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    Structured Review

    TaKaRa bamhi recognition site
    Bamhi Recognition Site, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 14678 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/bamhi+recognition+site/BamH+I/us12600991-473-27-37
    Average 99 stars, based on 14678 article reviews
    bamhi recognition site - by Bioz Stars, 2026-09
    99/100 stars

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    Related Articles

    Transcription Assay:

    Article Title: The Homeodomain Transcription Factor Xvent-2 Mediates Autocatalytic Regulation of BMP-4 Expression in XenopusEmbryos
    Article Snippet: .. Yeast Transcriptional Assay (28)—Xvent-1 and Xvent-2 were integrated in-frame into the BamHI recognition site of the bacteria/yeast shuttle vector pAS2 (CLONTECH). .. Subsequently, the constructs have been transformed according to established procedures (yeast protocols handbook, CLONTECH) into yeast strain Y187 employing selection markers trp1 and leu2 (29) and plated on drop-out plates missing tryptophan.

    Bacteria:

    Article Title: The Homeodomain Transcription Factor Xvent-2 Mediates Autocatalytic Regulation of BMP-4 Expression in XenopusEmbryos
    Article Snippet: .. Yeast Transcriptional Assay (28)—Xvent-1 and Xvent-2 were integrated in-frame into the BamHI recognition site of the bacteria/yeast shuttle vector pAS2 (CLONTECH). .. Subsequently, the constructs have been transformed according to established procedures (yeast protocols handbook, CLONTECH) into yeast strain Y187 employing selection markers trp1 and leu2 (29) and plated on drop-out plates missing tryptophan.

    Plasmid Preparation:

    Article Title: The Homeodomain Transcription Factor Xvent-2 Mediates Autocatalytic Regulation of BMP-4 Expression in XenopusEmbryos
    Article Snippet: .. Yeast Transcriptional Assay (28)—Xvent-1 and Xvent-2 were integrated in-frame into the BamHI recognition site of the bacteria/yeast shuttle vector pAS2 (CLONTECH). .. Subsequently, the constructs have been transformed according to established procedures (yeast protocols handbook, CLONTECH) into yeast strain Y187 employing selection markers trp1 and leu2 (29) and plated on drop-out plates missing tryptophan.

    Article Title: Recombinant feline herpesvirus type 1 and polyvalent vaccine using the same
    Article Snippet: .. That is, a plasmid vector pSal-I (obtained from Dr. T. Miyazawa, Department of Agriculture, Tokyo University) wherein the I fragment as one of the SalI digested DNA fragments of the FHV-1 genome DNA had been integrated was cloned again in a commercial plasmid vector whose BamHI recognition site had been deleted, and then a LacZ gene fragment (Pro-LacZ) accompanied by an IE promoter derived from a commercial eucaryotic cell expression vector pCMVβ (CLONETECH) was integrated in a unique BamHI cleavage site in the newly constructed plasmid pdBSI containing the I fragment, to prepare a transfer vector pdBSI-LacZ. ..

    Article Title: Genetically modified microorganism for production of aspartic acid and downstream metabolites from aspartic acid as target substance, and method for producing target substance using same
    Article Snippet: Hereinafter, the procedures therefor are shown. (1) Preparation of Gene-Deficient Strain (Corynebacterium glutamicum Strain ATCC13032 ΔldhΔsdhΔpoxB) At first, a SacB gene fragment was amplified by the PCR method using plasmid pNIC-Bsa4 (Source BioScience) serving as a template, and a pair of primers shown in Table 12 below. .. TABLE 12 SEQ Primer ID name Sequence and description NO: Primer 5′-GGGGAAGCTTGACGTCCACATATACCTGCC-3′ 14 F1 Underlined part: HindIII- recognition site Primer 5′-ATTCGGATCCGTATCCACCTTTAC-3′ 15 R1 Underlined part: BamHI- recognition site The amplified DNA fragment and plasmid pHSG299 (Takara Bio Inc.) were subjected to a restriction enzyme treatment with BamHI and HindIII, and then, the resulting fragments were ligated using DNA ligation Kit Ver. .. 2 (Takara Bio Inc.), thereby obtaining plasmid pGE015.

