BamHI Restriction Fragment Length Polymorphism Research Articles

Association of gene polymorphisms for plasminogen activators with alveolar bone loss

The plasminogen activating system is a protease/inhibitor system central to extracellular matrix remodeling with a suggested role in periodontal disease pathology. A few studies have reported polymorphisms in the genes of plasminogen activator inhibitors to be associated with periodontal disease severity. Two gene polymorphisms - a BamHI restriction fragment length polymorphism in the urokinase plasminogen activator gene (uPA) and a HindIII restriction fragment length polymorphism in the plasminogen activator inhibitor type 1 gene (PAI-1) - have been associated with conditions having a vascular component, and our objective was to assess the association of these gene polymorphisms with alveolar bone loss in chronic periodontal disease of adults. Genotype was determined by polymerase chain reaction amplification of whole blood, pertinent histories were obtained by interview, and alveolar bone loss was assessed from current radiographs. In 77 elderly patients with a normal distribution of alveolar bone loss, we demonstrated a significant association between levels of alveolar bone loss and these polymorphisms in the uPA and PAI-1 genes. Controlling for the contributions of smoking or diabetes to periodontal bone loss, estimated odds ratios for predicting lower levels of alveolar bone loss, associated with a greater degree of periodontal health, were strongest when defined by the concurrent presence of a homozygous urokinase plasminogen activator genotype and the nuclease-sensitive plasminogen activator inhibitor type 1 (HindIII) allele (odds ratio = 2.6; 95% confidence interval: 5.8-1.3). The urokinase plasminogen activator (BamHI) and plasminogen activator inhibitor type 1 (HindIII) genotypes may serve as useful markers for heritability of bone loss associated with periodontal disease.

Single Nucleotide Polymorphism analysis of the human adenosine A2B receptor gene: prevalence of SNPs in asthmatics and normal subjects

AbstractThe adenosine A2B receptor is found on human lung mast cells and is believed to mediate the bronchoconstriction in response to adenosine characteristic of asthmatics. As such it represents an attractive therapeutic target for asthma and allergic rhinitis. As genetic variability in drug targets may affect an individual's response to treatment, the adenosine A2B receptor gene was analyzed for polymorphisms and their prevalence defined in a Caucasian population. The coding region of the A2B receptor gene as well as the intron‐exon boundaries of the gene were found to be free of genetic variation. Three single nucleotide polymorphisms were identified in the promoter region of the gene, one of which created a BamHI restriction fragment length polymorphism. The prevalence of the three single nucleotide polymorphisms in an unselected population was <5%. The prevalence of the BamHI polymorphism was investigated in a British population of 40 asthmatics and 40 non‐asthmatics: no excess of the BamHI variant was observed in asthmatic subjects. The data indicates that any variability in drug response would likely not be due to direct structural variation of the A2B receptor protein. Further, polymorphism at the A2B receptor genomic locus is unlikely to contribute to the population risk of developing asthma.

Aflatoxin genes and the aflatoxigenic potential of Koji moulds.

Sixty-four Aspergillus isolates, 54 of which originated from food fermentations, and 18 Aspergillus reference strains were identified and screened for the presence of aflatoxin genes aflR and omt-1. Among the Koji moulds, not only A. oryzae but also A. flavus strains were found. Furthermore, 27% of A. oryzae and 93% of A. flavus strains lacked either aflR or both aflR- and omt-1. A selection of 29 strains was also checked for the presence of pksA and nor-1. This revealed large deletions in the aflatoxin gene cluster of some strains. The hybridisation patterns also suggested a polarity in the deletion events, originating in the vicinity of pksA and extending towards omt-1. Other strains exhibited BamHI restriction fragment length polymorphisms (RFLPs) for either aflR or for aflR and omt-1. All aflR and/or omt-1 deletion strains turned out to be unable to produce aflatoxin. The RFLP-carrying strains either produced only traces of aflatoxin or none at all. In 73% of the A. oryzae strains, no apparent deletions were detected with the aflR and omt-1 probes. Nevertheless, after incubation in aflatoxin-inducing media, no aflatoxin B1 production could be detected in those A. oryzae strains.

