Journal articles: 'BamHI'

1

Kang, Y. K., H. B. Lee, M. J. Noh, N. Y. Cho, and O. J. Yoo. "Different Effects of Base Analog Substitutions in BamHI Restriction Site on Recognition by BamHI Endonuclease and Bamhi Methylase." Biochemical and Biophysical Research Communications 206, no. 3 (January 1995): 997–1002. http://dx.doi.org/10.1006/bbrc.1995.1141.

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2

Kim, W. K., R. L. Innes, and E. R. Kerber. "Ribosomal DNA repeat unit polymorphism in six Aegilops species." Genome 35, no. 3 (June 1, 1992): 510–15. http://dx.doi.org/10.1139/g92-075.

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Total genomic DNA of 27 accessions representing six Aegilops species was restricted with BamHI, EcoRI, and BamHI plus EcoRI, and the restriction fragments were probed with the ribosomal clones pMF2 containing the ribosomal RNA coding regions. The rDNA repeat lengths varied between 9.0 and 10.8 kb. Intraspecific variation among the 10 accessions of Ae. squarrosa var. strangulata ranged from 9.0 to 9.6 kb, suggesting a diversity of genotypes within as well as between species. These variations were not related to their geographical distributions. Each of 24 accessions had two BamHI sites in the coding region (type A), while three accessions of Ae. squarrosa var. strangulata had four BamHI sites (type B, two sites in the intergenic region). Results for these three accessions of Ae. squarrosa var. strangulata suggest genotypic diversity in this species. In BamHI restriction of each accession, a third DNA fragment, ranging between 9.0 and 10.8 kb in type A and 6.0 kb in type B, resulted from lack of digestion at the 26S BamHI site. In double digestion, all rDNA repeat units were restricted by EcoRI, yielding 3.9-, 0.9-, and 4.8-kb fragments, the last of which arose from the lack of digestion at the 26S BamHI site, estimated to occur in 5–20% of the repeat units, depending on the accession.Key words: Triticum tauschii, RFLP, diversity.

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3

Melani Maskoen, Ani, Saskia L Nasroen, Prima Nanda Fauziah, Eky Setiawan Soeria Soemantri, and Basri A Gani. "EXPRESSION OF TRANSFORMING GROWTH FACTOR ALPHA BAMHI AND RSAI GENE VARIANTS ASSOCIATED WITH NON-SYNDROMIC CLEFT PALATE OF INDONESIAN SUBJECTS USING POLYMERASE CHAIN REACTION METHOD." Asian Journal of Pharmaceutical and Clinical Research 11, no. 4 (April 1, 2018): 351. http://dx.doi.org/10.22159/ajpcr.2018.v11i4.24242.

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Objective: This study aimed to detect and analyze transforming growth factor alpha (TGFA) BamHI and RsaI gene variants which associated with the risk factor of non-syndromic cleft palate only (NS CPO) of Indonesian subject.Methods: This was case-control study using samples from 32 NS CPO subjects and 28 control subjects. DNA was extracted from venous blood, and the TGFA gene was amplified using polymerase chain reaction technique, then digestion product from TaqI and RsaI restriction enzyme was evaluated. Statistical analysis to determine significant differences of gene variant frequency among NS CPO subject and control was χ2. The odds ratio (OR) was used to determine a risk factor of NS CPO.Results: The study results showed that the TGFA BamHI gene variant was not identified in NS CPO among Indonesian but TGFA RsaI gene variant was identified. The frequency of TT/B1B1 homozygous mutant genotype was 80.0% in NS CPO subjects and 20.0% in control subjects (OR=3.857; 95% confidence interval=0.405–36.749).Conclusion: TGFA RsaI gene can be considered a risk factor of NS CPO compared TGFA BamH1 gene of Indonesian subjects.

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4

Molnar, Stephen J., and George Fedak. "Polymorphism in ribosomal DNA repeat units of 12 Hordeum species." Genome 32, no. 6 (December 1, 1989): 1124–27. http://dx.doi.org/10.1139/g89-565.

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Total genomic DNA was isolated from leaves of individual accessions of 12 Hordeum species. SacI, HindIII, and BamHI restriction fragments hybridizing to the wheat rDNA probe pTA71 were compared. Thirteen rDNA repeat unit length variants were recovered, which combined to produce 11 distinct phenotypes. All rDNA repeat units had two SacI sites and no HindIII sites. The rDNA repeat units of H. secalinum, H. hrasdanicum, and H. distichum all had 3 BamHI sites, but in different configurations. The rDNA repeat units of the other species had at least 4 BamHI sites. Ladders of small hybridizing fragments in 8 of 9 of the latter accessions indicated the presence of occasional BamHI sites in some subrepeats within the intergenic spacer regions of the rDNA repeat units. Different distributions of BamHI restriction site maps within the Hordeum sections strengthen the concept of using variation in rDNA restriction sites as a taxonomic character.Key words: Hordeum, ribosomal DNA, polymorphism.

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5

Litz, CE, JS McClure, CM Copenhaver, and RD Brunning. "Duplication of small segments within the major breakpoint cluster region in chronic myelogenous leukemia." Blood 81, no. 6 (March 15, 1993): 1567–72. http://dx.doi.org/10.1182/blood.v81.6.1567.1567.

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Abstract The t(9;22) in chronic myelogenous leukemia (CML) may be reciprocal or, in a minority of cases, may result in an extensive deletion of a portion of the major breakpoint cluster region (M-bcr) of the BCR. This report provides evidence of the duplication of small segments within the M-bcr in a small group of patients with CML. Southern blots of Bgl II and Bgl II/BamHI double-digested DNA from the blood or bone marrow of 46 patients with CML were probed with a 5' 1.4-kb Taq I/HindIII M- bcr probe and a 3' 2-kb HindIII/BamHI M-bcr probe. In three patients, rearrangements were noted with both probes in Bgl II-digested DNA, but were not present in Bgl II/BamHI-digested DNA with either probe. Southern analysis of DNA samples double-digested with Bgl II and BspHI from two of these three cases showed no rearrangements with either probe; the M-bcr BspHI site is located 26 bp 3' of the BamHI site in the second intron of the M-bcr. The presence of a rearranged M-bcr with both probes in Bgl II-digested DNA and the lack of rearrangement in Bgl II/BamHI and Bgl II/BspHI double-digested DNA suggest the presence of M- bcr BamHI and BspHI sites on both 9q+ chromosome (9q+) and the Philadelphia chromosome (Ph). This implies a duplication of at least the 26-bp M-bcr BamHI/BspHI fragment in these two samples. Sequence data from one of these two cases confirmed the M-bcr breakpoints to be staggered; the Ph M-bcr breakpoint occurred 258 bp downstream from the 9q+ M-bcr breakpoint. It is concluded that a duplication of small segments within the M-bcr occurs in a small group of patients with CML, which may lead to pseudogermline patterns on Southern blot. Such a duplication may provide insight into the mechanism of some chromosomal translocations in neoplasia.