    Article Title: Recombinant feline herpesvirus type 1 and polyvalent vaccine using the same
    Article Snippet: .. That is, a plasmid vector pSal-I (obtained from Dr. T. Miyazawa, Department of Agriculture, Tokyo University) wherein the I fragment as one of the SalI digested DNA fragments of the FHV-1 genome DNA had been integrated was cloned again in a commercial plasmid vector whose BamHI recognition site had been deleted, and then a LacZ gene fragment (Pro-LacZ) accompanied by an IE promoter derived from a commercial eucaryotic cell expression vector pCMVβ (CLONETECH) was integrated in a unique BamHI cleavage site in the newly constructed plasmid pdBSI containing the I fragment, to prepare a transfer vector pdBSI-LacZ. ..

    Polymerase Chain Reaction:

    Article Title: Novel single nucleotide polymorphisms in the bovine leukemia virus genome are associated with proviral load and affect the expression profile of viral non-coding transcripts.
    Article Snippet: Bovine leukemia virus (BLV) infects bovine B-cells and causes malignant lymphoma, resulting in severe economic losses in the livestock industry.. To control the spread of BLV, several studies have attempted to clarify the molecular mechanisms of BLV pathogenesis, but the details of the mechanism are still enigmatic.. Currently, viral non-coding RNAs are attracting attention as a novel player for BLV pathogenesis because these transcripts can evade the host immune response and are persistently expressed in latent infection.

    Amplification:

    Article Title: Novel single nucleotide polymorphisms in the bovine leukemia virus genome are associated with proviral load and affect the expression profile of viral non-coding transcripts.
    Article Snippet: Bovine leukemia virus (BLV) infects bovine B-cells and causes malignant lymphoma, resulting in severe economic losses in the livestock industry.. To control the spread of BLV, several studies have attempted to clarify the molecular mechanisms of BLV pathogenesis, but the details of the mechanism are still enigmatic.. Currently, viral non-coding RNAs are attracting attention as a novel player for BLV pathogenesis because these transcripts can evade the host immune response and are persistently expressed in latent infection.

    Article Title: Genetically modified microorganism for production of aspartic acid and downstream metabolites from aspartic acid as target substance, and method for producing target substance using same
    Article Snippet: Hereinafter, the procedures therefor are shown. (1) Preparation of Gene-Deficient Strain (Corynebacterium glutamicum Strain ATCC13032 ΔldhΔsdhΔpoxB) At first, a SacB gene fragment was amplified by the PCR method using plasmid pNIC-Bsa4 (Source BioScience) serving as a template, and a pair of primers shown in Table 12 below. .. TABLE 12 SEQ Primer ID name Sequence and description NO: Primer 5′-GGGGAAGCTTGACGTCCACATATACCTGCC-3′ 14 F1 Underlined part: HindIII- recognition site Primer 5′-ATTCGGATCCGTATCCACCTTTAC-3′ 15 R1 Underlined part: BamHI- recognition site The amplified DNA fragment and plasmid pHSG299 (Takara Bio Inc.) were subjected to a restriction enzyme treatment with BamHI and HindIII, and then, the resulting fragments were ligated using DNA ligation Kit Ver. .. 2 (Takara Bio Inc.), thereby obtaining plasmid pGE015.

    Clone Assay:

    Article Title: Novel single nucleotide polymorphisms in the bovine leukemia virus genome are associated with proviral load and affect the expression profile of viral non-coding transcripts.
    Article Snippet: Bovine leukemia virus (BLV) infects bovine B-cells and causes malignant lymphoma, resulting in severe economic losses in the livestock industry.. To control the spread of BLV, several studies have attempted to clarify the molecular mechanisms of BLV pathogenesis, but the details of the mechanism are still enigmatic.. Currently, viral non-coding RNAs are attracting attention as a novel player for BLV pathogenesis because these transcripts can evade the host immune response and are persistently expressed in latent infection.

