Restriction Endonucleases Bam Research Articles

JMT-1: a novel, spherical lytic halotolerant phage isolated from Yuncheng saline lake

This work described a novel halotolerant phage, JMT-1, with a spherical morphology. JMT-1, which was isolated from a hypersaline lake, could produce clear plaques on Chromohalobacter sp. LY7-3. The purified virions are spherical, have no visible tail, and are about 30–50 nm in diameter. JMT-1 has a wide host range, and this study showed that the phage can infect at least five halophilic bacteria. The proteins of JMT-1 were analyzed using sodium dodecyl sulfate polyacrylamide gel electrophoresis, and six proteins were detected. Results show that JMT-1 is a bacteriophage with a linear double-stranded DNA. Meanwhile, the genome is approximately 23 kb in length and is sensitive to the restriction endonucleases Bam I, EcoR I, Hind III and Kpa I. JMT-1 has a high titer, approaching 1.5 × 109 pfu/mL after dilution to 10−6 pfu/mL. The phage is also sensitive to chloroform but not to temperature, pH, and lowered salt concentration. JMT-1 is a spherical lytic halotolerant phage with a wide host range and has the tolerance to specific extreme environments. These data could provide references for studying phage resources in extreme environments and would also provide the useful methods for isolation and identification of other valuable phage in the salt lake environment.

Loop-mediated isothermal amplification based on the mitochondrial COI region to detect Pratylenchus zeae

Pratylenchus zeae parasitizes various crops and damages the host roots, resulting in decreased yield and quality of the host plants. Alignments of mitochondrial DNA (mtDNA) Cytochrome Oxidase I (COΙ) sequences revealed the genetic variation among Pratylenchus species. The results indicated 0.2–2.4% intraspecific variations for mtDNA COI sequences among eight P. zeae populations, and 25.4–35.1% interspecific variations between P. zeae and other Pratylenchus species. Based on the mtDNA COΙ region, a loop-mediated isothermal amplification (LAMP) assay was developed for the rapid and specific detection of P. zeae. The optimal conditions for the LAMP assay were 64 °C for 40 min. The LAMP products were confirmed using conventional polymerase chain reaction (PCR), analysis with the restriction enzyme Bam HI and visual inspection by adding SYBR Green I to the products. The LAMP assay could detect P. zeae populations from different hosts and different geographical origins specifically. The LAMP assay was also sensitive, detecting 0.1 individual P. zeae, which was 10 times more sensitive than conventional PCR. This is the first report of the detection of Pratylenchus spp. using LAMP. In addition, the results also suggested that use of the COI gene might allow for good resolution at the Pratylenchus species level.

Penyisipan Gen Inhibitor α-amilase pada Plasmid Biner pCambia 1301

<p class="p1">The experiment was conducted at the Molecular Biology Laboratory of the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor. The objective was to construct <em>-ai </em>gene on a binary plasmid <em>p</em>Cambia 1301. This experiment was carried out using construction method by ligation process between fragments of <em>α-ai </em>gene from <em>p</em>TA<span class="s1">3 </span>plasmid and <em>p</em>Cambia 1301 on <em>Hind</em>III site. The result of ligant transformation into <em>E. coli </em>DH5<em>α </em>was 182 surviving colonies on YEP medium containing kanamycin. DNA samples were obtained from 60 randomly selected colonies. The restriction pattern was tested by digesting each DNA sample using <em>Hind</em>III showed colonies containing two fragments expected of sizes wich are 11.837 and 4.887 kb. Two colonies are predicted containing of <em>α-ai </em>gene on its the binary plasmid. Advanced tests using restriction enzymes <em>Bam</em>HI and <em>Xba</em>I showed two directions (right and left) of <em>α-ai </em>gene. The right direction was shown by <em>p</em>Cambia-<em>α-ai</em>1 from colony number 43. This plasmid showed expected fragments of sizes 13.485 and 3.219 kb when digested with <em>Bam</em>HI and two fragments of sizes 15.421 and 1.303 kb when digested with <em>Xba</em>I. The left direction was shown <em>p</em>Cambia-<em>α-ai</em>2 from colony number 58. This plasmid also demon-strated expected fragments of sizes 15.026 and 1.698 kb when digested with <em>Bam</em>HI and two fragments of sizes 13.082 and 3.642 kb when digested with <em>Xba</em>I. Both <em>p</em>Cambia-<em>α-ai</em>1 and <em>p</em>Cambia-<em>α-ai</em>2 were transformed into <em>A. tumefaciens </em>LBA4404.</p>

A comparative study of hematological parameters of α and β thalassemias in a high prevalence zone: Saudi Arabia.