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6

Litz, CE, JS McClure, CM Copenhaver, and RD Brunning. "Duplication of small segments within the major breakpoint cluster region in chronic myelogenous leukemia." Blood 81, no. 6 (March 15, 1993): 1567–72. http://dx.doi.org/10.1182/blood.v81.6.1567.bloodjournal8161567.

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The t(9;22) in chronic myelogenous leukemia (CML) may be reciprocal or, in a minority of cases, may result in an extensive deletion of a portion of the major breakpoint cluster region (M-bcr) of the BCR. This report provides evidence of the duplication of small segments within the M-bcr in a small group of patients with CML. Southern blots of Bgl II and Bgl II/BamHI double-digested DNA from the blood or bone marrow of 46 patients with CML were probed with a 5' 1.4-kb Taq I/HindIII M- bcr probe and a 3' 2-kb HindIII/BamHI M-bcr probe. In three patients, rearrangements were noted with both probes in Bgl II-digested DNA, but were not present in Bgl II/BamHI-digested DNA with either probe. Southern analysis of DNA samples double-digested with Bgl II and BspHI from two of these three cases showed no rearrangements with either probe; the M-bcr BspHI site is located 26 bp 3' of the BamHI site in the second intron of the M-bcr. The presence of a rearranged M-bcr with both probes in Bgl II-digested DNA and the lack of rearrangement in Bgl II/BamHI and Bgl II/BspHI double-digested DNA suggest the presence of M- bcr BamHI and BspHI sites on both 9q+ chromosome (9q+) and the Philadelphia chromosome (Ph). This implies a duplication of at least the 26-bp M-bcr BamHI/BspHI fragment in these two samples. Sequence data from one of these two cases confirmed the M-bcr breakpoints to be staggered; the Ph M-bcr breakpoint occurred 258 bp downstream from the 9q+ M-bcr breakpoint. It is concluded that a duplication of small segments within the M-bcr occurs in a small group of patients with CML, which may lead to pseudogermline patterns on Southern blot. Such a duplication may provide insight into the mechanism of some chromosomal translocations in neoplasia.

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7

Lupton, S., and A. J. Levine. "Mapping genetic elements of Epstein-Barr virus that facilitate extrachromosomal persistence of Epstein-Barr virus-derived plasmids in human cells." Molecular and Cellular Biology 5, no. 10 (October 1985): 2533–42. http://dx.doi.org/10.1128/mcb.5.10.2533-2542.1985.

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The Epstein-Barr virus (EBV) genome becomes established as a multicopy plasmid in the nucleus of infected B lymphocytes. A cis-acting DNA sequence previously described within the BamHI-C fragment of the EBV genome (J. Yates, N. Warren, D. Reisman, and B. Sugden, Proc. Natl. Acad. Sci. USA 81:3806-3810, 1984) allows stable extrachromosomal plasmid maintenance in latently infected cells, but not in EBV-negative cells. In agreement with the findings of Yates et al., deletion analysis permitted the assignment of this function to a 2,208-base-pair region (nucleotides 7315 to 9517 of the B95-8 strain of EBV) of the BamHI-C fragment that contained a striking repetitive sequence and an extended region of dyad symmetry. A recombinant vector, p410+, was constructed which carried the BamHI-K fragment (nucleotides 107565 to 112625 of the B95-8 strain, encoding the EBV-associated nuclear antigen EBNA-1), the cis-acting sequence from the BamHI-C fragment, and a dominant selectable marker gene encoding G-418 resistance in animal cells. After being transfected into HeLa cells, this plasmid persisted extrachromosomally at a low copy number, with no detectable rearrangements or deletions. Two mutations in the BamHI-K-derived portion of p410+, a large in-frame deletion and a linker insertion frameshift mutation, both of which alter the carboxy-terminal portion of EBNA-1, destroyed the ability of the plasmid to persist extrachromosomally in HeLa cells. A small in-frame deletion and linker insertion mutation in the region encoding the carboxy-terminal portion of EBNA-1, which replaced 19 amino acid codons with 2, had no effect on the maintenance of p410+ in HeLa cells. These observations indicate that EBNA-1, in combination with a cis-acting sequence in the BamHI-C fragment, is in part responsible for extrachromosomal EBV-derived plasmid maintenance in HeLa cells. Two additional activities have been localized to the BamHI-C DNA fragment: (i) a DNA sequence that could functionally substitute for the simian virus 40 enhancer and promoter elements controlling the expression of G-418 resistance and (ii) a DNA sequence which, although not sufficient to allow extrachromosomal plasmid maintenance, enhanced the frequency of transformation to G-418 resistance in EBV-positive (but not EBV-negative) cells. These findings suggest that the BamHI-C fragment contains a lymphoid-specific or EBV-inducible promoter or enhancer element or both.

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8

Lupton, S., and A. J. Levine. "Mapping genetic elements of Epstein-Barr virus that facilitate extrachromosomal persistence of Epstein-Barr virus-derived plasmids in human cells." Molecular and Cellular Biology 5, no. 10 (October 1985): 2533–42. http://dx.doi.org/10.1128/mcb.5.10.2533.

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The Epstein-Barr virus (EBV) genome becomes established as a multicopy plasmid in the nucleus of infected B lymphocytes. A cis-acting DNA sequence previously described within the BamHI-C fragment of the EBV genome (J. Yates, N. Warren, D. Reisman, and B. Sugden, Proc. Natl. Acad. Sci. USA 81:3806-3810, 1984) allows stable extrachromosomal plasmid maintenance in latently infected cells, but not in EBV-negative cells. In agreement with the findings of Yates et al., deletion analysis permitted the assignment of this function to a 2,208-base-pair region (nucleotides 7315 to 9517 of the B95-8 strain of EBV) of the BamHI-C fragment that contained a striking repetitive sequence and an extended region of dyad symmetry. A recombinant vector, p410+, was constructed which carried the BamHI-K fragment (nucleotides 107565 to 112625 of the B95-8 strain, encoding the EBV-associated nuclear antigen EBNA-1), the cis-acting sequence from the BamHI-C fragment, and a dominant selectable marker gene encoding G-418 resistance in animal cells. After being transfected into HeLa cells, this plasmid persisted extrachromosomally at a low copy number, with no detectable rearrangements or deletions. Two mutations in the BamHI-K-derived portion of p410+, a large in-frame deletion and a linker insertion frameshift mutation, both of which alter the carboxy-terminal portion of EBNA-1, destroyed the ability of the plasmid to persist extrachromosomally in HeLa cells. A small in-frame deletion and linker insertion mutation in the region encoding the carboxy-terminal portion of EBNA-1, which replaced 19 amino acid codons with 2, had no effect on the maintenance of p410+ in HeLa cells. These observations indicate that EBNA-1, in combination with a cis-acting sequence in the BamHI-C fragment, is in part responsible for extrachromosomal EBV-derived plasmid maintenance in HeLa cells. Two additional activities have been localized to the BamHI-C DNA fragment: (i) a DNA sequence that could functionally substitute for the simian virus 40 enhancer and promoter elements controlling the expression of G-418 resistance and (ii) a DNA sequence which, although not sufficient to allow extrachromosomal plasmid maintenance, enhanced the frequency of transformation to G-418 resistance in EBV-positive (but not EBV-negative) cells. These findings suggest that the BamHI-C fragment contains a lymphoid-specific or EBV-inducible promoter or enhancer element or both.