    Article Title: Recombinant feline herpesvirus type 1 and polyvalent vaccine using the same
    Article Snippet: .. That is, a plasmid vector pSal-I (obtained from Dr. T. Miyazawa, Department of Agriculture, Tokyo University) wherein the I fragment as one of the SalI digested DNA fragments of the FHV-1 genome DNA had been integrated was cloned again in a commercial plasmid vector whose BamHI recognition site had been deleted, and then a LacZ gene fragment (Pro-LacZ) accompanied by an IE promoter derived from a commercial eucaryotic cell expression vector pCMVβ (CLONETECH) was integrated in a unique BamHI cleavage site in the newly constructed plasmid pdBSI containing the I fragment, to prepare a transfer vector pdBSI-LacZ. ..

    Article Title: Recombinant feline herpesvirus type 1 and polyvalent vaccine using the same
    Article Snippet: .. That is, a plasmid vector pSal-I (obtained from Dr. T. Miyazawa, Department of Agriculture, Tokyo University) wherein the I fragment as one of the SalI digested DNA fragments of the FHV-1 genome DNA had been integrated was cloned again in a commercial plasmid vector whose BamHI recognition site had been deleted, and then a LacZ gene fragment (Pro-LacZ) accompanied by an IE promoter derived from a commercial eucaryotic cell expression vector pCMVβ (CLONETECH) was integrated in a unique BamHI cleavage site in the newly constructed plasmid pdBSI containing the I fragment, to prepare a transfer vector pdBSI-LacZ. ..

    Cloning:

    Article Title: Novel single nucleotide polymorphisms in the bovine leukemia virus genome are associated with proviral load and affect the expression profile of viral non-coding transcripts.
    Article Snippet: Bovine leukemia virus (BLV) infects bovine B-cells and causes malignant lymphoma, resulting in severe economic losses in the livestock industry.. To control the spread of BLV, several studies have attempted to clarify the molecular mechanisms of BLV pathogenesis, but the details of the mechanism are still enigmatic.. Currently, viral non-coding RNAs are attracting attention as a novel player for BLV pathogenesis because these transcripts can evade the host immune response and are persistently expressed in latent infection.

    Derivative Assay:

    Article Title: Recombinant feline herpesvirus type 1 and polyvalent vaccine using the same
    Article Snippet: .. That is, a plasmid vector pSal-I (obtained from Dr. T. Miyazawa, Department of Agriculture, Tokyo University) wherein the I fragment as one of the SalI digested DNA fragments of the FHV-1 genome DNA had been integrated was cloned again in a commercial plasmid vector whose BamHI recognition site had been deleted, and then a LacZ gene fragment (Pro-LacZ) accompanied by an IE promoter derived from a commercial eucaryotic cell expression vector pCMVβ (CLONETECH) was integrated in a unique BamHI cleavage site in the newly constructed plasmid pdBSI containing the I fragment, to prepare a transfer vector pdBSI-LacZ. ..

    Article Title: Recombinant feline herpesvirus type 1 and polyvalent vaccine using the same
    Article Snippet: .. That is, a plasmid vector pSal-I (obtained from Dr. T. Miyazawa, Department of Agriculture, Tokyo University) wherein the I fragment as one of the SalI digested DNA fragments of the FHV-1 genome DNA had been integrated was cloned again in a commercial plasmid vector whose BamHI recognition site had been deleted, and then a LacZ gene fragment (Pro-LacZ) accompanied by an IE promoter derived from a commercial eucaryotic cell expression vector pCMVβ (CLONETECH) was integrated in a unique BamHI cleavage site in the newly constructed plasmid pdBSI containing the I fragment, to prepare a transfer vector pdBSI-LacZ. ..

    Expressing:

    Article Title: Recombinant feline herpesvirus type 1 and polyvalent vaccine using the same
    Article Snippet: .. That is, a plasmid vector pSal-I (obtained from Dr. T. Miyazawa, Department of Agriculture, Tokyo University) wherein the I fragment as one of the SalI digested DNA fragments of the FHV-1 genome DNA had been integrated was cloned again in a commercial plasmid vector whose BamHI recognition site had been deleted, and then a LacZ gene fragment (Pro-LacZ) accompanied by an IE promoter derived from a commercial eucaryotic cell expression vector pCMVβ (CLONETECH) was integrated in a unique BamHI cleavage site in the newly constructed plasmid pdBSI containing the I fragment, to prepare a transfer vector pdBSI-LacZ. ..