BACKGROUND AND AIMS:Saudi Arabia falls in the high prevalent zone of αα and β thalassemias. Early screening for the type of thalassemia is essential for further investigations and management. The study was carried out to differentiate the type of thalassemia based on red cell indices and other hematological parameters.MATERIALS AND METHODS:The study was carried out on 991 clinically suspected cases of thalassemias in Riyadh, Saudi Arabia. The hematological parameters were studied on Coulter STKS. Cellulose acetate hemoglobin electrophoresis and high-performance liquid chromatography (HPLC) were performed on all the blood samples. Gene deletion studies were carried out by restriction fragment length polymorphism (RFLP) technique using the restriction endonucleases Bam HI.STATISTICAL ANALYSIS:Statistical analysis was performed on SPSS 11.5 version.RESULTS:The hemoglobin electrophoresis and gene studies revealed that there were 406 (40.96%) and 59 (5.95 %) cases of β thalassemia trait and β thalassemia major respectively including adults and children. 426 cases of various deletion forms of α thalassemias were seen. Microcytosis was a common feature in β thalassemias trait and (-α/-α) and (--/αα) types of α thalassemias. MCH was a more significant distinguishing feature among thalassemias. β thalassemia major and α thalassemia (-α/αα) had almost normal hematological parameters.CONCLUSION:MCV and RBC counts are not statistically significant features for discriminating between α and β thalassemias. There is need for development of a discrimination index to differentiate between α and β thalassemias traits on the lines of discriminatory Indices available for distinguishing β thalassemias trait from iron deficiency anemia.

Caracterization of Aujeszky's disease virus isolated from South Brazil in the last twenty years by restriction enzyme analysis

Aujeszky's disease virus (ADV) belongs to Herpesviridae family and is an important etiological agent which infects pigs causing economic losses in swine producing countries worldwide and international trade restrictions to products of swine origin. An eradication program for ADV was established in Santa Catarina State since 2001. The last outbreak was reported in July 2004 and since then none has been reported. The disease has been controlled with the use of a genetic modified vaccine and elimination of seropositives. Aiming the characterization of ADV isolated in the South of Brazil in the last twenty years (1983-2003), a retrospective study based on the genomic analysis of the isolates through a digestion of viral genomic DNA with restriction enzyme Bam HI was done. Thirty-seven ADV samples isolated from swine from the States of Santa Catarina, Parana and Rio Grande do Sul were analyzed. These isolates were compared to the reference strains NIA-4, Bartha and Begonia. The most predominant genomic arrangement was type II found in 33 samples isolated in Santa Catarina State and in one isolate from Rio Grande do Sul State. Genomic arrangement type I, characteristic of vaccine strains was identified in 2 isolates from Parana State and in 1 isolate from Rio Grande do Sul State.

Asociación de hemoglobinopatía S y alfatalasemia. Análisis de 45 casos

Hemoglobin S (HbS) alpha-thalassemia together with ss-thalassemia and hemoglobins C, E and D are named common hemoglobinopathies. In this study, we analyzed the frequency of the association between alpha-thalassemia and HbS and its phenotypic expression. Since January 1995 to March 2003 we studied 83 cases of HbS, which were diagnosed by electrophoretic and chromatographic criteria. The molecular study was carried out by Southern blot with the restriction enzymes Bam HI and Bgl II and a (1.5 Kb Pst) and z (1.8 Kb Sac Y) probes. 45 cases (54.2%) had a-thalassemia (36 -alpha3,7/aa; 1-alpha4,2/alphaalpha; 6 -alpha3,7/-alpha3,7; 1-alpha4,2/-alpha4,2); 36 had not alpha-thalassemia and in two cases there were a triplication of a genes. The patients with HbS heterozygote associated with alpha-thalassemia showed a percentage of HbS (p < 0.0001), CMV (p = 0.004), MCH (p = 0.002) and MCHC (p = 0.02) significantly lower than the cases of HbS without this association. However, no differences between both groups were found with regard to the rest of parameters analyzed (Hb p = 0.56; PVC p = 0.84; RDW p = 0.06; Reticulocytes p = 0.26; HbF p = 0.76; HbA2 p = 0.13). In the cases with a severe form of disease (HbS homozygote; HbS/Hb C; HbS/beta-thalassemia), patients with alpha-thalassemia had a number of leukocytes that was significantly lower than that of patients without alpha-thalassemia (p = 0.034). An association between HbS and alpha-thalassemia was common (> 50%). Screening for this association is of great interest because the clinical expression in the cases of HbS homozigote will be modulated. This association must be suspected in cases of homozygous HbS in which levels of HbS are lower than expected.