Lack of Association Between the Heparan Sulfate Proteoglycan Gene Polymorphism and Diabetic Nephropathy in Japanese NIDDM with Proliferative Diabetic Retinopathy

The development of diabetic nephropathy shows remarkable variation among individuals. Therefore, not only hvperglycemia hut also genetic factors may contribute to the development of diabetic nephropathy. Heparan sulfate proteoglycan (HSPG) is thought to play an important role as a component of the charge selectivity barrier in the glomerular basement membrane. Recently, a BamHI restriction fragment length polymorphism (RFLP) in the HSPG gene (HSPG 2) was reported to be associated with diabetic nephropathy in Caucasian insulin-dependent diabetes niellitus (IDDM). The aim of the present study was to examine the contribution of the BamHI HSPG2 polymorphism to the development of diabetic nephropathy in Japanese non-insulin-dependent diabetes mellitus (NIDDM). For this purpose, we recruited 102 patients with diabetic nephropathy and 64 age-matched patients without diabetic nephropathy from Japanese NIDDM patients. Since all the subjects had proliferative diabetic retinopathy, it seems likely that they would be exposed to hyperglycemia for a long time. In the present study, the BamHI HSPG2 genotype and allele frequencies were not significantly different between the patients with nephropathy and the patients without nephropathy. Therefore, we conclude that the BamHI HSPG2 polymorphism is not associated with the development of diabetic nephropathy in Japanese NIDDM.

Organisation of the equine immunoglobulin constant heavy chain genes: II. Equine c γ genes

The number of immunoglobulin G constant heavy chain genes ( cγ genes) varies broadly among mammalian species, reflecting structural and functional differences between expressed immunoglobulin G (IgG) isotypes and allotypes. Up to now equine IgG isotypes have been defined only at the biochemical and serological level. It is still not clear how many IgG isotypes exist in horses and whether there are any allotypes. Here, we describe the isolation and characterisation of equine cγ genes. An equine genomic lambda phage library was screened with a human c γ4 probe. Cross-hybridising equine c γ sequences were cloned twice and characterised by restriction mapping with the human c γ4 and a murine s γ1 probe. Genomic equine DNA probes for both, cγ genes and corresponding switch regions (s γ), were isolated and used for a more detailed BamHI restriction analysis, comparing genomic DNA of various horses. This analysis reveals the existence of at least five, or probably six cγ genes in the equine haploid genome. Beside the porcine system, this is the highest number of cγ genes described for any mammalian species. Moreover, for two of these cγ genes, BamHI restriction fragment length polymorphism became evident.

Identification of a BamHI Polymorphism for the Urokinase Gene Associated with Symptomatic Coronary Artery Disease.

Urokinase-type plasminogen activator (u-PA) and plasmin have been implicated in a number of processes, including activation of a variety of metalloproteinases, matrix remodeling, and cell migration, which may underlie the early initiation and progression of atherosclerosis and coronary artery disease (CAD). These studies were carried out to determine whether variations in the u-PA gene, using a BamHI restriction fragment length polymorphism (RFLP) as a new marker for genetic variation, may be associated with CAD. Southern blot analysis of individual digested genomic DNA (BamHI), hybridized with a 2-kb human u-PA cDNA probe, identified a two-allele RFLP with allelic bands at 6 and 1.5 kb. A constant band at 9 kb was detected. Three genotypes were identified and designated as 1/1 (6.0-kb band only), 1/2 (6.0 and 1.5-kb bands), and 2/2(1.5-kb band only). For these studies, 43, individual human umbilical cord samples, representing a "control" population, were analyzed and compared in terms of their u-PA genotypes with 34 saphenous vein samples from patients requiring coronary artery bypass grafting (CABG). Controls, presumed to reflect the normal population distribution, showed a u-PA genotype distribution of 1/1(n = 8, 18.6%), 1/2 (n = 33, 76.7%) and 2/2 (n = 2, 4.7%), whereas CAD patients showed a distribution of 1/1 (n = 16, 47.1%), 1/2 (n = 13, 38.2%), and 2/2 (n = 5, 14.7%). Comparison of the "control" genotype distribution with data derived from CABG patients demonstrated a significant difference in the distribution of u-PA genotypes (P = 0.002), with an increased prevalence of the homozygous 1/1 and 2/2 genotypes in CAD patients. These early studies demonstrate a significant association between u-PA gene polymorphism and the presence or absence of CAD.