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9

Patel, P., G. I. Bell, R. C. Turner, and J. S. Wainscoat. "BamHI RFLP at the GLUT3 locus." Nucleic Acids Research 18, no. 16 (1990): 4967. http://dx.doi.org/10.1093/nar/18.16.4967.

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10

Cao, Y., J. K. Wagner, A. Eblé, P. Hindmarsh, and P. E. Mullis. "BamHI RFLP for the GHRHR locus." Human Molecular Genetics 3, no. 4 (1994): 682. http://dx.doi.org/10.1093/hmg/3.4.682.

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11

Yanagi, Yusuke, H. Masud, Takahiro Watanabe, Yoshitaka Sato, Fumi Goshima, Hiroshi Kimura, and Takayuki Murata. "Initial Characterization of the Epstein–Barr Virus BSRF1 Gene Product." Viruses 11, no. 3 (March 21, 2019): 285. http://dx.doi.org/10.3390/v11030285.

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Epstein–Barr virus (EBV) is a ubiquitous virus that causes infectious mononucleosis and several types of cancer, such as Burkitt lymphoma, T/NK-cell lymphoma, and nasopharyngeal carcinoma. As a herpesvirus, it encodes more than 80 genes, many of which have not been characterized. EBV BamHI S rightward reading frame 1 (BSRF1) encodes a tegument protein that, unlike its homologs herpes simplex virus unique long 51 (UL51) and human cytomegalovirus UL71, has not been extensively investigated. To examine the role of BSRF1, we prepared knockout and revertant strains using the bacterial artificial chromosome system. Unexpectedly, the disruption of the gene had little or no effect on EBV lytic replication and the transformation of primary B cells. However, the knockdown of BSRF1 in B95-8 cells decreased progeny production. An immunofluorescence assay revealed that BSRF1 localized to the Golgi apparatus in the cytoplasm, as did its homologs. BSRF1 also associated with BamHI G leftward reading frame 3.5 (BGLF3.5), BamHI B rightward reading frame 2 (BBRF2), and BamHI A leftward reading frame 1 (BALF1), and BALF1 was incorporated into the tegument fraction with BSRF1. Taken together, our results indicate that BSRF1 plays a role in secondary envelopment or virion egress in the cytoplasm, as do its homolog genes.

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12

Pan, Qiang, Hodjattallah Rabbani, and Lennart Hammarström. "Characterization of Human γ4 Switch Region Polymorphisms Suggests a Meiotic Recombinational Hot Spot Within the Ig Locus: Influence of S Region Length on IgG4 Production." Journal of Immunology 161, no. 7 (October 1, 1998): 3520–26. http://dx.doi.org/10.4049/jimmunol.161.7.3520.

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Abstract Human γ4 gene RFLPs, revealed after BamHI digestion, show IGHG4 alleles of 9.0 (9.2), 9.4, and 9.6 kb at various frequencies in different ethnic populations. Studies in immunodeficient individuals have previously suggested that the 9.4 BamHI allele is associated with a higher serum level of IgG4 than the 9.0 (9.2) BamHI allele, but it is not clear whether this is associated with the S region itself or other control elements. In addition, a duplication of the 9.4-kb γ4 allele has recently been observed in a high proportion of normal donors. We therefore undertook a study of the structural basis for the difference in Ab levels in the various γ4 alleles. We demonstrate that the Sγ4 alleles differ in length due to deletions and insertions of a varying number of 79-bp Sγ4 repeat units. Two novel RFLPs, 8.8 and 9.1 kb, were also observed. The alleles are likely to be generated by unequal crossing over, and the breakpoints cluster in Sγ4 repeat units that contain chi-like motifs, implicating chi-like sequences in the meiotic recombination. Our data support the idea that the 9.4-kb BamHI allele is more productive than the 9.0 (9.2)-kb allele in normal healthy donors, possibly due to the extended switch regions, whereas duplication of the γ4 gene has no effect on switching and IgG4 serum levels.

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13

Girard-Santosuosso, O., J. Lantier, N. Millet, C. Mouline, J. F. Guillot, J. Protais, P. Colin, C. Beaumont, and F. Lantier. "BamHI RFLP at the chicken ACRG locus." Animal Genetics 27, no. 5 (April 24, 2009): 375. http://dx.doi.org/10.1111/j.1365-2052.1996.tb00988.x.

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14

Rogde, S., B. Olaisen, P. Teisberg, and J. Sodetz. "A BamHI RFLP of the C8A gene." Nucleic Acids Research 19, no. 13 (1991): 3762. http://dx.doi.org/10.1093/nar/19.13.3762-a.

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15

Viadiu, Hector, and Aneel K. Aggarwal. "Structure of BamHI Bound to Nonspecific DNA." Molecular Cell 5, no. 5 (May 2000): 889–95. http://dx.doi.org/10.1016/s1097-2765(00)80329-9.

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16

Zantinge, Jennifer L., Éva Nagy, J. Brian Derbyshire, and Peter J. Krell. "Analysis of fowlpox virus DNA replication and mapping." Canadian Journal of Microbiology 41, no. 4-5 (April 1, 1995): 378–87. http://dx.doi.org/10.1139/m95-051.

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A physical map was generated for the fowlpox virus Chick-N-Pox vaccine strain DNA genome for EcoRI, BamHI, NcoI, and PstI. The gel profiles resulting from EcoRI, BamHI, BglII, NcoI, StyI, PstI, and PvuII digestions were analyzed by agarose and polyacrylamide gel electrophoresis. The size of the fowlpox virus genome was estimated from these digests to be 289–301 kb. Replication of fowlpox virus DNA in QT-35 cells was followed and indicated that viral DNA replication initiated at 6–8 h postinfection in these cells.Key words: physical mapping, fowlpox virus, QT-35 cells, DNA replication.

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17

Sebastio, G., A. Riccio, P. Verde, N. Scarpato, and F. Blasi. "BamHI RFLP linked to the human urokinase gene." Nucleic Acids Research 13, no. 14 (1985): 5404. http://dx.doi.org/10.1093/nar/13.14.5404.

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18

Clark, B. A., C. L. Maslen, L. Y. Sakai, M. Al Dhalimi, R. Litt, and M. Litt. "A BamHI polymorphism at the fibrillin (FBN) locus." Nucleic Acids Research 19, no. 15 (1991): 4309. http://dx.doi.org/10.1093/nar/19.15.4309.