    Article Title: Recombinant feline herpesvirus type 1 and polyvalent vaccine using the same
    Article Snippet: .. That is, a plasmid vector pSal-I (obtained from Dr. T. Miyazawa, Department of Agriculture, Tokyo University) wherein the I fragment as one of the SalI digested DNA fragments of the FHV-1 genome DNA had been integrated was cloned again in a commercial plasmid vector whose BamHI recognition site had been deleted, and then a LacZ gene fragment (Pro-LacZ) accompanied by an IE promoter derived from a commercial eucaryotic cell expression vector pCMVβ (CLONETECH) was integrated in a unique BamHI cleavage site in the newly constructed plasmid pdBSI containing the I fragment, to prepare a transfer vector pdBSI-LacZ. ..

    Construct:

    Article Title: Recombinant feline herpesvirus type 1 and polyvalent vaccine using the same
    Article Snippet: .. That is, a plasmid vector pSal-I (obtained from Dr. T. Miyazawa, Department of Agriculture, Tokyo University) wherein the I fragment as one of the SalI digested DNA fragments of the FHV-1 genome DNA had been integrated was cloned again in a commercial plasmid vector whose BamHI recognition site had been deleted, and then a LacZ gene fragment (Pro-LacZ) accompanied by an IE promoter derived from a commercial eucaryotic cell expression vector pCMVβ (CLONETECH) was integrated in a unique BamHI cleavage site in the newly constructed plasmid pdBSI containing the I fragment, to prepare a transfer vector pdBSI-LacZ. ..

    Article Title: Recombinant feline herpesvirus type 1 and polyvalent vaccine using the same
    Article Snippet: .. That is, a plasmid vector pSal-I (obtained from Dr. T. Miyazawa, Department of Agriculture, Tokyo University) wherein the I fragment as one of the SalI digested DNA fragments of the FHV-1 genome DNA had been integrated was cloned again in a commercial plasmid vector whose BamHI recognition site had been deleted, and then a LacZ gene fragment (Pro-LacZ) accompanied by an IE promoter derived from a commercial eucaryotic cell expression vector pCMVβ (CLONETECH) was integrated in a unique BamHI cleavage site in the newly constructed plasmid pdBSI containing the I fragment, to prepare a transfer vector pdBSI-LacZ. ..

    Sequencing:

    Article Title: Genetically modified microorganism for production of aspartic acid and downstream metabolites from aspartic acid as target substance, and method for producing target substance using same
    Article Snippet: Hereinafter, the procedures therefor are shown. (1) Preparation of Gene-Deficient Strain (Corynebacterium glutamicum Strain ATCC13032 ΔldhΔsdhΔpoxB) At first, a SacB gene fragment was amplified by the PCR method using plasmid pNIC-Bsa4 (Source BioScience) serving as a template, and a pair of primers shown in Table 12 below. .. TABLE 12 SEQ Primer ID name Sequence and description NO: Primer 5′-GGGGAAGCTTGACGTCCACATATACCTGCC-3′ 14 F1 Underlined part: HindIII- recognition site Primer 5′-ATTCGGATCCGTATCCACCTTTAC-3′ 15 R1 Underlined part: BamHI- recognition site The amplified DNA fragment and plasmid pHSG299 (Takara Bio Inc.) were subjected to a restriction enzyme treatment with BamHI and HindIII, and then, the resulting fragments were ligated using DNA ligation Kit Ver. .. 2 (Takara Bio Inc.), thereby obtaining plasmid pGE015.

    DNA Ligation:

    Article Title: Genetically modified microorganism for production of aspartic acid and downstream metabolites from aspartic acid as target substance, and method for producing target substance using same
    Article Snippet: Hereinafter, the procedures therefor are shown. (1) Preparation of Gene-Deficient Strain (Corynebacterium glutamicum Strain ATCC13032 ΔldhΔsdhΔpoxB) At first, a SacB gene fragment was amplified by the PCR method using plasmid pNIC-Bsa4 (Source BioScience) serving as a template, and a pair of primers shown in Table 12 below. .. TABLE 12 SEQ Primer ID name Sequence and description NO: Primer 5′-GGGGAAGCTTGACGTCCACATATACCTGCC-3′ 14 F1 Underlined part: HindIII- recognition site Primer 5′-ATTCGGATCCGTATCCACCTTTAC-3′ 15 R1 Underlined part: BamHI- recognition site The amplified DNA fragment and plasmid pHSG299 (Takara Bio Inc.) were subjected to a restriction enzyme treatment with BamHI and HindIII, and then, the resulting fragments were ligated using DNA ligation Kit Ver. .. 2 (Takara Bio Inc.), thereby obtaining plasmid pGE015.



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    Image Search Results


    The results of finding possible recognition sites for a specific restriction enzyme . BamHI recognition sites are displayed. Lines with different colors are employed for better visualization, especially when results are close to each other. The information for the sequence and position for each recognition site will popup when the mouse hovers over the sequence.

    Journal: BMC Bioinformatics

    Article Title: ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites

    doi: 10.1186/1471-2105-10-286

    Figure Lengend Snippet: The results of finding possible recognition sites for a specific restriction enzyme . BamHI recognition sites are displayed. Lines with different colors are employed for better visualization, especially when results are close to each other. The information for the sequence and position for each recognition site will popup when the mouse hovers over the sequence.

    Article Snippet: As discussed previously, the existing tools such as NEBcutter or WatCut do not support this functionality, whereas ICRPfinder can create 6 BamHI recognition sites without changing the protein sequence encoded.

    Techniques: Sequencing

    (A) An unrooted maximum likelihood phylogeny of 366 SbmA/BacA-like proteins is shown. The scale bar represents the average number of amino acid substitutions per site. Red triangles indicate proteins whose corresponding genes were codon optimized and synthesized: 1 - Polymorphum gilvum BclA; 2 - Synechococcus elongatus BclA; 3 - Cyanobacterium aponinum BclA; 4 - Basilea psittacipulmonis BclA; 5 - Succinivibrio dextrinosolvens BclA; 6 - Methylomusa anaerophila BclA; 7 - Polaromonas naphthalenivorans BclA; 8 - Eikenella exigua BclA-like; 9 - Phyllobacterium zundukense ExsE. The bars beneath the phylogeny summarize the clustering and annotation of these proteins. The top bar indicates the phylogenetic clade to which each protein belongs. The second bar indicates the preliminary hidden Markov model (HMM) classification of each protein. The third bar indicates the cluster in the sequence similarity network that each protein belongs to. The bottom bar indicates which proteins were ultimately classified as SbmA/BacA (red) or BclA (blue). An interactive version of this phylogeny, with node support values, is provided through iTol ( https://itol.embl.de/shared/1IAjjFrHYGLI9 ) while a Newick-formatted version of the phylogeny can be downloaded from GitHub ( https://github.com/amira-boukh/SbmA_BacA_phylogenetic_distribution ). (B) A sequence similarity network, calculated using EFI-EST, of 366 SbmA-BacA-like proteins is shown. Each node (the circles) represents one protein, while edges (the lines) represent sequence similarity between pairs of proteins above the threshold, with longer lines indicating lower similarity. Nodes are colour coded based on cluster.

    Journal: bioRxiv

    Article Title: Taxonomic distribution of SbmA/BacA and BacA-like antimicrobial peptide transporters suggests independent recruitment and convergent evolution in host-microbe interactions

