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    Name:
    BfaI
    Description:
    BfaI 2 500 units
    Catalog Number:
    r0568l
    Price:
    302
    Size:
    2 500 units
    Category:
    Restriction Enzymes
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    New England Biolabs bfa i
    BfaI
    BfaI 2 500 units
    https://www.bioz.com/result/bfa i/product/New England Biolabs
    Average 96 stars, based on 24 article reviews
    Price from $9.99 to $1999.99
    bfa i - by Bioz Stars, 2020-07
    96/100 stars

    Images

    1) Product Images from "Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces"

    Article Title: Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.69.2.1251-1262.2003

    Frequency distribution profiles of the 5′ T-RFs derived from in silico digestion of 16S rRNA gene sequences from strains belonging to the major large intestinal bacterial genera. TAP T-RFLPs were run with the primer-enzyme combinations of 516f- Rsa I plus Bfa I (A) or 516f- Bsl I (B), and histograms of the predicted T-RF lengths were drawn. The T-RFs of 995 bp in panel B are uncut fragments.
    Figure Legend Snippet: Frequency distribution profiles of the 5′ T-RFs derived from in silico digestion of 16S rRNA gene sequences from strains belonging to the major large intestinal bacterial genera. TAP T-RFLPs were run with the primer-enzyme combinations of 516f- Rsa I plus Bfa I (A) or 516f- Bsl I (B), and histograms of the predicted T-RF lengths were drawn. The T-RFs of 995 bp in panel B are uncut fragments.

    Techniques Used: Derivative Assay, In Silico

    Fractionation of T-RFs by agarose gel electrophoresis. T-RFs produced by Bsl I digestion of 16S rRNA gene amplicons from a fecal sample of individual G (lane 3) or by Rsa I-plus- Bfa I digestion of those from a fecal sample of individual H (lane 4) were electrophoresed on a 3% agarose gel as described in Materials and Methods. Arrowheads in lanes 3 and 4 represent the positions of 124-bp OTU Bsl and 377-bp OTU R-B , respectively. Lane 1, 100-bp ladder marker (MBI Fermentas); lane 2, pBR322× Msp I marker (Nippon Gene).
    Figure Legend Snippet: Fractionation of T-RFs by agarose gel electrophoresis. T-RFs produced by Bsl I digestion of 16S rRNA gene amplicons from a fecal sample of individual G (lane 3) or by Rsa I-plus- Bfa I digestion of those from a fecal sample of individual H (lane 4) were electrophoresed on a 3% agarose gel as described in Materials and Methods. Arrowheads in lanes 3 and 4 represent the positions of 124-bp OTU Bsl and 377-bp OTU R-B , respectively. Lane 1, 100-bp ladder marker (MBI Fermentas); lane 2, pBR322× Msp I marker (Nippon Gene).

    Techniques Used: Fractionation, Agarose Gel Electrophoresis, Produced, Marker

    2) Product Images from "Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of Mycoplasma species"

    Article Title: Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of Mycoplasma species

    Journal: BMC Infectious Diseases

    doi: 10.1186/1471-2334-5-46

    ARDRA profiles after restriction with Bfa I of 18 different Mycoplasma species. Since all samples of the same species gave identical restriction patterns, the number of strains tested for each species is indicated in parenthesis. A Generuler 50-bp ladder (Fermentas) was used as size-marker.
    Figure Legend Snippet: ARDRA profiles after restriction with Bfa I of 18 different Mycoplasma species. Since all samples of the same species gave identical restriction patterns, the number of strains tested for each species is indicated in parenthesis. A Generuler 50-bp ladder (Fermentas) was used as size-marker.

    Techniques Used: Marker

    Calculated ARDRA profiles of Mycoplasma spp. that can be differentiated using Bfa I, but had undistinguishable Alu I restriction profiles.
    Figure Legend Snippet: Calculated ARDRA profiles of Mycoplasma spp. that can be differentiated using Bfa I, but had undistinguishable Alu I restriction profiles.

    Techniques Used:

    3) Product Images from "Isolation of Helicobacter canis from a Colony of Bengal Cats with Endemic Diarrhea"

    Article Title: Isolation of Helicobacter canis from a Colony of Bengal Cats with Endemic Diarrhea

    Journal: Journal of Clinical Microbiology

    doi:

    Comparison of RFLP patterns of the 1.2-kb Helicobacter -specific PCR product with restriction enzymes Bfa I and Hha I. Lanes: M, 100-bp DNA ladder; 1, H. canis ); 2, H. canis ATCC 51401; 3, MIT 98-152; 4, MIT 98-153.
    Figure Legend Snippet: Comparison of RFLP patterns of the 1.2-kb Helicobacter -specific PCR product with restriction enzymes Bfa I and Hha I. Lanes: M, 100-bp DNA ladder; 1, H. canis ); 2, H. canis ATCC 51401; 3, MIT 98-152; 4, MIT 98-153.

    Techniques Used: Polymerase Chain Reaction

    4) Product Images from "Genetic Characteristics of Borrelia coriaceae Isolates from the Soft Tick Ornithodoros coriaceus (Acari: Argasidae)"

    Article Title: Genetic Characteristics of Borrelia coriaceae Isolates from the Soft Tick Ornithodoros coriaceus (Acari: Argasidae)

    Journal: Journal of Clinical Microbiology

    doi:

    16S rRNA amplification products restricted with Hph I (a), Bfa I (b), and Mse I (c). Lanes: 1, CA434; 2, CA435; 3, Co53; 4, B. parkeri ; 5, CA4. Restriction fragments were resolved in 2.5% NuSieve-GTG agarose–1× TBE at 5 V/cm for 3.5 h.
    Figure Legend Snippet: 16S rRNA amplification products restricted with Hph I (a), Bfa I (b), and Mse I (c). Lanes: 1, CA434; 2, CA435; 3, Co53; 4, B. parkeri ; 5, CA4. Restriction fragments were resolved in 2.5% NuSieve-GTG agarose–1× TBE at 5 V/cm for 3.5 h.