Organization of the equine immunoglobulin constant heavy chain genes I. cε and cα genes

We provide a restriction map of the equine cε and cα genes as a molecular basis for isotype classification. Human and murine DNA probes were used for identification of homologous equine DNA sequences and for isolation of the equine cε and cα genes from a genomic DNA library. A detailed map of the equine 5′-sε/cε-sα/cα-3′ gene region was obtained. Equine cε and cα DNA probes were prepared and used for restriction analysis of immunoglobulin heavy chain gene loci from different horses. This analysis indicated the presence of only one equine cε and one cα gene in the haploid equine genome. In addition, for the equine cα gene, four haplotypes were identified according to BamHI restriction fragment length polymorphism (RFLP) of genomic DNA. The relative location of the cε and cα genes 3′ of the equine cμ and cγ genes was determined by restriction analysis of equi-murine heterohybridomas.

IgE, TNFα, IL1 β, IL4 and IFNγ gene polymorphisms in sheep selected for resistance to fleece rot and flystrike

Investigation of restriction fragment length polymorphisms (RFLPs) associated with immunoglobulin E (IgE) and cytokine genes in the sheep genome revealed polymorphisms in the IgE constant heavy chain, interferon γ and interleukin 4 genes. No polymorphisms were found in interleukin 1β or tumour necrosis factor α. PstI and BamHI RFLPs in the IgE gene showed differences in frequency between animals selected for resistance or susceptibility to fleece rot and blowfly strike.

Rapid communication: BamHI restriction fragment length polymorphism detected with a pig gastric mucin (MUC5AC) probe.

Rapid communication: BamHI restriction fragment length polymorphism detected with a pig gastric mucin (MUC5AC) probe.

Relationship of restriction fragment length polymorphisms (RFLP) at the bovine calpastatin locus to calpastatin activity and meat tenderness.

Restriction fragment length polymorphisms (RFLP) have been identified at the bovine calpastatin locus. The objective of the present study was to determine whether these polymorphisms are related to variations in calpastatin activity or beef tenderness in unrelated animals of mixed breeding. A sample of 83 crossbred steers from sires representing eight different breeds was examined to determine this relationship. A 2.2-kb cDNA coding for domains 2 through 4 plus a 3' untranslated region of bovine skeletal muscle calpastatin was used as a probe for calpastatin RFLP. Polymorphisms were found using the restriction enzymes BamHI and EcoRI. Polymorphic restriction fragments for BamHI were 9.0 and 5.0 kb and for EcoRI were 6.0 and 4.0 kb. Allelic frequencies for BamHI restriction fragments were .53 for the 9.0-kb allele and .47 for the 5.0-kb allele. Allelic frequencies for EcoRI restriction fragments were .43 for the 6.0-kb allele and >57 for the 4.0-kb allele. No polymorphisms were identified using the restriction enzymes BglII, DraI, or PstI. No associations between EcoRI and BamHI RFLP and 24-h calpastatin activity of Warner-Bratzler shear force at 14 d postmortem were detected. Therefore, the polymorphic EcoRI and BamHI restriction sites within the bovine calpastatin locus do not detect DNA sequence differences responsible for variation in calpastatin activity or tenderness of aged beef. Therefore, these polymorphisms cannot be used to predict tenderness of aged beef from unrelated animals of mixed breeding. These results do not exclude the possibility that other DNA sequences in or near the bovine calpastatin gene are responsible for variation in calpastatin activity or meat tenderness. The lack of a relationship between these calpastatin RFLP and meat tenderness must be distinguished from the well-documented relationship between calpastatin activity and meat tenderness. Therefore, further development of calpastatin-based methods for predicting beef tenderness in unrelated animals of mixed breeding should focus on basic factors influencing calpastatin activity at the molecular and cellular level.