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19

Lindstrom, William M., Ernst G. Malygin, Lidiya G. Ovechkina, Victor V. Zinoviev, and Norbert O. Reich. "Functional Analysis of BamHI DNA Cytosine-N4 Methyltransferase." Journal of Molecular Biology 325, no. 4 (January 2003): 711–20. http://dx.doi.org/10.1016/s0022-2836(02)01282-2.

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20

Xu, S. Y., and I. Schildkraut. "Isolation of BamHI variants with reduced cleavage activities." Journal of Biological Chemistry 266, no. 7 (March 1991): 4425–29. http://dx.doi.org/10.1016/s0021-9258(20)64339-3.

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21

Viadiu, Hector, Rebecca Kucera, Ira Schildkraut, and Aneel K. Aggarwal. "Crystallization of Restriction Endonuclease BamHI with Nonspecific DNA." Journal of Structural Biology 130, no. 1 (May 2000): 81–85. http://dx.doi.org/10.1006/jsbi.2000.4235.

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22

Nathan, Peter D., and Joan E. Brooks. "Characterization of clones of the BamHI methyltransferase gene." Gene 74, no. 1 (December 1988): 35–36. http://dx.doi.org/10.1016/0378-1119(88)90244-2.

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23

Adedeji Olulana, Abimbola F., Dianne Choi, Vincent Inverso, Shiv K. Redhu, Marco Vidonis, Luca Crevatin, Allen W. Nicholson, and Matteo Castronovo. "Noncanonical DNA Cleavage by BamHI Endonuclease in Laterally Confined DNA Monolayers Is a Step Function of DNA Density and Sequence." Molecules 27, no. 16 (August 17, 2022): 5262. http://dx.doi.org/10.3390/molecules27165262.

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Cleavage of DNA at noncanonical recognition sequences by restriction endonucleases (star activity) in bulk solution can be promoted by global experimental parameters, including enzyme or substrate concentration, temperature, pH, or buffer composition. To study the effect of nanoscale confinement on the noncanonical behaviour of BamHI, which cleaves a single unique sequence of 6 bp, we used AFM nanografting to generate laterally confined DNA monolayers (LCDM) at different densities, either in the form of small patches, several microns in width, or complete monolayers of thiol-modified DNA on a gold surface. We focused on two 44-bp DNAs, each containing a noncanonical BamHI site differing by 2 bp from the cognate recognition sequence. Topographic AFM imaging was used to monitor end-point reactions by measuring the decrease in the LCDM height with respect to the surrounding reference surface. At low DNA densities, BamHI efficiently cleaves only its cognate sequence while at intermediate DNA densities, noncanonical sequence cleavage occurs, and can be controlled in a stepwise (on/off) fashion by varying the DNA density and restriction site sequence. This study shows that endonuclease action on noncanonical sites in confined nanoarchitectures can be modulated by varying local physical parameters, independent of global chemical parameters.

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24

Pillay, Michael. "Variation of nuclear ribosomal RNA genes in Eragrostis tef (Zucc.) Trotter." Genome 40, no. 6 (December 1, 1997): 815–21. http://dx.doi.org/10.1139/g97-805.

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Variation in the ribosomal RNA genes (rDNA) was examined to assess the genetic variability among 314 plants representing 28 accessions of Eragrostis tef, an important food crop. A restriction site map was constructed for the species by localization of the BamHI, BglII, DraI, EcoRI, EcoRV, NdeI, SacI, SpeI, XbaI, and XhoI sites. A comparison of this map with those of other grasses showed conservation of sites, especially in the coding region. However, a unique EcoRI site combined with a BamHI site in the 18S region may be of diagnostic value for the species. A BamHI fragment that spans the intergenic spacer was used as an indicator of length variation of rDNA repeat units. rDNA repeat units in E. tef ranged in size from 8.4 to 11.07 kbp. Considerable size variation of rDNA repeats was present among accessions, between individual plants within some accessions, and within single plants. A total of 19 spacer length (sl) phenotypes was observed in 16 accessions in which 11–42 plants were analyzed. A single restriction site polymorphism was detected in PI442115 that was also distinguished by having a single sl variant. Variation in the rRNA genes is a useful indicator of genetic diversity in E. tef germplasm.Key words: Eragrostis tef, ribosomal DNA, restriction map, genetic variation.

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25

Chang, Yueh-Long, Seungho Cho, H. Corby Kistler, Chun-Sheng Hsieh, and Gary J. Muehlbauer. "Bacterial artificial chromosome–based physical map of Gibberella zeae (Fusarium graminearum)." Genome 50, no. 10 (October 2007): 954–62. http://dx.doi.org/10.1139/g07-079.

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Fusarium graminearum is the primary causal pathogen of Fusarium head blight of wheat and barley. To accelerate genomic analysis of F. graminearum, we developed a bacterial artificial chromosome (BAC)–based physical map and integrated it with the genome sequence and genetic map. One BAC library, developed in the HindIII restriction enzyme site, consists of 4608 clones with an insert size of approximately 107 kb and covers about 13.5 genome equivalents. The other library, developed in the BamHI restriction enzyme site, consists of 3072 clones with an insert size of approximately 95 kb and covers about 8.0 genome equivalents. We fingerprinted 2688 clones from the HindIII library and 1536 clones from the BamHI library and developed a physical map of F. graminearum consisting of 26 contigs covering 39.2 Mb. Comparison of our map with the F. graminearum genome sequence showed that the size of our physical map is equivalent to the 36.1 Mb of the genome sequence. We used 31 sequence-based genetic markers, randomly spaced throughout the genome, to integrate the physical map with the genetic map. We also end-sequenced 17 BamHI BAC clones and identified 4 clones that spanned gaps in the genome sequence. Our new integrated map is highly reliable and useful for a variety of genomics studies.

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26

Dreyfus, David H. "Genetics and Molecular Biology of Epstein-Barr Virus-Encoded BART MicroRNA: A Paradigm for Viral Modulation of Host Immune Response Genes and Genome Stability." Journal of Immunology Research 2017 (2017): 1–8. http://dx.doi.org/10.1155/2017/4758539.

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Epstein-Barr virus, a ubiquitous human herpesvirus, is associated through epidemiologic evidence with common autoimmune syndromes and cancers. However, specific genetic mechanisms of pathogenesis have been difficult to identify. In this review, the author summarizes evidence that recently discovered noncoding RNAs termed microRNA encoded by Epstein-Barr virus BARF (BamHI A right frame) termed BART (BamHI A right transcripts) are modulators of human immune response genes and genome stability in infected and bystander cells. BART expression is apparently regulated by complex feedback loops with the host immune response regulatory NF-κB transcription factors. EBV-encoded BZLF-1 (ZEBRA) protein could also regulate BART since ZEBRA contains a terminal region similar to ankyrin proteins such as IκBαthat regulate host NF-κB. BALF-2 (BamHI A left frame transcript), a viral homologue of the immunoglobulin and T cell receptor gene recombinase RAG-1 (recombination-activating gene-1), may also be coregulated with BART since BALF-2 regulatory sequences are located near the BART locus. Viral-encoded microRNA and viral mRNA transferred to bystander cells through vesicles, defective viral particles, or other mechanisms suggest a new paradigm in which bystander or hit-and-run mechanisms enable the virus to transiently or chronically alter human immune response genes as well as the stability of the human genome.

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27

Chen, Kevin G., and Michael M. Gottesman. "Useful tool to generate unidirectional deletion vectors by utilizing the star activity of BamHI in an NcoI-BamHI-XhoI cassette." BioTechniques 38, no. 2 (February 2005): 198–204. http://dx.doi.org/10.2144/05382bm05.

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28

Lin, F. L., K. Sperle, and N. Sternberg. "Intermolecular recombination between DNAs introduced into mouse L cells is mediated by a nonconservative pathway that leads to crossover products." Molecular and Cellular Biology 10, no. 1 (January 1990): 103–12. http://dx.doi.org/10.1128/mcb.10.1.103-112.1990.

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We describe experiments designed to measure the efficiency of intermolecular recombination between mutant herpesvirus thymidine kinase (tk) genes introduced into mouse L cells. Recombinants were scored as stable transformants containing a functional tk gene. The two recombination substrates used were ptkB8, a pBR322-based plasmid containing a mutant tk gene, with a BamHI linker in an SphI restriction site that is centrally located within the gene, and mp10tk delta 3' delta 5', an mp10 vector with a tk gene deleted at both the 3' and 5' ends. The only homology shared by the two DNAs is 885 base pairs within the tk gene. To determine whether the double-strand break repair model that has been used to explain recombination in yeast cells (J. W. Szostak, T. L. Orr-Weaver, R. J. Rothstein, and F. W. Stahl, Cell 33:25-35, 1983) can account for recombination during the introduction of these DNAs into mammalian cells, we transformed cells with BamHI-linearized ptkB8 and supercoiled mp10tk delta 3' delta 5' replicative-form DNA. These two DNAs should recombine efficiently according to that model and should generate gene conversion products. In this reaction, the supercoiled DNA acts as the donor of information to repair the cleaved tk gene. Our results indicated that the efficiency of this reaction was very low (less than 10 transformants were obtained per 0.1 microgram of each DNA used in the reaction per 10(6) cells). In contrast, if BamHI-cleaved ptkB8 DNA was cotransformed into cells along with a circular DNA molecule containing a tk gene deleted only at its 3' end or only at its 5' end (mp10tk delta 3' or mp10tk delta 5'), then the efficiency of recombination could be more than 4 orders of magnitude higher than it was with circular mp10tk delta 3' delta 5' DNA. Recombination frequencies were highest when the tk delta 3' or tk delta 5' DNA used was cleaved at the tk deletion junction. Southern analyses of DNA from TK+ transformants generated with BamHI-cleaved ptkB8 and BamHI-cleaved mp10tk delta 3' DNAs indicated that recombination was almost always associated with the reassortment of markers flanking the reconstructed tk DNA. Together, these results are more consistent with the nonconservative single-strand annealing model for recombination that we proposed several years ago (F.-L. Lin, K. Sperle, and N. Sternberg, Mol. Cell. Biol. 4:1020-1034, 1984) than they are with the double-strand break repair model.

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Lin, F. L., K. Sperle, and N. Sternberg. "Intermolecular recombination between DNAs introduced into mouse L cells is mediated by a nonconservative pathway that leads to crossover products." Molecular and Cellular Biology 10, no. 1 (January 1990): 103–12. http://dx.doi.org/10.1128/mcb.10.1.103.

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We describe experiments designed to measure the efficiency of intermolecular recombination between mutant herpesvirus thymidine kinase (tk) genes introduced into mouse L cells. Recombinants were scored as stable transformants containing a functional tk gene. The two recombination substrates used were ptkB8, a pBR322-based plasmid containing a mutant tk gene, with a BamHI linker in an SphI restriction site that is centrally located within the gene, and mp10tk delta 3' delta 5', an mp10 vector with a tk gene deleted at both the 3' and 5' ends. The only homology shared by the two DNAs is 885 base pairs within the tk gene. To determine whether the double-strand break repair model that has been used to explain recombination in yeast cells (J. W. Szostak, T. L. Orr-Weaver, R. J. Rothstein, and F. W. Stahl, Cell 33:25-35, 1983) can account for recombination during the introduction of these DNAs into mammalian cells, we transformed cells with BamHI-linearized ptkB8 and supercoiled mp10tk delta 3' delta 5' replicative-form DNA. These two DNAs should recombine efficiently according to that model and should generate gene conversion products. In this reaction, the supercoiled DNA acts as the donor of information to repair the cleaved tk gene. Our results indicated that the efficiency of this reaction was very low (less than 10 transformants were obtained per 0.1 microgram of each DNA used in the reaction per 10(6) cells). In contrast, if BamHI-cleaved ptkB8 DNA was cotransformed into cells along with a circular DNA molecule containing a tk gene deleted only at its 3' end or only at its 5' end (mp10tk delta 3' or mp10tk delta 5'), then the efficiency of recombination could be more than 4 orders of magnitude higher than it was with circular mp10tk delta 3' delta 5' DNA. Recombination frequencies were highest when the tk delta 3' or tk delta 5' DNA used was cleaved at the tk deletion junction. Southern analyses of DNA from TK+ transformants generated with BamHI-cleaved ptkB8 and BamHI-cleaved mp10tk delta 3' DNAs indicated that recombination was almost always associated with the reassortment of markers flanking the reconstructed tk DNA. Together, these results are more consistent with the nonconservative single-strand annealing model for recombination that we proposed several years ago (F.-L. Lin, K. Sperle, and N. Sternberg, Mol. Cell. Biol. 4:1020-1034, 1984) than they are with the double-strand break repair model.

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30

Slavíková, L., J. Mikulka, and J. K. Kundu. "Tolerance of blackgrass (Alopecurus myosuroide) to sylfonylurea herbicides in the Czech Republic." Plant Protection Science 47, No. 2 (January 27, 2012): 55–61. http://dx.doi.org/10.17221/13/2010-pps.

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Seeds of three blackgrass populations fromSouthern Bohemiawere collected in 2007–2008. Biological tests with chlorsulfuron were performed at the 2–3 leaf stage. Some plants survived after treatment with the highest dose 37.5 g/ha. Biological tests showed a resistant phenotype to chlorsulfuron. Leaves of these plants were analysed by dCAPS assay. Two domains of ALS gene: domain A ‒ P197 and domain B ‒ W574 were targeted by PCR with regenerated primers P197 containing BamHI site and W574 containing site BstXI. PCR products of all tested samples were cleaved by BamHI in the codon P197. No mutation of proline in P197 was found out. The codon W574 PCR product of the samples was not cleaved by BstXI.

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Szeles, Anna, Kerstin I. Falk, Stephan Imreh, and George Klein. "Visualization of Alternative Epstein-Barr Virus Expression Programs by Fluorescent In Situ Hybridization at the Cell Level." Journal of Virology 73, no. 6 (June 1, 1999): 5064–69. http://dx.doi.org/10.1128/jvi.73.6.5064-5069.1999.

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ABSTRACT Epstein-Barr virus (EBV) transforms human B lymphocytes into immortalized lymphoblastoid cell lines (LCLs). They regularly express six virally encoded nuclear proteins (EBNA1 to EBNA6) and three membrane proteins (LMP1, LMP2A, and LMP2B). In contrast, EBV-carrying Burkitt lymphoma (BL) cells in vivo and derived type I cell lines that maintain the BL phenotype express only EBNA1. During prolonged in vitro culturing, most EBV-carrying BL lines drift toward a more immunoblastic (type II or III) phenotype. Their viral antigen expression is upregulated in parallel. We have used fluorescent in situ hybridization to visualize viral transcripts in type I and III BL lines and LCLs. In type I cells, EBNA1 is encoded by a monocistronic message that originates from the Qp promoter. In type III cells, the EBNA1 transcript is spliced from a giant polycistronic message that originates from one of several alternative Wp or Cp promoters and encodes all six EBNAs. We have obtained a “track” signal with aBamHI W DNA probe that could hybridize with the polycistronic but not with the monocistronic message in two type III BL lines (Namalwa-Cl8 and MUTU III) and three LCLs (LCL IB4-D, LCL-970402, and IARC-171). A BamHI K probe that can hybridize to both the monocistronic and the polycistronic message visualized the same pattern in the type III BLs and the LCLs as the BamHI W probe. A positive signal was obtained with the BamHI K but not the BamHI W probe in the type I BL lines MUTU I and Rael. The RNA track method can thus distinguish between cells that use a type III and those that use a type I program. The former cells hybridize with both the W and the K probes, but the latter cells hybridize with only the K probe. Our findings may open the way for studies of the important but still unanswered question of whether cells with type I latency arise from immunoblasts with a full type III program or are generated by a separate pathway during primary infection.

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Fonseca, Antônio Augusto, Cristina Gonçalves Magalhães, Érica Bravo Sales, Régia Maria D'Ambros, Janice Ciacci-Zanella, Marcos Bryan Heinemann, Rômulo Cerqueira Leite, and Jenner Karlisson Pimenta dos Reis. "Genotyping of the Pseudorabies Virus by Multiplex PCR Followed by Restriction Enzyme Analysis." ISRN Microbiology 2011 (November 24, 2011): 1–4. http://dx.doi.org/10.5402/2011/458294.

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Suid herpesvirus 1 (SuHV-1) is the causative agent of Aujeszky's disease. The infectious agent has only one serotype, but it was classified by restriction enzyme analysis of the whole genome into four genotypes, named I to IV. The aim of this study was to standardize a rapid method for genotyping SuHV-1 without virus isolation, using a multiplex-PCR followed by enzymatic restriction analysis. The complete genome of the virus was analyzed in silico to determine the restriction sites for the enzyme BamHI. Primers were designed to flank sites with emphasis on certain points of differentiation of genotypes. The standard PCRs were able to detect the SuHV-1 and also to differentiate genotypes from brain tissue of infected pigs. The BamHI-PCR is a rapid, practical, and sensitive way to genotype SuHV-1.

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Triasih, D., Y. Erwanto, and N. A. Fitrianto. "Identification of Goat Skin and Pig Skin as the Raw Material of Rambak Using PCR-RFLP Method." Jurnal Sain Peternakan Indonesia 15, no. 4 (December 29, 2020): 420–25. http://dx.doi.org/10.31186/jspi.id.15.4.420-425.

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The aim of this research was to detect the skin which comes from goat and pig using PCR-RFLP method so the raw material used in rambak product was discovered. The comparison of combination between goat and pig skin was 100, 75:25, 91:9, 94:6, 97:3, and 99:1. PCR-RFLP uses the universal primary from from mitochondria cytochrome b gen which results in the length of fragment of 359 bp. The restriction enzyme used in the DNA cut is BamHI enzyme and BseDI enzyme. The result of the research showed that seven samples have been successfully isolated perfectly so the total bands of genomic DNA have been obtained which is clearly seen and amplification with target of cytochrome b gen results in PCR product of goat and pig of 359 bp. The digestion's result using BamHI enzyme gets fragment size on 359 bp in length on goat samples and length of fragment size of 359, 244, and 115 bp on samples which contain pig. The digestion results of using BseDI results in fragment size of 359 bp in length on goat samples and the fragment size of 359, 228, and 131 bp in length on samples which contain pig. The conclusion of the research is PCR-RFLP using BamHI enzyme and BseDI enzyme can be used to detect the types of pig skin, but can't be used to detect the goat skin.

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Ikuta, Kazufumi, Shamala K. Srinivas, Tim Schacker, Jun-ichi Miyagi, Rona S. Scott, and John W. Sixbey. "Points of Recombination in Epstein-Barr Virus (EBV) Strain P3HR-1-Derived Heterogeneous DNA as Indexes to EBV DNA Recombinogenic Events In Vivo." Journal of Virology 82, no. 23 (September 25, 2008): 11516–25. http://dx.doi.org/10.1128/jvi.01036-08.

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ABSTRACT Deletions and rearrangements in the genome of Epstein-Barr virus (EBV) strain P3HR-1 generate subgenomic infectious particles that, unlike defective interfering particles in other viral systems, enhance rather than restrict EBV replication in vitro. Reports of comparable heterogeneous (het) DNA in EBV-linked human diseases, based on detection of an abnormal juxtaposition of EBV DNA fragments BamHI W and BamHI Z that disrupts viral latency, prompted us to determine at the nucleotide level all remaining recombination joints formed by the four constituent segments of P3HR-1-derived het DNA. Guided by endonuclease restriction maps, we chose PCR primer pairs that approximated and framed junctions creating the unique BamHI M/B1 and E/S fusion fragments. Sequencing of PCR products revealed points of recombination that lacked regions of extensive homology between constituent fragments. Identical recombination junctions were detected by PCR in EBV-positive salivary samples from human immunodeficiency virus-infected donors, although the W/Z rearrangement that induces EBV reactivation was frequently found in the absence of the other two. In vitro infection of lymphoid cells similarly indicated that not all three het DNA rearrangements need to reside on a composite molecule. These results connote a precision in the recombination process that dictates both composition and regulation of gene segments altered by genomic rearrangement. Moreover, the apparent frequency of het DNA at sites of EBV replication in vivo is consistent with a likely contribution to the pathogenesis of EBV reactivation.

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Hwang, Hye-Yeon, and Jeongbin Yim. "SolI, a novel isoschizomer of ,BamHI isolated fromStreptoverticillium olivoverticillatum." Nucleic Acids Research 22, no. 12 (1994): 2197. http://dx.doi.org/10.1093/nar/22.12.2197.

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36

Priestley, L., T. Knott, S. Wallis, L. Powell, R. Pease, A. Simon, and J. Scott. "RFLP for the human apollpoprotein B gene: I;BamHI." Nucleic Acids Research 13, no. 18 (1985): 6789. http://dx.doi.org/10.1093/nar/13.18.6789.

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37

Polten, A., and V. Gieselmann. "A BamHI RFLP in the human arylsulfatase A gene." Nucleic Acids Research 18, no. 22 (1990): 6746. http://dx.doi.org/10.1093/nar/18.22.6746.

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Yamauchi, Toyoaki, Hajime Tanaka, Masao Hiraiwa, Yutaka Uda, Tadashi Miyatake, and Shoji Tsuji. "BamHI polymorphism at N-acetyl-α-galactosaminidase locus (NAGA)." Nucleic Acids Research 19, no. 9 (1991): 2518. http://dx.doi.org/10.1093/nar/19.9.2518-a.

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Atac, E., D. Shalhevet, D. Krull, P. Clamp, R. Feltes, J. Beever, and L. B. Schook. "A BamHI polymorphism at the porcine crystallin γ locus." Animal Genetics 24, no. 2 (April 24, 2009): 139. http://dx.doi.org/10.1111/j.1365-2052.1993.tb00257.x.

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40

Nakatani, Kazuhiko, Chikara Dohno, Atsushi Ogawa, and Isao Saito. "Suppression of DNA-Mediated Charge Transport by BamHI Binding." Chemistry & Biology 9, no. 3 (March 2002): 361–66. http://dx.doi.org/10.1016/s1074-5521(02)00119-9.

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Brooks, J. E., J. S. Benner, K. R. Silber, D. F. Heiter, L. A. Sznyter, T. Jager-Quinton, G. G. Wilson, L. S. Moran, B. E. Slatko, and D. O. Nwankwo. "Cloning and characterization of the BamHI restriction modification system." Gene 74, no. 1 (December 1988): 13. http://dx.doi.org/10.1016/0378-1119(88)90239-9.

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Kim, E. L., and S. S. Maliuta. "A new isoschizomer, BnaI, of the BamHI restriction endonuclease." Gene 80, no. 2 (August 1989): 363–68. http://dx.doi.org/10.1016/0378-1119(89)90300-4.

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Guiral, Sébastien, Vincent Hénard, Maria-Halima Laaberki, Chantal Granadel, Marc Prudhomme, Bernard Martin, and Jean-Pierre Claverys. "Construction and evaluation of a chromosomal expression platform (CEP) for ectopic, maltose-driven gene expression in Streptococcus pneumoniae." Microbiology 152, no. 2 (February 1, 2006): 343–49. http://dx.doi.org/10.1099/mic.0.28433-0.

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In this paper, the construction and evaluation of a chromosomal expression platform (CEP), which allows controlled gene expression following ectopic integration into the chromosome of Streptococcus pneumoniae, is described. CEP is based on the well-studied maltosaccharide-inducible system. To facilitate integration at CEP, a plasmid, pCEP, capable of replication in Escherichia coli, but not in S. pneumoniae, was assembled. This plasmid contains an expression/selection cassette flanked on each side by more than 2 kb of pneumococcal DNA. The cassette comprises a maltose-inducible promoter, PM, separated from a kanamycin-resistance gene by NcoI and BamHI cloning sites. Clones harbouring the gene of interest integrated at CEP under the control of PM can be obtained through direct transformation of an S. pneumoniae recipient with ligation products between that gene and NcoI/BamHI-digested pCEP DNA, followed by selection for kanamycin-resistant transformants.

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Mansfield, Shawn D., Greg S. Bezanson, and Thomas J. Marrie. "Characterization and cloning of a 37.6-kb plasmid carried byLegionella pneumophilarecovered from patients and hospital water over a 12-year period." Canadian Journal of Microbiology 43, no. 2 (February 1, 1997): 193–97. http://dx.doi.org/10.1139/m97-025.

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For 12 years, strains of Legionella pneumophila serogroup 1 harbouring a 37.6-kb (23 MDa) plasmid have predominated among patient and potable water isolates at the Victoria General Hospital, Halifax, N.S. Plasmid DNA recovered from 24 strains isolated between 1983 and 1995 was digested with the restriction endonucleases EcoRI, HindIII, KpnI, PvuII, XbaI, and BamHI. The distribution of cutting sites indicated that the 23-MDa size group had remained essentially unchanged during this period, suggesting the persistence of a single plasmid type. Further fragmentation pattern analysis permitted the construction of a physical map of the prototype 23-MDA plasmid, pLp4269. Double digestion with BamHI–HindIII enabled the cloning of 94.4% of pLp4269 into pBluescript vector. A 2.1-kb fragment was not clonable. Plasmid pLp4269 is the first of the smaller Legionella extrachromosomal DNAs to be characterized in this way.Key words: Legionella, plasmid, stability, map, cloning.

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Chiou, Shiow-Her, Kuan-Chih Chow, Chih-Huan Yang, Shu-Fen Chiang, and Chun-Hao Lin. "Discovery of Epstein–Barr virus (EBV)-encoded RNA signal and EBV nuclear antigen leader protein DNA sequence in pet dogs." Journal of General Virology 86, no. 4 (April 1, 2005): 899–905. http://dx.doi.org/10.1099/vir.0.80792-0.

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The aim of this study was to investigate Epstein–Barr virus (EBV)-related virus infection in pet dogs. The presence of antibodies to EBV antigens and EBV-related DNA was determined by Western blot analysis and PCR, respectively. Among 36 pet dogs examined for serum antibodies, 32 (88·9 %) were positive for EBV-specific thymidine kinase, 15 (41·7 %) for EBV-encoded DNA-binding protein and 10 (27·8 %) for EBV-specific DNA polymerase. A BamHI W fragment sequence encoding part of the EBV nuclear antigen leader protein was detected by PCR in corresponding leukocyte DNA samples. Among 21 dogs tested, 15 (71·4 %) were positive for the BamHI W fragment sequence. The specificity of the amplified DNA fragments was confirmed by DNA sequencing. Within the amplified region of the BamHI W fragment (241 bp), DNA sequences detected in 10 dogs had 99·2 % (two nucleotide variations), 99·6 % (one nucleotide variation) or 100 % identity to that of EBV. Furthermore, an EBV-encoded RNA signal was detected by in situ hybridization in dog lymphocytes, as well as in bone-marrow sections, indicating a latent infection with EBV or an EBV-like virus. In conclusion, although the sample size was small, these results showed that a widespread EBV-related gammaherpesvirus could be detected in the peripheral blood and bone marrow of pet dogs. Although no evident zoonotic transmission was detected, further studies are imperative for disclosing the biological significance of this canine EBV-like virus, which may correlate with human disorders.