    Techniques Used: Amplification

    5) Product Images from "Identification of mutations in the c-mpl gene in congenital amegakaryocytic thrombocytopenia"

    Article Title: Identification of mutations in the c-mpl gene in congenital amegakaryocytic thrombocytopenia

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi:

    c-mpl gene mutations in the family with CAMT. ( A ) A pedigree of the family. Circles represent females and squares males. Half-shaded (left side of the symbol) symbols represent carriers of the Q186X mutation, and half-hatched (right side of the symbol) symbols represent carriers of the 1,499 delT mutation. The proband is II-1. ( B ) Verification of the C-to-T mutation at cDNA position 556 by PCR amplification and restriction-enzyme analysis. PCR products of exon 4 were digested with Pvu II and checked by agarose gel electrophoresis. The 380-bp PCR product of exon 4 is cleaved to 175-bp, 105-bp, and 100-bp fragments by Pvu II. The Q186X mutation abolishes one of two Pvu II sites, resulting in 275-bp and 105-bp fragments. The patient (lane 2), her mother (lane 4), and her brother (lane 5) possess this mutation in one allele, whereas her father (lane 3) and her sister (lane 6) do not have this mutation. Lane 1 shows the molecular size marker. ( C ) Restriction-enzyme analysis of the 1,499 delT. The 265-bp PCR product of exon 10 is cleaved to 162-bp, 70-bp, and 33-bp fragments by Bfa I. The 1,499 delT abolishes one of two Bfa I sites, resulting in 195-bp and 70-bp fragments (70-bp and 33-bp bands are not shown). Although the patient (lane 2) and her father (lane 3) have this mutation in one allele, her mother (lane 4), her brother (lane 5), and her sister (lane 6) do not have this mutation. Lane 1 shows the molecular size marker.
    Figure Legend Snippet: c-mpl gene mutations in the family with CAMT. ( A ) A pedigree of the family. Circles represent females and squares males. Half-shaded (left side of the symbol) symbols represent carriers of the Q186X mutation, and half-hatched (right side of the symbol) symbols represent carriers of the 1,499 delT mutation. The proband is II-1. ( B ) Verification of the C-to-T mutation at cDNA position 556 by PCR amplification and restriction-enzyme analysis. PCR products of exon 4 were digested with Pvu II and checked by agarose gel electrophoresis. The 380-bp PCR product of exon 4 is cleaved to 175-bp, 105-bp, and 100-bp fragments by Pvu II. The Q186X mutation abolishes one of two Pvu II sites, resulting in 275-bp and 105-bp fragments. The patient (lane 2), her mother (lane 4), and her brother (lane 5) possess this mutation in one allele, whereas her father (lane 3) and her sister (lane 6) do not have this mutation. Lane 1 shows the molecular size marker. ( C ) Restriction-enzyme analysis of the 1,499 delT. The 265-bp PCR product of exon 10 is cleaved to 162-bp, 70-bp, and 33-bp fragments by Bfa I. The 1,499 delT abolishes one of two Bfa I sites, resulting in 195-bp and 70-bp fragments (70-bp and 33-bp bands are not shown). Although the patient (lane 2) and her father (lane 3) have this mutation in one allele, her mother (lane 4), her brother (lane 5), and her sister (lane 6) do not have this mutation. Lane 1 shows the molecular size marker.

    Techniques Used: Mutagenesis, Polymerase Chain Reaction, Amplification, Agarose Gel Electrophoresis, Marker

    6) Product Images from "Maternal Separation Enhances Conditioned Fear and Decreases the mRNA Levels of the Neurotensin Receptor 1 Gene with Hypermethylation of This Gene in the Rat Amygdala"

    Article Title: Maternal Separation Enhances Conditioned Fear and Decreases the mRNA Levels of the Neurotensin Receptor 1 Gene with Hypermethylation of This Gene in the Rat Amygdala

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0097421

    Effect of MS on DNA methylation in the NTSR1 promoter region in AMY. A , The diagram of NTSR1 DNA and the locations of the CpG islands (CGI) and fragments A, B and C. B , Nucleotide sequence of the promoter region of the rat NTSR1 gene [34] . The hooked shape indicates the Bfa I recognition sites. Underlined sequences indicate the position of the primers of fragments A, B and C. The potential binding sites for transcription factors, GATA, activating protein 2 (AP2), specificity protein 1 (SP1), CAAT box, cAMP response elements (CRE), and nuclear factor-interleukin 6 (NF IL6) are marked by boxes, and their names are indicated above. The coding sequence of the first exon is indicated by an asterisk. C , Methylation analysis of NTSR1 promoter region using a MethylCollector Ultra Kit (Active Motif). The percentage enrichment was calculated as follows: enrichment (%) = 2 CT (UF) – CT (EF) /(1 + 2 CT (UF) – CT (EF) ) × 100. The eluted fragment (EF) represents a DNA fragment with more than five methylated CpG sites, and the unbounded fragment (UF) represents a DNA fragment with four or fewer methylated CpG sites. The % enrichment of fragments B and C was significantly increased in the MS group compared with the AFR group (n = 8 per group; * p
    Figure Legend Snippet: Effect of MS on DNA methylation in the NTSR1 promoter region in AMY. A , The diagram of NTSR1 DNA and the locations of the CpG islands (CGI) and fragments A, B and C. B , Nucleotide sequence of the promoter region of the rat NTSR1 gene [34] . The hooked shape indicates the Bfa I recognition sites. Underlined sequences indicate the position of the primers of fragments A, B and C. The potential binding sites for transcription factors, GATA, activating protein 2 (AP2), specificity protein 1 (SP1), CAAT box, cAMP response elements (CRE), and nuclear factor-interleukin 6 (NF IL6) are marked by boxes, and their names are indicated above. The coding sequence of the first exon is indicated by an asterisk. C , Methylation analysis of NTSR1 promoter region using a MethylCollector Ultra Kit (Active Motif). The percentage enrichment was calculated as follows: enrichment (%) = 2 CT (UF) – CT (EF) /(1 + 2 CT (UF) – CT (EF) ) × 100. The eluted fragment (EF) represents a DNA fragment with more than five methylated CpG sites, and the unbounded fragment (UF) represents a DNA fragment with four or fewer methylated CpG sites. The % enrichment of fragments B and C was significantly increased in the MS group compared with the AFR group (n = 8 per group; * p

