain Reaction, Expressing, SDS Page, Positive Control

    Physical representation of the first 1 Mbp of pseudochromosome 1 in ‘Hongyang’ genome sequence with mapped reads found by stdGBS and rtGBS methods, all treatments, supported by ≥10 reads. The occurrence of BamH I sites per method and/or plant is denoted by coloured dots: Sites found in all treatments by stdGBS and rtGBS (green dot), found by either one type of library (red and yellow dots), and sites poorly represented by KFE and KFF (pink dot). The extract_aliquot data is denoted by an asterisk, in the following order from top to bottom of each plant_method panel: 2_4, 2_3, 2_2, 2_1, 1_4, 1_3, 1_2, 1_1.

    Journal: PLoS ONE

    Article Title: Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome

    doi: 10.1371/journal.pone.0143193

    Figure Lengend Snippet: Physical representation of the first 1 Mbp of pseudochromosome 1 in ‘Hongyang’ genome sequence with mapped reads found by stdGBS and rtGBS methods, all treatments, supported by ≥10 reads. The occurrence of BamH I sites per method and/or plant is denoted by coloured dots: Sites found in all treatments by stdGBS and rtGBS (green dot), found by either one type of library (red and yellow dots), and sites poorly represented by KFE and KFF (pink dot). The extract_aliquot data is denoted by an asterisk, in the following order from top to bottom of each plant_method panel: 2_4, 2_3, 2_2, 2_1, 1_4, 1_3, 1_2, 1_1.

    Article Snippet: We used 20 units of BamH I- HF with CutSmart reaction buffer (New England Biolabs) for each RE digestion.

    Techniques: Sequencing

    Difference on coverage depth obtained by stdGBS and rtGBS. A) Heatmaps of the mapped BamH I sites covered by ≥10 reads. B) Read coverage depth of the concatenated dataset for each library method. The cut-off value of 10 reads is marked with a red dotted line.

    Journal: PLoS ONE

    Article Title: Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome

    doi: 10.1371/journal.pone.0143193

    Figure Lengend Snippet: Difference on coverage depth obtained by stdGBS and rtGBS. A) Heatmaps of the mapped BamH I sites covered by ≥10 reads. B) Read coverage depth of the concatenated dataset for each library method. The cut-off value of 10 reads is marked with a red dotted line.

    Article Snippet: We used 20 units of BamH I- HF with CutSmart reaction buffer (New England Biolabs) for each RE digestion.

    Techniques:

    Venn diagrams summarizing the BamH I sites supported by ≥10 reads from the combined datasets of all treatments for stdGBS and rtGBS. The combined datasets were constructed by concatenating all plants_extract_aliquot ([KF.][ 12 ][1234]) for both lanes from each library method (green circles). The intersection between the two sets corresponds to the BamH I sites in common by all plants and ‘Hongyang’ denoted as “population” (blue circles).

    Journal: PLoS ONE

    Article Title: Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome

    doi: 10.1371/journal.pone.0143193

    Figure Lengend Snippet: Venn diagrams summarizing the BamH I sites supported by ≥10 reads from the combined datasets of all treatments for stdGBS and rtGBS. The combined datasets were constructed by concatenating all plants_extract_aliquot ([KF.][ 12 ][1234]) for both lanes from each library method (green circles). The intersection between the two sets corresponds to the BamH I sites in common by all plants and ‘Hongyang’ denoted as “population” (blue circles).

    Article Snippet: We used 20 units of BamH I- HF with CutSmart reaction buffer (New England Biolabs) for each RE digestion.

    Techniques: Construct

    Fragment size distribution analysis. A) Semi-logarithmic display of the BamH I fragment size distribution among the ‘Hongyang’ genome (population) and the two library methods. B) Probability distribution plots for the two GBS library methods vs. Hongyang genome RE fragment size distribution.

    Journal: PLoS ONE

    Article Title: Random Tagging Genotyping by Sequencing (rtGBS), an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome

    doi: 10.1371/journal.pone.0143193

    Figure Lengend Snippet: Fragment size distribution analysis. A) Semi-logarithmic display of the BamH I fragment size distribution among the ‘Hongyang’ genome (population) and the two library methods. B) Probability distribution plots for the two GBS library methods vs. Hongyang genome RE fragment size distribution.

    Article Snippet: We used 20 units of BamH I- HF with CutSmart reaction buffer (New England Biolabs) for each RE digestion.

    Techniques: