bfa i  (New England Biolabs)

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

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

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

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:

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

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