    Techniques Used: Mass Spectrometry, DNA Methylation Assay, Sequencing, Binding Assay, Methylation

    7) Product Images from "Mutations in FOXC2 (MFH-1), a Forkhead Family Transcription Factor, Are Responsible for the Hereditary Lymphedema-Distichiasis Syndrome"

    Article Title: Mutations in FOXC2 (MFH-1), a Forkhead Family Transcription Factor, Are Responsible for the Hereditary Lymphedema-Distichiasis Syndrome

    Journal: American Journal of Human Genetics

    doi:

    Mutation analysis in two families with hereditary lymphedema. Mutations in the FOXC2 gene were detected by direct sequencing of the PCR-amplified coding region of the gene. Results were confirmed by sequencing the reverse strand and by restriction-enzyme analysis. a, Sequencing revealed a TAC→TAG nonsense mutation (C297G) ( arrow, left panel ) in the proband (II-7) in family 1, creating a novel Bfa I restriction site. The right panel shows the cosegregation of the novel restriction site with the LD phenotype. Fetus II-6 was also shown to have the mutation, by restriction digest analysis (not shown). A 439-bp region of the FOXC2 gene was PCR amplified and digested with Bfa I. Products from normal alleles are not cut and remain 439 bp, whereas the mutant allele is cut into 383- and 53-bp fragments (not retained on gel). b, Sequence analysis revealing a 4-bp insertion in the proband (IV-2) in family 2. The GGCC insertion creates a shifted sequence beginning at the arrow ( left panel ). A novel Nae I restriction site is created by the insertion. The right panel shows the cosegregation of the Nae I fragments with the LD phenotype in family 2. PCR was used to amplify a 125-bp region of the FOXC2 gene (129 bp for the mutant allele). Nae I digestion of the PCR products results in 35- and 90-bp fragments for normal alleles, because of the presence of a naturally occurring Nae I site in the product. In alleles with the insertion, the 129-bp product is cut twice, generating two 35-bp fragments and a 59-bp fragment. Bands labeled “HD” show uncut heteroduplexes.
    Figure Legend Snippet: Mutation analysis in two families with hereditary lymphedema. Mutations in the FOXC2 gene were detected by direct sequencing of the PCR-amplified coding region of the gene. Results were confirmed by sequencing the reverse strand and by restriction-enzyme analysis. a, Sequencing revealed a TAC→TAG nonsense mutation (C297G) ( arrow, left panel ) in the proband (II-7) in family 1, creating a novel Bfa I restriction site. The right panel shows the cosegregation of the novel restriction site with the LD phenotype. Fetus II-6 was also shown to have the mutation, by restriction digest analysis (not shown). A 439-bp region of the FOXC2 gene was PCR amplified and digested with Bfa I. Products from normal alleles are not cut and remain 439 bp, whereas the mutant allele is cut into 383- and 53-bp fragments (not retained on gel). b, Sequence analysis revealing a 4-bp insertion in the proband (IV-2) in family 2. The GGCC insertion creates a shifted sequence beginning at the arrow ( left panel ). A novel Nae I restriction site is created by the insertion. The right panel shows the cosegregation of the Nae I fragments with the LD phenotype in family 2. PCR was used to amplify a 125-bp region of the FOXC2 gene (129 bp for the mutant allele). Nae I digestion of the PCR products results in 35- and 90-bp fragments for normal alleles, because of the presence of a naturally occurring Nae I site in the product. In alleles with the insertion, the 129-bp product is cut twice, generating two 35-bp fragments and a 59-bp fragment. Bands labeled “HD” show uncut heteroduplexes.

    Techniques Used: Mutagenesis, Sequencing, Polymerase Chain Reaction, Amplification, Labeling

    8) Product Images from "In Vivo Bypass of 8-oxodG"

    Article Title: In Vivo Bypass of 8-oxodG

    Journal: PLoS Genetics

    doi: 10.1371/journal.pgen.1003682

    Models for incorporation of oligo GO and UGO. (A) Incorporation of Oligo GO creates three mismatches; if the oligo is not removed before the second round, replication of the C, indicated in yellow, would result in a Trp+ phenotype, replication of the 8-oxoG, indicated in red, would create a Bfa I site if an A were incorporated, and replication of the G indicated in blue would create an Sph I site. In the first round, usually the entire portion of the oligo containing the marked bases remains or is removed by MMR. However, when MMR is present, the segment of the oligo containing the 5′-two mismatches can be removed, but the segment creating the Trp+ phenotype can be left, presumably due to failure of MMR to recognized the C-C mismatch (see text). If the marked segment of Oligo GO persists to the second round of replication, translesion synthesis creates an Sph I site and a Bfa I site if the 8-oxoG is bypassed with an A. If the 8-oxoG induces template switching, no Sph I site is created. (B) Incorporation of Oligo UGO creates an additional mismatch with the C indicated in blue, 3′ of the C-C mismatch. Due to this additional mismatch, in the first round, either the entire oligo remains, or is removed. The results of the second round of replication are identical to that of Oligo GO in (A). Cells with a gray background are Trp- and thus do not survive selection.
    Figure Legend Snippet: Models for incorporation of oligo GO and UGO. (A) Incorporation of Oligo GO creates three mismatches; if the oligo is not removed before the second round, replication of the C, indicated in yellow, would result in a Trp+ phenotype, replication of the 8-oxoG, indicated in red, would create a Bfa I site if an A were incorporated, and replication of the G indicated in blue would create an Sph I site. In the first round, usually the entire portion of the oligo containing the marked bases remains or is removed by MMR. However, when MMR is present, the segment of the oligo containing the 5′-two mismatches can be removed, but the segment creating the Trp+ phenotype can be left, presumably due to failure of MMR to recognized the C-C mismatch (see text). If the marked segment of Oligo GO persists to the second round of replication, translesion synthesis creates an Sph I site and a Bfa I site if the 8-oxoG is bypassed with an A. If the 8-oxoG induces template switching, no Sph I site is created. (B) Incorporation of Oligo UGO creates an additional mismatch with the C indicated in blue, 3′ of the C-C mismatch. Due to this additional mismatch, in the first round, either the entire oligo remains, or is removed. The results of the second round of replication are identical to that of Oligo GO in (A). Cells with a gray background are Trp- and thus do not survive selection.

    Techniques Used: Translesion Synthesis, Selection

    Accuracy of 8-oxoG replication. Trp+ revertants containing an Sph I site were assayed for the presence of a Bfa I site resulting from insertion of an A opposite 8-oxoG in strains of the indicated genotype transformed with an 8-oxoG-containing oligo; those transformants lacking the Bfa I site had a C inserted opposite the 8-oxoG. In most cases, more than 40 Sph I containing revertants were assayed. Note that the 8-oxoG lesion is replicated in the second round; thus for example replication is on the leading strand in R strains. The error bars and horizontal bars are as in Figure 3 . For a : P
    Figure Legend Snippet: Accuracy of 8-oxoG replication. Trp+ revertants containing an Sph I site were assayed for the presence of a Bfa I site resulting from insertion of an A opposite 8-oxoG in strains of the indicated genotype transformed with an 8-oxoG-containing oligo; those transformants lacking the Bfa I site had a C inserted opposite the 8-oxoG. In most cases, more than 40 Sph I containing revertants were assayed. Note that the 8-oxoG lesion is replicated in the second round; thus for example replication is on the leading strand in R strains. The error bars and horizontal bars are as in Figure 3 . For a : P

    Techniques Used: Transformation Assay

    Sequences of TRP5 mutant regions and oligonucleotides used for reversion analysis. The trp5 - G148Cm mutant contains several changes designed to create additional completely degenerate third codon positions, with those of interest underlined; the sequence shown here begins at nt 128. The C at position 148 that must change to G in order to restore a Trp+ phenotype is highlighted in yellow. Oligo N creates 7 mismatches (highlighted in yellow and blue) upon annealing with the G148Cm sequence; oligos are numbered from the 5′ end. Oligo G and UG create a subset of those mismatches as indicated. Oligos GO and UGO are identical to Oligos G and UG except that the base highlighted in red is an 8-oxoG. If A is inserted opposite the 8-oxoG during replication, a novel Bfa I restriction site is created; similarly, the G highlighted in blue, if incorporated, creates a novel Sph I restriction site.
    Figure Legend Snippet: Sequences of TRP5 mutant regions and oligonucleotides used for reversion analysis. The trp5 - G148Cm mutant contains several changes designed to create additional completely degenerate third codon positions, with those of interest underlined; the sequence shown here begins at nt 128. The C at position 148 that must change to G in order to restore a Trp+ phenotype is highlighted in yellow. Oligo N creates 7 mismatches (highlighted in yellow and blue) upon annealing with the G148Cm sequence; oligos are numbered from the 5′ end. Oligo G and UG create a subset of those mismatches as indicated. Oligos GO and UGO are identical to Oligos G and UG except that the base highlighted in red is an 8-oxoG. If A is inserted opposite the 8-oxoG during replication, a novel Bfa I restriction site is created; similarly, the G highlighted in blue, if incorporated, creates a novel Sph I restriction site.

    Techniques Used: Mutagenesis, Sequencing

    9) Product Images from "Isolation and basic characterization of a β-glucosidase from a strain of Lactobacillus brevis isolated from a malolactic starter culture"

    Article Title: Isolation and basic characterization of a β-glucosidase from a strain of Lactobacillus brevis isolated from a malolactic starter culture

    Journal: Journal of applied microbiology

    doi: 10.1111/j.1365-2672.2009.04461.x

    16S ARDRA patterns on 2% Agarose. Digestion with Mse I ( A ) and Bfa I ( B ). Lanes 1 8: 50 bp ladder (A) , 100 bp ladder (B) . Lane 2: L. brevis DSMZ 20054. Lane 3: O. oeni DSMZ 20252. Lane 4: L. brevis SK3. Lane 5: Pediococcus acidilacti . Lane 6: O. oeni SK3Ba, Lane 7: O. oeni SK3Bb.
    Figure Legend Snippet: 16S ARDRA patterns on 2% Agarose. Digestion with Mse I ( A ) and Bfa I ( B ). Lanes 1 8: 50 bp ladder (A) , 100 bp ladder (B) . Lane 2: L. brevis DSMZ 20054. Lane 3: O. oeni DSMZ 20252. Lane 4: L. brevis SK3. Lane 5: Pediococcus acidilacti . Lane 6: O. oeni SK3Ba, Lane 7: O. oeni SK3Bb.

    Techniques Used:

    10) Product Images from "Resistance to Infection by Subgroups B, D, and E Avian Sarcoma and Leukosis Viruses Is Explained by a Premature Stop Codon within a Resistance Allele of the tvb Receptor Gene"

    Article Title: Resistance to Infection by Subgroups B, D, and E Avian Sarcoma and Leukosis Viruses Is Explained by a Premature Stop Codon within a Resistance Allele of the tvb Receptor Gene

    Journal: Journal of Virology

    doi: 10.1128/JVI.76.15.7918-7921.2002

    A 2.1-kb Bfa I restriction fragment is diagnostic of the tvb r allele. Bfa I-digested genomic DNA samples prepared from CEFs with the tvb genotypes indicated were subjected to Southern blot analysis with a 32 P-labeled tvb -specific DNA probe under standard conditions. Autoradiography was performed for 10 days at −80°C with intensifying screens. The position of the 2.1-kb DNA fragment that is unique to tvb r is indicated with an arrow.
    Figure Legend Snippet: A 2.1-kb Bfa I restriction fragment is diagnostic of the tvb r allele. Bfa I-digested genomic DNA samples prepared from CEFs with the tvb genotypes indicated were subjected to Southern blot analysis with a 32 P-labeled tvb -specific DNA probe under standard conditions. Autoradiography was performed for 10 days at −80°C with intensifying screens. The position of the 2.1-kb DNA fragment that is unique to tvb r is indicated with an arrow.

    Techniques Used: Diagnostic Assay, Southern Blot, Labeling, Autoradiography

    The tvb r allele contains a premature stop codon. A schematic drawing of TVB is shown depicting the signal peptide (SP), cysteine-rich domains (CRDs), membrane spanning domain (MSD), and cytoplasmic death domain. The nucleotide and amino acid sequences are also shown surrounding the single nucleotide change that distinguishes tvb r from tvb s1 (numbered from the start methionine codon). The premature stop codon in tvb r is indicated by an asterisk and a Bfa I site unique to tvb r is shown in a box.
    Figure Legend Snippet: The tvb r allele contains a premature stop codon. A schematic drawing of TVB is shown depicting the signal peptide (SP), cysteine-rich domains (CRDs), membrane spanning domain (MSD), and cytoplasmic death domain. The nucleotide and amino acid sequences are also shown surrounding the single nucleotide change that distinguishes tvb r from tvb s1 (numbered from the start methionine codon). The premature stop codon in tvb r is indicated by an asterisk and a Bfa I site unique to tvb r is shown in a box.

    Techniques Used:

    Related Articles

    Nucleic Acid Electrophoresis:

    Article Title: In Vivo Bypass of 8-oxodG
    Article Snippet: .. For restriction digestion, 5 µl of the PCR reaction was incubated with 2 units of either Bfa I or Sph I (New England Biolabs) in the recommended buffer in a total volume of 15 µl at 37° overnight and analyzed by gel electrophoresis. ..

    Article Title: Mutations in FOXC2 (MFH-1), a Forkhead Family Transcription Factor, Are Responsible for the Hereditary Lymphedema-Distichiasis Syndrome
    Article Snippet: .. PCR products were column purified (Qiagen) and were digested with Bfa I (New England Biolabs) at 37°C for 1 h prior to gel electrophoresis. ..

    Amplification:

    Article Title: Genetic Characteristics of Borrelia coriaceae Isolates from the Soft Tick Ornithodoros coriaceus (Acari: Argasidae)
    Article Snippet: .. Ten microliters of the amplification products was restricted separately with Bfa I, Hph I, and Mse I (New England Biolabs, Beverly, Mass.). .. Restriction fragments were resolved in a 2.5% NuSieve GTG agarose gel (FMC BioProducts, Rockland, Maine) with 1× TBE ( ) at 5 V/cm for 3.5 h.

    Article Title: Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of Mycoplasma species
    Article Snippet: .. For a final identification, the amplified 16S rDNA of some strains were digested in addition with Bfa I (New England Biolabs, USA; sequence: C^TAG) or Hpy F10VI (Fermentas; sequence: GCNNNNN^NNGC). .. The restriction fragments were separated on a 3% Nusieve 3:1 agar (Tebu-Bio, France) for 2 hours at 130 V and visualized using a GeneGenius gel documentation system (Westburg, The Netherlands).

    Purification:

    Article Title: Mutations in FOXC2 (MFH-1), a Forkhead Family Transcription Factor, Are Responsible for the Hereditary Lymphedema-Distichiasis Syndrome
    Article Snippet: .. PCR products were column purified (Qiagen) and were digested with Bfa I (New England Biolabs) at 37°C for 1 h prior to gel electrophoresis. ..

    Polymerase Chain Reaction:

    Article Title: Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces
    Article Snippet: .. In the case of digestion with Rsa I (recognition site, 5′-GT|AC-3′) plus Bfa I (5′-C|TAG-3′), a reaction mixture (10 μl) containing 2.5 U each of Rsa I (Nippon Gene, Toyama, Japan) and Bfa I (New England BioLabs, Beverly, Mass.), 1× NEB buffer 4 (New England BioLabs), 2 μl of the PCR product from the fecal DNA, and 0.5 μl of each of two kinds of the internal control DNAs was incubated at 37°C for 1 h. In the case of digestion with Bsl I (5′-CCNNNNN|NNGG-3′) or Bse LI, which is an isoschizomer of Bsl I, a reaction mixture (10 μl) containing 2 U of Bsl I (New England BioLabs) or Bse LI (MBI Fermentas, Amherst, N.Y.), 1× NEB buffer 3 (New England BioLabs), 2 μl of the PCR product from the fecal DNA, and 0.5 μl of either of two kinds of the internal control DNAs was incubated at 55°C for 1 h. The digestion of the internal control DNA derived from Lactobacillus sp. with Rsa I, Bfa I, or Bsl I gave a T-RF of 383, 311, or 657 bp, respectively. .. The digestion of the internal control DNA derived from Staphylococcus sp. with Rsa I, Bfa I, or Bsl I gave a T-RF of 136, 498, or 518 bp, respectively.

    Article Title: In Vivo Bypass of 8-oxodG
    Article Snippet: .. For restriction digestion, 5 µl of the PCR reaction was incubated with 2 units of either Bfa I or Sph I (New England Biolabs) in the recommended buffer in a total volume of 15 µl at 37° overnight and analyzed by gel electrophoresis. ..

    Article Title: Identification of mutations in the c-mpl gene in congenital amegakaryocytic thrombocytopenia
    Article Snippet: .. PCR fragments of exons 4 and 10 were incubated at 37°C for 2 h with Pvu II (Boehringer Mannheim) and Bfa I (New England Biolabs), respectively, in accordance with the suppliers’ instructions. .. The digests were analyzed by electrophoresis in 1× TBE (90 mM Tris/64.6 mM boric acid/2.5 mM EDTA, pH 8.3) on 4% agarose (GIBCO/BRL) in parallel with a 100-bp ladder marker (New England Biolabs) and visualized with ethidium bromide staining.

    Article Title: Mutations in FOXC2 (MFH-1), a Forkhead Family Transcription Factor, Are Responsible for the Hereditary Lymphedema-Distichiasis Syndrome
    Article Snippet: .. PCR products were column purified (Qiagen) and were digested with Bfa I (New England Biolabs) at 37°C for 1 h prior to gel electrophoresis. ..

    Incubation:

    Article Title: Isolation of Helicobacter canis from a Colony of Bengal Cats with Endemic Diarrhea
    Article Snippet: .. DNA digestion was accomplished by the addition of 10 U each of the restriction endonucleases Hha I and Bfa I (New England Biolabs, Beverly, Mass.) and 1 μl of restriction buffer (New England Biolabs) to 16 μl of DNA and incubation at 37°C for 3 h. The samples were separated on a 6% Visigel separation matrix (Stratagene), stained with ethidium bromide, and viewed by UV illumination. .. Bacteria isolated from both fecal samples from one cat were cultured on blood agar plates, and the cells were harvested and washed twice with 1 ml of double-distilled H2 O.

    Article Title: Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces
    Article Snippet: .. In the case of digestion with Rsa I (recognition site, 5′-GT|AC-3′) plus Bfa I (5′-C|TAG-3′), a reaction mixture (10 μl) containing 2.5 U each of Rsa I (Nippon Gene, Toyama, Japan) and Bfa I (New England BioLabs, Beverly, Mass.), 1× NEB buffer 4 (New England BioLabs), 2 μl of the PCR product from the fecal DNA, and 0.5 μl of each of two kinds of the internal control DNAs was incubated at 37°C for 1 h. In the case of digestion with Bsl I (5′-CCNNNNN|NNGG-3′) or Bse LI, which is an isoschizomer of Bsl I, a reaction mixture (10 μl) containing 2 U of Bsl I (New England BioLabs) or Bse LI (MBI Fermentas, Amherst, N.Y.), 1× NEB buffer 3 (New England BioLabs), 2 μl of the PCR product from the fecal DNA, and 0.5 μl of either of two kinds of the internal control DNAs was incubated at 55°C for 1 h. The digestion of the internal control DNA derived from Lactobacillus sp. with Rsa I, Bfa I, or Bsl I gave a T-RF of 383, 311, or 657 bp, respectively. .. The digestion of the internal control DNA derived from Staphylococcus sp. with Rsa I, Bfa I, or Bsl I gave a T-RF of 136, 498, or 518 bp, respectively.

    Article Title: In Vivo Bypass of 8-oxodG
    Article Snippet: .. For restriction digestion, 5 µl of the PCR reaction was incubated with 2 units of either Bfa I or Sph I (New England Biolabs) in the recommended buffer in a total volume of 15 µl at 37° overnight and analyzed by gel electrophoresis. ..

    Article Title: Identification of mutations in the c-mpl gene in congenital amegakaryocytic thrombocytopenia
    Article Snippet: .. PCR fragments of exons 4 and 10 were incubated at 37°C for 2 h with Pvu II (Boehringer Mannheim) and Bfa I (New England Biolabs), respectively, in accordance with the suppliers’ instructions. .. The digests were analyzed by electrophoresis in 1× TBE (90 mM Tris/64.6 mM boric acid/2.5 mM EDTA, pH 8.3) on 4% agarose (GIBCO/BRL) in parallel with a 100-bp ladder marker (New England Biolabs) and visualized with ethidium bromide staining.

    Sequencing:

    Article Title: Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of Mycoplasma species
    Article Snippet: .. For a final identification, the amplified 16S rDNA of some strains were digested in addition with Bfa I (New England Biolabs, USA; sequence: C^TAG) or Hpy F10VI (Fermentas; sequence: GCNNNNN^NNGC). .. The restriction fragments were separated on a 3% Nusieve 3:1 agar (Tebu-Bio, France) for 2 hours at 130 V and visualized using a GeneGenius gel documentation system (Westburg, The Netherlands).

    Staining:

    Article Title: Isolation of Helicobacter canis from a Colony of Bengal Cats with Endemic Diarrhea
    Article Snippet: .. DNA digestion was accomplished by the addition of 10 U each of the restriction endonucleases Hha I and Bfa I (New England Biolabs, Beverly, Mass.) and 1 μl of restriction buffer (New England Biolabs) to 16 μl of DNA and incubation at 37°C for 3 h. The samples were separated on a 6% Visigel separation matrix (Stratagene), stained with ethidium bromide, and viewed by UV illumination. .. Bacteria isolated from both fecal samples from one cat were cultured on blood agar plates, and the cells were harvested and washed twice with 1 ml of double-distilled H2 O.

    Derivative Assay:

    Article Title: Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces
    Article Snippet: .. In the case of digestion with Rsa I (recognition site, 5′-GT|AC-3′) plus Bfa I (5′-C|TAG-3′), a reaction mixture (10 μl) containing 2.5 U each of Rsa I (Nippon Gene, Toyama, Japan) and Bfa I (New England BioLabs, Beverly, Mass.), 1× NEB buffer 4 (New England BioLabs), 2 μl of the PCR product from the fecal DNA, and 0.5 μl of each of two kinds of the internal control DNAs was incubated at 37°C for 1 h. In the case of digestion with Bsl I (5′-CCNNNNN|NNGG-3′) or Bse LI, which is an isoschizomer of Bsl I, a reaction mixture (10 μl) containing 2 U of Bsl I (New England BioLabs) or Bse LI (MBI Fermentas, Amherst, N.Y.), 1× NEB buffer 3 (New England BioLabs), 2 μl of the PCR product from the fecal DNA, and 0.5 μl of either of two kinds of the internal control DNAs was incubated at 55°C for 1 h. The digestion of the internal control DNA derived from Lactobacillus sp. with Rsa I, Bfa I, or Bsl I gave a T-RF of 383, 311, or 657 bp, respectively. .. The digestion of the internal control DNA derived from Staphylococcus sp. with Rsa I, Bfa I, or Bsl I gave a T-RF of 136, 498, or 518 bp, respectively.

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    New England Biolabs bfa i
    Frequency distribution profiles of the 5′ T-RFs derived from in silico digestion of 16S rRNA gene sequences from strains belonging to the major large intestinal bacterial genera. TAP T-RFLPs were run with the primer-enzyme combinations of 516f- <t>Rsa</t> I plus <t>Bfa</t> I (A) or 516f- Bsl I (B), and histograms of the predicted T-RF lengths were drawn. The T-RFs of 995 bp in panel B are uncut fragments.
    Bfa I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Frequency distribution profiles of the 5′ T-RFs derived from in silico digestion of 16S rRNA gene sequences from strains belonging to the major large intestinal bacterial genera. TAP T-RFLPs were run with the primer-enzyme combinations of 516f- Rsa I plus Bfa I (A) or 516f- Bsl I (B), and histograms of the predicted T-RF lengths were drawn. The T-RFs of 995 bp in panel B are uncut fragments.

    Journal: Applied and Environmental Microbiology

    Article Title: Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces

    doi: 10.1128/AEM.69.2.1251-1262.2003

    Figure Lengend Snippet: Frequency distribution profiles of the 5′ T-RFs derived from in silico digestion of 16S rRNA gene sequences from strains belonging to the major large intestinal bacterial genera. TAP T-RFLPs were run with the primer-enzyme combinations of 516f- Rsa I plus Bfa I (A) or 516f- Bsl I (B), and histograms of the predicted T-RF lengths were drawn. The T-RFs of 995 bp in panel B are uncut fragments.

    Article Snippet: In the case of digestion with Rsa I (recognition site, 5′-GT|AC-3′) plus Bfa I (5′-C|TAG-3′), a reaction mixture (10 μl) containing 2.5 U each of Rsa I (Nippon Gene, Toyama, Japan) and Bfa I (New England BioLabs, Beverly, Mass.), 1× NEB buffer 4 (New England BioLabs), 2 μl of the PCR product from the fecal DNA, and 0.5 μl of each of two kinds of the internal control DNAs was incubated at 37°C for 1 h. In the case of digestion with Bsl I (5′-CCNNNNN|NNGG-3′) or Bse LI, which is an isoschizomer of Bsl I, a reaction mixture (10 μl) containing 2 U of Bsl I (New England BioLabs) or Bse LI (MBI Fermentas, Amherst, N.Y.), 1× NEB buffer 3 (New England BioLabs), 2 μl of the PCR product from the fecal DNA, and 0.5 μl of either of two kinds of the internal control DNAs was incubated at 55°C for 1 h. The digestion of the internal control DNA derived from Lactobacillus sp. with Rsa I, Bfa I, or Bsl I gave a T-RF of 383, 311, or 657 bp, respectively.

    Techniques: Derivative Assay, In Silico

    Fractionation of T-RFs by agarose gel electrophoresis. T-RFs produced by Bsl I digestion of 16S rRNA gene amplicons from a fecal sample of individual G (lane 3) or by Rsa I-plus- Bfa I digestion of those from a fecal sample of individual H (lane 4) were electrophoresed on a 3% agarose gel as described in Materials and Methods. Arrowheads in lanes 3 and 4 represent the positions of 124-bp OTU Bsl and 377-bp OTU R-B , respectively. Lane 1, 100-bp ladder marker (MBI Fermentas); lane 2, pBR322× Msp I marker (Nippon Gene).

    Journal: Applied and Environmental Microbiology

    Article Title: Application of New Primer-Enzyme Combinations to Terminal Restriction Fragment Length Polymorphism Profiling of Bacterial Populations in Human Feces

    doi: 10.1128/AEM.69.2.1251-1262.2003

    Figure Lengend Snippet: Fractionation of T-RFs by agarose gel electrophoresis. T-RFs produced by Bsl I digestion of 16S rRNA gene amplicons from a fecal sample of individual G (lane 3) or by Rsa I-plus- Bfa I digestion of those from a fecal sample of individual H (lane 4) were electrophoresed on a 3% agarose gel as described in Materials and Methods. Arrowheads in lanes 3 and 4 represent the positions of 124-bp OTU Bsl and 377-bp OTU R-B , respectively. Lane 1, 100-bp ladder marker (MBI Fermentas); lane 2, pBR322× Msp I marker (Nippon Gene).

    Article Snippet: In the case of digestion with Rsa I (recognition site, 5′-GT|AC-3′) plus Bfa I (5′-C|TAG-3′), a reaction mixture (10 μl) containing 2.5 U each of Rsa I (Nippon Gene, Toyama, Japan) and Bfa I (New England BioLabs, Beverly, Mass.), 1× NEB buffer 4 (New England BioLabs), 2 μl of the PCR product from the fecal DNA, and 0.5 μl of each of two kinds of the internal control DNAs was incubated at 37°C for 1 h. In the case of digestion with Bsl I (5′-CCNNNNN|NNGG-3′) or Bse LI, which is an isoschizomer of Bsl I, a reaction mixture (10 μl) containing 2 U of Bsl I (New England BioLabs) or Bse LI (MBI Fermentas, Amherst, N.Y.), 1× NEB buffer 3 (New England BioLabs), 2 μl of the PCR product from the fecal DNA, and 0.5 μl of either of two kinds of the internal control DNAs was incubated at 55°C for 1 h. The digestion of the internal control DNA derived from Lactobacillus sp. with Rsa I, Bfa I, or Bsl I gave a T-RF of 383, 311, or 657 bp, respectively.

    Techniques: Fractionation, Agarose Gel Electrophoresis, Produced, Marker

    ARDRA profiles after restriction with Bfa I of 18 different Mycoplasma species. Since all samples of the same species gave identical restriction patterns, the number of strains tested for each species is indicated in parenthesis. A Generuler 50-bp ladder (Fermentas) was used as size-marker.

    Journal: BMC Infectious Diseases

    Article Title: Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of Mycoplasma species

    doi: 10.1186/1471-2334-5-46

    Figure Lengend Snippet: ARDRA profiles after restriction with Bfa I of 18 different Mycoplasma species. Since all samples of the same species gave identical restriction patterns, the number of strains tested for each species is indicated in parenthesis. A Generuler 50-bp ladder (Fermentas) was used as size-marker.

    Article Snippet: For a final identification, the amplified 16S rDNA of some strains were digested in addition with Bfa I (New England Biolabs, USA; sequence: C^TAG) or Hpy F10VI (Fermentas; sequence: GCNNNNN^NNGC).

    Techniques: Marker

    Calculated ARDRA profiles of Mycoplasma spp. that can be differentiated using Bfa I, but had undistinguishable Alu I restriction profiles.

    Journal: BMC Infectious Diseases

    Article Title: Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of Mycoplasma species

    doi: 10.1186/1471-2334-5-46

    Figure Lengend Snippet: Calculated ARDRA profiles of Mycoplasma spp. that can be differentiated using Bfa I, but had undistinguishable Alu I restriction profiles.

    Article Snippet: For a final identification, the amplified 16S rDNA of some strains were digested in addition with Bfa I (New England Biolabs, USA; sequence: C^TAG) or Hpy F10VI (Fermentas; sequence: GCNNNNN^NNGC).

    Techniques:

    Comparison of RFLP patterns of the 1.2-kb Helicobacter -specific PCR product with restriction enzymes Bfa I and Hha I. Lanes: M, 100-bp DNA ladder; 1, H. canis ); 2, H. canis ATCC 51401; 3, MIT 98-152; 4, MIT 98-153.

    Journal: Journal of Clinical Microbiology

    Article Title: Isolation of Helicobacter canis from a Colony of Bengal Cats with Endemic Diarrhea

    doi:

    Figure Lengend Snippet: Comparison of RFLP patterns of the 1.2-kb Helicobacter -specific PCR product with restriction enzymes Bfa I and Hha I. Lanes: M, 100-bp DNA ladder; 1, H. canis ); 2, H. canis ATCC 51401; 3, MIT 98-152; 4, MIT 98-153.

    Article Snippet: DNA digestion was accomplished by the addition of 10 U each of the restriction endonucleases Hha I and Bfa I (New England Biolabs, Beverly, Mass.) and 1 μl of restriction buffer (New England Biolabs) to 16 μl of DNA and incubation at 37°C for 3 h. The samples were separated on a 6% Visigel separation matrix (Stratagene), stained with ethidium bromide, and viewed by UV illumination.

    Techniques: Polymerase Chain Reaction

    16S rRNA amplification products restricted with Hph I (a), Bfa I (b), and Mse I (c). Lanes: 1, CA434; 2, CA435; 3, Co53; 4, B. parkeri ; 5, CA4. Restriction fragments were resolved in 2.5% NuSieve-GTG agarose–1× TBE at 5 V/cm for 3.5 h.

    Journal: Journal of Clinical Microbiology

    Article Title: Genetic Characteristics of Borrelia coriaceae Isolates from the Soft Tick Ornithodoros coriaceus (Acari: Argasidae)

    doi:

    Figure Lengend Snippet: 16S rRNA amplification products restricted with Hph I (a), Bfa I (b), and Mse I (c). Lanes: 1, CA434; 2, CA435; 3, Co53; 4, B. parkeri ; 5, CA4. Restriction fragments were resolved in 2.5% NuSieve-GTG agarose–1× TBE at 5 V/cm for 3.5 h.

    Article Snippet: Ten microliters of the amplification products was restricted separately with Bfa I, Hph I, and Mse I (New England Biolabs, Beverly, Mass.).

    Techniques: Amplification