Genomic analysis of adenovirus isolated from Argentinian children with acute lower respiratory infections.

Adenoviruses are the second cause of acute lower respiratory infection (ALRI) of viral origin in small children from Buenos Aires, Argentina. The aim of this study was to characterize, by restriction enzyme analysis, 17 adenovirus strains isolated from the nasopharyngeal aspirates of children under 2 years of age hospitalized due to ALRI. Seventeen adenovirus strains isolated between May 1991 and December 1992 in one hospital of Buenos Aires were studied. Adenoviruses were amplified in HEp-2 cells and viral DNA was studied with the restriction enzymes Bam HI and Sma I. Eighty two percent (14/17) of the isolates were classified as adenoviruses from subgenus b and 17.7% (3/17) belonged to subgenus c. Genome type 7 h was detected in 85.7% (12/14) and 7 i in 14.3% (2/14) of the strains from subgenus b. The case lethality associated with adenovirus genome type 7 was 28.6% (4/14 cases). Three fatal cases corresponded to Ad 7 h and one to Ad 7i. Ad 7h shows a high prevalence in small children hospitalized with ALRI and is associated with a high fatality rate.

Structure of Bam HI Endonuclease Bound to DNA: Partial Folding and Unfolding on DNA Binding

The crystal structure of restriction endonuclease Bam HI complexed to DNA has been determined at 2.2 angstrom resolution. The DNA binds in the cleft and retains a B-DNA type of conformation. The enzyme, however, undergoes a series of conformational changes, including rotation of subunits and folding of disordered regions. The most striking conformational change is the unraveling of carboxyl-terminal alpha helices to form partially disordered "arms." The arm from one subunit fits into the minor groove while the arm from the symmetry related subunit follows the DNA sugar-phosphate backbone. Recognition of DNA base pairs occurs primarily in the major groove, with a few interactions occurring in the minor groove. Tightly bound water molecules play an equally important role as side chain and main chain atoms in the recognition of base pairs. The complex also provides new insights into the mechanism by which the enzyme catalyzes the hydrolysis of DNA phosphodiester groups.

Restriction Fragment Length Polymorphism Analysis of the Mitochondrial DNA of Fusarium oxysporum f. sp. ciceris

AbstractSeven isolates of Fusarium oxysporum f. sp. ciceris, representing pathogenic races 1, 2, 3, and 4 from India and 0, 5, and 6 from Spain, were assayed for restriction fragment length polymorphisms (RFLPs) in the mitochondrial DNA,(mt DNA). The mt DNA fraction of total fungal DNA was purified and digested with the restriction endonucleases Bam HI, Bgl II, Eco RI. Kpn I, Sac I, Sal I, Sma I, and Xho I. The mt DNA is a circular molecule of 40.5 kb. No RFLP in the mt DNA was detected among the seven races of F. o. ciceris. The identical restriction patterns of mt DNA indicates an extensive conservation in the gene composition of mt DNA without sequence variation, and suggests that mt DNA of F. o. ciceris may not be responsible for pathogenic diversity. The restriction map of mt DNA from the race 6 isolate Fo 8272 was constructed by digestion of the mt DNA with five restriction enzymes: Eco RI, Kpn I, Sac I, Sal I, and Xho I, either singly or in selected pairs.