    doi: 10.1101/2024.02.25.581009

    Figure Lengend Snippet: (A) An unrooted maximum likelihood phylogeny of 366 SbmA/BacA-like proteins is shown. The scale bar represents the average number of amino acid substitutions per site. Red triangles indicate proteins whose corresponding genes were codon optimized and synthesized: 1 - Polymorphum gilvum BclA; 2 - Synechococcus elongatus BclA; 3 - Cyanobacterium aponinum BclA; 4 - Basilea psittacipulmonis BclA; 5 - Succinivibrio dextrinosolvens BclA; 6 - Methylomusa anaerophila BclA; 7 - Polaromonas naphthalenivorans BclA; 8 - Eikenella exigua BclA-like; 9 - Phyllobacterium zundukense ExsE. The bars beneath the phylogeny summarize the clustering and annotation of these proteins. The top bar indicates the phylogenetic clade to which each protein belongs. The second bar indicates the preliminary hidden Markov model (HMM) classification of each protein. The third bar indicates the cluster in the sequence similarity network that each protein belongs to. The bottom bar indicates which proteins were ultimately classified as SbmA/BacA (red) or BclA (blue). An interactive version of this phylogeny, with node support values, is provided through iTol ( https://itol.embl.de/shared/1IAjjFrHYGLI9 ) while a Newick-formatted version of the phylogeny can be downloaded from GitHub ( https://github.com/amira-boukh/SbmA_BacA_phylogenetic_distribution ). (B) A sequence similarity network, calculated using EFI-EST, of 366 SbmA-BacA-like proteins is shown. Each node (the circles) represents one protein, while edges (the lines) represent sequence similarity between pairs of proteins above the threshold, with longer lines indicating lower similarity. Nodes are colour coded based on cluster.

    Article Snippet: Ten vectors encoding putative bacA , bclA , or exsE genes, codon optimized for S. meliloti 1021 and flanked by XbaI and BamHI recognition sites, were produced by Twist Biosciences (Table S2, Dataset S1).

    Techniques: Synthesized, Sequencing

    An unrooted maximum likelihood phylogeny of 1,533 bacteria is shown, inferred from the concatenated protein alignments of 31 single-copy proteins. The scale bar represents the average number of amino acid substitutions per site. Three clades of intracellular symbionts/pathogens with long branch lengths were removed for presentation purposes; none of these taxa encode SbmA/BacA or BclA. The outer rings represent the following, starting from the inner ring: (i) the phylum that each strain belongs to, limited to phyla where at least one strain encodes SbmA/BacA or BclA; (ii) the class that each strain belongs to, limited to classes where at least one strain encodes SbmA/BacA or BclA and that are mentioned in the text; (iii) the class that each strain belongs to, limited to classes where at least one strain encodes SbmA/BacA or BclA and that are mentioned in the text; (iv) whether the strain encodes BclA (blue) or not (white); (v) whether the strain encodes SbmA/BacA (red) or not (white). An interactive version of this phylogeny, with node support values and without collapsing of any clades, is provided through iTol ( https://itol.embl.de/shared/1IAjjFrHYGLI9 ) while a Newick-formatted version of the phylogeny can be downloaded from GitHub ( https://github.com/amira-boukh/SbmA_BacA_phylogenetic_distribution ).

    Journal: bioRxiv

    Article Title: Taxonomic distribution of SbmA/BacA and BacA-like antimicrobial peptide transporters suggests independent recruitment and convergent evolution in host-microbe interactions

    doi: 10.1101/2024.02.25.581009

    Figure Lengend Snippet: An unrooted maximum likelihood phylogeny of 1,533 bacteria is shown, inferred from the concatenated protein alignments of 31 single-copy proteins. The scale bar represents the average number of amino acid substitutions per site. Three clades of intracellular symbionts/pathogens with long branch lengths were removed for presentation purposes; none of these taxa encode SbmA/BacA or BclA. The outer rings represent the following, starting from the inner ring: (i) the phylum that each strain belongs to, limited to phyla where at least one strain encodes SbmA/BacA or BclA; (ii) the class that each strain belongs to, limited to classes where at least one strain encodes SbmA/BacA or BclA and that are mentioned in the text; (iii) the class that each strain belongs to, limited to classes where at least one strain encodes SbmA/BacA or BclA and that are mentioned in the text; (iv) whether the strain encodes BclA (blue) or not (white); (v) whether the strain encodes SbmA/BacA (red) or not (white). An interactive version of this phylogeny, with node support values and without collapsing of any clades, is provided through iTol ( https://itol.embl.de/shared/1IAjjFrHYGLI9 ) while a Newick-formatted version of the phylogeny can be downloaded from GitHub ( https://github.com/amira-boukh/SbmA_BacA_phylogenetic_distribution ).

    Article Snippet: Ten vectors encoding putative bacA , bclA , or exsE genes, codon optimized for S. meliloti 1021 and flanked by XbaI and BamHI recognition sites, were produced by Twist Biosciences (Table S2, Dataset S1).

    Techniques: Bacteria