Rapid communication: BamHI and TaqI restriction fragment length polymorphisms in the bovine Uroplakin IA gene

Journal Article Rapid communication: BamHI and TaqI restriction fragment length polymorphisms in the bovine Uroplakin IA gene Get access A. M. Ryan, A. M. Ryan *Department of Veterinary Pathobiology and the Center for Animal Genetics, Institute for Biosciences and Technology, Texas A&M University, College Station 77840 2To whom correspondence should be addressed. Search for other works by this author on: Oxford Academic PubMed Google Scholar J. E. Womack, J. E. Womack *Department of Veterinary Pathobiology and the Center for Animal Genetics, Institute for Biosciences and Technology, Texas A&M University, College Station 77840 Search for other works by this author on: Oxford Academic PubMed Google Scholar J. Yu, J. Yu †the Ronald O. Perleman Department of Dermatology and the Department of Pharmacology, Kaplan Comprehensive Cancer Center, New York University Medical School, New York 10016 Search for other works by this author on: Oxford Academic PubMed Google Scholar J.-H. Lin, J.-H. Lin †the Ronald O. Perleman Department of Dermatology and the Department of Pharmacology, Kaplan Comprehensive Cancer Center, New York University Medical School, New York 10016 Search for other works by this author on: Oxford Academic PubMed Google Scholar X.-R. Wu, X.-R. Wu †the Ronald O. Perleman Department of Dermatology and the Department of Pharmacology, Kaplan Comprehensive Cancer Center, New York University Medical School, New York 10016 Search for other works by this author on: Oxford Academic PubMed Google Scholar T.-T. Sun T.-T. Sun †the Ronald O. Perleman Department of Dermatology and the Department of Pharmacology, Kaplan Comprehensive Cancer Center, New York University Medical School, New York 10016 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Animal Science, Volume 72, Issue 7, July 1994, Page 1908, https://doi.org/10.2527/1994.7271908x Published: 01 July 1994 Article history Received: 07 February 1994 Accepted: 01 April 1994 Published: 01 July 1994

Characterization of Leptospiraceae by 16S DNA restriction fragment length polymorphisms

Chromosomal DNA from 37 Leptospiracae representing genetic species, groups and reference strains together with five leptospire isolates and Escherichia coli were digested with the restriction endonucleases BamHI, ClaI and EcoRI. The Southern blots were hybridized with a biotinylated E. coli 1.5 kb 16S rDNA probe and gave 36 reproducible and unique patterns. With the exception of the type strain (Leptospira interrogans serovar icterohaemorrhagiae RGA) and neotype strain (serovar icterohaemorrhagiae Ictero no. 1) all the species and taxa examined could be differentiated from each other on the basis of their BamHI, ClaI and EcoRI restriction fragment length polymorphisms (RFLP). L. interrogans and L. borgpetersenii reference strains were heterogeneous, whereas Leptonema illini and L. parva incertae sedis were distinct and separate. Strains representing L. biflexa sensu lato presented divergent RFLP patterns. A porcine isolate was identified to be L. interrogans pomona Pomona.

A single serine:pyruvate aminotransferase gene on rat chromosome 9q34-q36

It was found in our previous study (Oda et al., 1990. J. Biol. Chem. 265: 7513–7519) that in the rat two mRNAs encoding mitochondrial and peroxisomal serine:pyruvate aminotransferase (SPT/AGT) are formed from a single SPT/AGT gene through alternative transcription initiation in exon 1. In an attempt to analyze the mechanisms underlying this unique phenomenon, we have isolated genomic clones harboring the entire rat SPT/AGT gene. In the present study, the location of the rat SPT/AGT gene was determined to be in the q34–q36 region of chromosome 9 by fluorescence in situ hybridization. Southern blot analysis of rat genomic DNA revealed an allelic BamHI restriction fragment length polymorphism among three different inbred rat strains. These results indicated that a single copy SPT/AGT gene is located on chromosome 9q34-q36 in the rat genome. This locus has been assigned the gene symbol Spat.