Organization of the Human Annexin V (ANX5) Gene

We characterized the region of human chromosome 4q26-q28 that contains the gene encoding annexin V (placental anticoagulant protein I), a member of a family of calcium-dependent phospholipid binding proteins. A total of 14.5 kb, containing 9 introns, could be directly amplified from genomic DNA; the remainder was characterized from genomic clones in phage λ and a yeast artificial chromosome. The gene was mapped with restriction enzymes Bam HI, EcoRI, HindIII, SacI, StuI, and Xba I; the transcribed region spans 28 kb and contains 13 exons (44 to 530 bp in size) and 12 introns (0.23 to 8.8 kb in size). Several putative transcription factor binding sites are present in the 5′-region, but the promoter has no recognizable TATA box. This study will facilitate further analysis of the functions of annexin V and its role in disease.

Homozygosity for a Missense Mutation (G20R) Associated with Neonatal Onset Adenosine Deaminase-Deficient Severe Combined Immunodeficiency (ADA-SCID)

Mutations at the adenosine deaminase (ADA) locus can result in varying degrees of immunodeficiency, including rapidly fulminant severe combined immunodeficiency (SCID) as well as a slowly progressive immunodeficiency not diagnosed until later in childhood. Genetic heterogeneity is a factor in the clinical heterogeneity. We have now identified, by direct sequencing of PCR-amplified genomic DNA, a G to A transition at a CpG dinucleotide predicting a glycine to arginine substitution at codon 20 (G20R). The mutation, in homozygosity, was associated with neonatal-onset rapidly fatal SCID. Consistent with homozygosity, the child was derived from a small isolated inbred community in Newfoundland. The mutation abolishes a site for the restriction enzyme Bam HI and can be simply detected by agarose gel electrophoresis following amplification of exon 2 from genomic DNA and digestion with Bam HI. The majority of ADA missense mutations can now be detected by similar amplification and enzyme digestion. We demonstrated that the G20R mutation is deleterious since introduction of the mutation into a normal ADA minigene abolished enzyme activity, as determined by transient expression in monkey kidney (Cos) cells. The amino acid substitution occurs in an area of the molecule conserved from Escherichia coli to man and that, as shown by crystallographic analysis, is involved in the binding of Zn 2+ at the catalytic site. Although the mutation is in a CpG dinucleotide, known "hotspots" for G to A transitions, it was not found in a series of 43 additional ADA - chromosomes. Identification of mutations in additional ADA - patients with immunodeficiency of varying severity should further define the role that genotype plays in determining the extent of immunologic dysfunction.

Molecular characterization of UV‐treated sugar beet somaclones using RFLP markers

Sugar beet plants regenerated from UV‐treated calluses were examined by restriction fragment length polymorphism (RFLP) analysis to determine the extent of somaclonal variation occurring at the DNA level. In total, 50 random sugar beet DNA sequences were used to screen 42 somaclones for genetic alterations. Three polymorphisms were detected among the 7 644 alleles analysed. From these data a mutation frequency of 0.03 ± 0.02% per allele was estimated. This frequency is in agreement with similar studies of somaclonal DNA variation using molecular markers and lies in the upper range of the spontaneous gene mutation frequencies found in plants. The two probegenotype combinations showing independent polymorphisms, were further analysed using the restriction enzymes Bam HI, Eco RI, Eco RV and Hind III. Both polymorphisms are likely to result from structural rearrangements rather than from point mutations. Differences in methylation among 10 of the investigated somaclones were tested for by comparing Hpa II and Msp I generated RFLP patterns. The somaclones showed extensive methylation, but no differences in their degree of methylation. Cytological analysis revealed 34 diploid, 8 tetraploid, but no aneuploid plants.

Characterization of Actinomyces with Genomic DNA Fingerprints and rRNA Gene Probes