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GONÇALVES, Célia R., Tania M. I. VAZ, Daniela LEITE, Beatriz PISANI, Marise SIMÕES, Maria Angela M. PRANDI, Marilu M. M. ROCHA, et al. "Molecular epidemiology of a nosocomial outbreak due to Enterobacter cloacae and Enterobacter agglomerans in Campinas, São Paulo, Brazil." Revista do Instituto de Medicina Tropical de São Paulo 42, no. 1 (February 2000): 1–7. http://dx.doi.org/10.1590/s0036-46652000000100001.

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A total of 73 isolates (57 Enterobacter cloacae and 16 Enterobacter agglomerans), recovered during an outbreak of bacteremia in the Campinas area, São Paulo, Brazil, were studied. Of these isolates, 61 were from parenteral nutrition solutions, 9 from blood cultures, 2 from a sealed bottle of parenteral nutrition solution, and one was of unknown origin. Of the 57 E. cloacae isolates, 54 were biotype 26, two were biotype 66 and one was non-typable. Of 39 E. cloacae isolates submitted to ribotyping, 87.2% showed the same banding pattern after cleavage with EcoRI and BamHI. No important differences were observed in the antimicrobial susceptibility patterns among E. cloacae isolates exhibiting the same biotype, serotype and ribotype. All E. agglomerans isolates, irrespective of their origin, showed same patterns when cleaved with EcoRI and BamHI. The results of this investigation suggest an intrinsic contamination of parenteral nutrition solutions and incriminate these products as a vehicle of infection in this outbreak.

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Raharjo, Tri Joko, Winda Cahyaningtyas, Surajiman Surajiman, Istini Istini, and Deni Pranowo. "VALIDATION OF PCR-RFLP TESTING METHOD TO DETECT PORCINE CONTAMINATION IN CHICKEN NUGGET." Indonesian Journal of Chemistry 12, no. 3 (December 28, 2012): 302–7. http://dx.doi.org/10.22146/ijc.21347.

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PCR-RFLP technique to detect porcine contamination in chicken nugget has been developed and validated in this research. Various concentrations of pork were fortified during preparation of the nugget. DNA was then isolated from the nugget followed by PCR employed primers which targeted a 359 bp cytB gene fragment of mitochondrial DNA. For RFLP, the PCR product was digested by means of BamHI and BseDI enzymes. Cutting DNA fragments from nugget containing pork using BseDI enzyme produced DNA fragment with size 228 and 131 bp, while cutting with BamHI enzyme produce DNA fragments with sizes 244 and 115 bp. All of these fragments were not present in RFLP analysis of pork-free nugget. The method shows good specificity and precision and could detect porcine contamination in the nugget up to 5%. The method has been applied to test commercial nugget. Four brand of Halal-labeled commercial nugget as well as four brand of non labeled one gave negative porcine contamination.

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Barnett, Melanie J., and Sharon R. Long. "Identification and Characterization of a Gene on Rhizobium meliloti pSyma, syrB, That Negatively Affects syrM Expression." Molecular Plant-Microbe Interactions® 10, no. 5 (July 1997): 550–59. http://dx.doi.org/10.1094/mpmi.1997.10.5.550.

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The Rhizobium meliloti SyrM protein activates transcription of nodD3 and syrA. Regulation of syrM is complex and may involve as yet undiscovered genes. Here we report the isolation of insertion mutants showing increased expression of a syrM-gusA gene fusion. Characterization of one mutant strain, designated SYR-B, revealed a mutation consisting of a transposon insertion linked to a large deletion. The corresponding wild-type DNA was cloned as a 5.3-kb BamHI fragment. Genetic and physical analysis of this DNA demonstrated that an open reading frame (ORF) near one end of the fragment, encoding the 16.5-kDa SyrB protein, is responsible for the repression of syrM activity. Results of complementation experiments with the 5.3-kb BamHI DNA led us to hypothesize that other genes within this DNA fragment interfere with the expression or activity of SyrB. Our analysis showed that the region upstream of syrB contains three ORFs. One ORF is similar to the Ros repressor of Agrobacterium tumefaciens and the MucR repressor of R. meliloti.

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Montgomery, G. P., and B. C. Lu. "Involvement of Coprinus endonuclease in preparing substrate for in vitro recombination." Genome 33, no. 1 (February 1, 1990): 101–8. http://dx.doi.org/10.1139/g90-016.

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A functional recombination assay involving the tetracycline mutant plasmids, pUW1 and pUW4, was used to assess (i) the nature of the DNA substrates needed and (ii) the involvement of Coprinus endonuclease in preparing substrate, for the RecA-directed recombination process. A gapped circular plasmid and a linear or a nicked circular plasmid are efficient substrate combinations in this system to achieve a 160-fold increase in the in vitro recombination frequency over the control levels. The Coprinus endonuclease obtained from early meiotic prophase can produce such substrates. The recombination frequency obtained with the combination of gapped pUW1 plasmids initially relaxed by the Coprinus endonuclease and linear pUW4 plasmids produced by the site-specific BamHI digest is 10-fold lower than that obtained when both substrates are digested by BamHI. The results suggest that the Coprinus endonuclease creates random nicks on plasmid DNA. Glyoxal gel electrophoretic analysis was used to confirm this random nicking activity of Coprinus endonuclease.Key words: Coprinus, genetic recombination, endonuclease, recA.

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Bramwell, H., H. G. Nimmo, I. S. Hunter, and J. R. Coggins. "Phosphoenolpyruvate carboxylase from Streptomyces coelicolor A3(2): purification of the enzyme, cloning of the ppc gene and over-expression of the protein in a streptomycete." Biochemical Journal 293, no. 1 (July 1, 1993): 131–36. http://dx.doi.org/10.1042/bj2930131.

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Phosphoenolpyruvate carboxylase [PEPC; orthophosphate:oxaloacetate carboxy-lyase (phosphorylating); EC 4.1.1.31] is a major anaplerotic enzyme in the polyketide producer Streptomyces coelicolor A3(2). PEPC was purified from S. coelicolor and the amino-acid sequences of four tryptic peptides were determined. Synthetic oligonucleotides based on the sequences of two of the peptides hybridized to the same bands in various restriction-enzyme digests of S. coelicolor genomic DNA. This hybridization allowed molecular cloning of an 8 kb BamHI fragment of genomic DNA. Partial DNA sequencing of this fragment showed that it could encode amino acid sequences similar to those of PEPC from other microorganisms. A BamHI/PstI fragment was subcloned into the streptomycete high-copy-number plasmid vector pIJ486 and transferred into Streptomyces lividans. The resulting strain over-expressed PEPC activity 21-fold and also over-expressed a protein with a subunit of 100,000 M(r), the same as that of purified S. coelicolor PEPC.

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Journal articles on the topic 'BamHI'

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