Cellular DNA from 25 Actinomyces naeslundii and Actinomyces viscosus strains belonging to the 7 taxonomic clusters of Fillery et al. (1978) and several unclustered strains was obtained by enzymatic and N-lauroylsarcosine/guanidine isothiocyanate treatment of whole cells, followed by extraction of the nucleic acid. The DNA samples were digested with restriction endonucleases BamHI or PvuII, and agarose gel electrophoresis was used to obtain DNA fingerprints. The DNA fragments were subjected to Southern blot hybridization with a digoxigenin-labeled cDNA probe transcribed from Escherichia coli 16S and 23S rRNA. The patterns of bands from genomic (DNA fingerprints) and rDNA fingerprints (ribotypes) were used for comparison between the taxonomic cluster strains and strains within clusters. Representative strains from each taxonomic cluster provided different BamHI DNA fingerprints and ribotype patterns with 3 to 9 distinct bands. Some strains within a cluster showed identical ribotype patterns with both endonucleases (A. naeslundii B120 and A. naeslundii B102 from cluster 3), while others showed the same pattern with BamHI but a different pattern with PvuII (A. naeslundii ATCC 12104 and 398A from cluster 5). A viscosus ATCC 15987 (cluster 7) and its parent strain T6 yielded identical fingerprint and ribotype patterns. The genomic diversity revealed by DNA fingerprinting and ribotyping demonstrates that these techniques, which do not require phenotypic expression, are suited for study of the oral ecology of the Actinomyces, and for epidemiological tracking of specific Actinomyces strains associated with caries lesions and sites of periodontal destruction.

Transmission of Porphyromonas gingivalis between spouses.

Porphyromonas gingivalis has been associated with severe forms of periodontitis. The question can be raised about the origin of this suspected periodontal pathogen. The purpose of the present investigation was to study the possibility of transmission of P. gingivalis between spouses. 18 patients were selected with severe periodontitis and colonized with P. gingivalis. 10 of their spouses appeared to be colonized with P. gingivalis too. 8 of the patients and their spouses were investigated further clinically and microbiologically. Microbiological evaluation revealed mostly high %s of P. gingivalis in the pockets, not only of the patients (5-48% of the cultivable flora), but also in 7 of the 8 spouses (0.2-61%). Furthermore, this species was isolated often from the saliva, the tongue, the buccal mucosa and the tonsillar area from both patients and spouses. For typing purposes, bacterial DNA was isolated, treated with the restriction endonucleases Bam HI or Pst I, after which the DNA fragments were separated by agarose gelelectrophoresis. With one exception, each individual was colonized with only one clonal type of P. gingivalis. The DNA patterns of all P. gingivalis isolates from unrelated individuals were found to be distinct. In contrast, in 6 of the 8 couples, the DNA patterns of isolates from husband and wife were indistinguishable. From these data, it can be concluded that it is most likely, that P. gingivalis can be transmitted between spouses. It remains to be investigated whether transmission of P. gingivalis is a risk factor for developing periodontal destruction.

The genomic diversity among equine herpesvirus-1 strains isolated in Japan.

The DNAs from nine Japanese field isolates of equine herpesvirus-1 (EHV-1) were analyzed by digestion with the restriction endonuclease Bam HI and Southern hybridization. Comparing restriction profiles among the EHV-1 strains, there was no considerable difference between isolates before and after vaccine application, but some minor variations in the mobility of Bam HI fragments were observed. To identify these variable fragments, all genomic DNA sequences of the Japanese prototype of EHV-1 have been cloned as Bam HI restriction fragments into the plasmid pUC-18. Physical maps of the virus DNA were constructed by a combination of Southern blot analysis and double enzyme digestion of the cloned fragments. By using these cloned fragments as probes in Southern blot analysis, the areas of heterogeneity observed among the field EHV-1 isolates were located in both terminals of UL, the center of UL, IR, US and TR regions of the genome.

DNA fingerprinting for differentiating aggressivity groups of the rape seed pathogen Leptosphaeria maculans

Genomic DNA was prepared from a total of 16 different isolates of the rape seed pathogen Leptosphaeria maculans , the teleomorph of Phoma lingam . These DNA preparations were digested with the restriction endonucleases Bam H I, Eco R I, Hpa II, Mbo I, Msp I and Sau3 A I, separated on agarose gels and analysed by hybridization with the radioactively labelled synthetic oligonucleotides (GTG) 5 , (GACA) 4 or (CT) 8 or with labelled DNA of phage M13. These probes reveal a high degree of DNA polymorphism within the species. Although all investigated isolates can clearly and unequivocally be distinguished from each other, aggressive and nonaggressive strains appear as consistent groups with high degrees of similarity. The fingerprinting technique is thus an appropriate tool for molecular diagnosis of this important plant pathogen. In general, oligonucleotide fingerprinting may be regarded as a convenient technique to identify individual fungal strains with a reliability similar to that of mammalian systems.

Bam HI Restriction Fragment Length Polymorphisms for Hypoxanthine‐Guanine Phosphoribosyltransferase (HPRT) Gene of Carriers and Controls of HPRT Deficiency in Japan

Three-allele restriction fragment length polymorphisms (RFLPs) for the restriction endonuclease Bam HI are known at the hypoxanthine-guanine phosphoribosyltransferase (HPRT, E.C.2.4.2.8.) gene locus. The alleles are expressed phenotypically on Southern blots as three distinct pairs of fragments that hybridize to HPRT cDNA: i) a 22-kilobase (kb)/25-kb pair, ii) a 12-kb/25-kb pair, and iii) a 22-kb/18-kb pair. Allele frequencies in 119 unrelated Japanese people were 0.38 for the 22-kb/25-kb allele, 0.43 for the 12-kb/25-kb allele, and 0.19 for the 22-kb/18-kb allele, an average heterozygosity of 66% in Japanese females, a higher rate than in Caucasian females. Five out of nine carriers of partial or complete HPRT deficiency showed heterozygous patterns for Bam HI RFLPs.

Genetic Variation in Strains ofClavibacter michiganensesubsp.sepedonicum: Polymorphisms in Restriction Fragments Containing a Highly Repeated Sequence

(...) Under the conditions employed in this study, restriction enzymes Bam HI, BclI, BstXI, and SmaI were particularly effective in yielding RFLP patterns that permit discrimination of strains. Restriction enzyme NheI was useful for differentiating pathogen strains that contain autonomously replicating pCS1 from those in which the plasmid is integrated into the bacterial chromosome. The RFLP patterns produced by NheI also provided evidence that integration of pCS1 into the chromosome is a site-specific process. No alterations in RFLP patterns were observed upon repeated subculture of selected strains. Numerical analysis of the RFLP data indicated that the strains are of high similarity

2'-5' oligoadenylate synthetase and its relationship to HLA and genetic markers of insulin-dependent diabetes mellitus.

Cytokines and their related enzyme pathways may play a part in the development of insulin-dependent diabetes mellitus (IDDM). We have therefore studied the activity of the enzyme 2'-5' oligoadenylate synthetase (which is induced by both interferon and the tumour necrosis factors) in circulating mononuclear cells from 40 subjects with IDDM and 32 healthy control subjects. There was no difference in mean basal enzyme activity between the two groups. A polymorphism of the 2'-5' oligoadenylate synthetase gene, not previously described, was found using the restriction enzyme Bam HI. There was no association of 2'-5' oligoadenylate synthetase genotypes with IDDM, but there was a significant correlation between basal 2'-5' oligoadenylate synthetase activity and 2'-5' oligoadenylate synthetase genotypes. Significantly higher mean basal levels of 2'-5' oligoadenylate synthetase activity were associated with HLA-DQA 4.6 phenotype (determined using the restriction enzyme Taq 1 and a DQA probe) and HLA-DR3 (determined serologically), whereas significantly lower mean levels of enzyme activity were associated with HLA-DQA 5.5 and HLA-DR7, in both IDDM and control subjects. An analysis of variance confirmed that these associations were independent 2'-5' oligoadenylate synthetase genotype. Likewise, a significantly higher mean level of enzyme activity was associated with the heterozygous 1/3 insulin-related genotype in the IDDM subjects only. This study therefore suggests that the possession of certain HLA haplotypes might be associated with differing levels of basal 2'-5' oligoadenylate synthetase activity.

Restriction fragment length polymorphism analysis of the VX locus in human lupus

To evaluate the degree of genetic polymorphism of the V kappa repertoire in systemic lupus erythematosus (SLE), we performed Southern blot hybridizations with human gene probes corresponding to the four human V kappa gene families. In a comparative analysis, non-lymphoid cell DNA samples from three patients with idiopathic SLE, eight subjects with susceptibility to drug-induced lupus and seven control individuals were digested with the restriction endonucleases Bam HI, Bg 1 II, Eco RI and Hind III, and hybridized sequentially to the four V kappa family-specific probes. The restriction patterns on Southern blots revealed a low degree of polymorphism of the human V kappa gene repertoires of SLE patients and control individuals. This analysis, together with previous parallel studies of the V kappa locus in lupus-prone mice, implies that autoantibody hyperproduction in lupus is not associated with major modifications in the structure or genomic organization of immunoglobulin light chain genes.