The relaxin gene is located on chromosome 19 in the mouse

Relaxin is a polypeptide hormone that exerts a variety of physiological effects during pregnancy. To investigate the possibility that known genetic mutations affecting aspects of reproductive physiology result in alterations in the structure or production of relaxin, we have determined the chromosomal location of the mouse gene. The finding of a BamHI restriction fragment length polymorphism in AKR mice enabled us to use recombinant inbred strains to make an assignment to chromosome 19. This was confirmed by Southern analysis of DNA from microcell hybrids.

Cloning of human heparan sulfate proteoglycan core protein, assignment of the gene ( HSPG2) to 1p36.1→p35 and identification of a BamHI restriction fragment length polymorphism

We have isolated a cDNA coding for the core protein of the large basement membrane heparan sulfate proteoglycan (HSPG) from a human fibrosarcoma cell (HT1080) library. The library was screened with a mouse cDNA probe and one clone obtained, with a 1.5-kb insert, was isolated and sequenced. The sequence contained an open reading frame coding for 507 amino acid residues with a 84% identity to the corresponding mouse sequence. This amino acid sequence contained several cysteine-rich internal repeats similar to those found in component chains of laminin. The HSPG cDNA clone was used to assign the gene ( HSPG2) to the p36.1→p35 region of chromosome 1 using both somatic cell hybrid and in situ hybridization. In the study of the polymorphisms of the locus, a BamHI restriction fragment length polymorphism was identified in the gene. This polymorphism displayed bands of 23 and 12 kb with allele frequencies of 76 and 24%, respectively.

Characterization of a programmed alteration in an 18S ribosomal gene that accompanies the experimental induction of drug resistance in Schistosoma mansoni.

Stable resistance to the anthelmintic hycanthone can be produced in the human blood fluke Schistosoma mansoni by exposing immature parasites in mice to the drug. Within a single generation, genomic rearrangements, detected as rRNA-encoding DNA restriction fragment length polymorphisms (RFLPs), accompany the appearance of resistance in this model. One of these RFLPs, an approximately 3.6-kilobase BamHI fragment, was shown previously to associate consistently with resistance in independent generations of the JHU strain of S. mansoni. To characterize the genetic changes responsible for this RFLP, the fragment was cloned and sequenced. A comparison of the cloned fragment with a normal 18S rRNA gene demonstrated that the drug resistance-associated RFLP fragment arises through the addition of 732 base pairs into an 18S rRNA gene, 134 base pairs downstream of the junction of the intergenic spacer and the mature 18S rRNA gene. The mutation is nonrandom, targets one, or a few only, of the 100 or so copies of the ribosomal genes, and may represent the incomplete duplication of the gene since the inserted element is identical in sequence to the region contiguous to it. The sequence spanning the junction of the insertion and the original 18S rRNA gene was used as a specific primer for the BamHI RFLP in PCR experiments. The analysis conclusively demonstrated that the mutation is induced rather than selected by the drug since the junctional sequence was not detectable in the drug-sensitive parent population of schistosomes. In addition, analysis of four, independently derived, resistant lines indicated that the same region of the gene was mutated each time. Together, these data demonstrate that reproducible changes are induced during the acquisition of resistance in schistosomes and suggest that the resistant phenotype is induced rather than selected from preexisting forms.

Genetic linkage of the human apolipoprotein AI-CIII-AIV gene cluster and the neural cell adhesion molecule (NCAM) gene

The genes encoding apolipoproteins AI, CIII, and AIV, three plasma proteins involved in lipid metabolism, are clustered within a 15-kb DNA segment (apoAI-CIII-AIV gene cluster) located on human chromosome 11 at band q23. The gene encoding the neural cell adhesion molecule (NCAM), a cell surface glycoprotein involved in cell-cell recognition during morphogenesis, is also located on chromosome 11, band q23. In this report, 12 previously described restriction fragment length polymorphisms (RFLPs) in the apoAI-CIII-AIV gene cluster were tested for cosegregation with a newly identified BamHI RFLP in the NCAM gene using 13 families. The results show that the apoAI-CIII-AIV gene cluster and the NCAM gene loci are linked with a maximum lod score of 15.9 at a recombination fraction of 0.028. In addition, an approach for the most efficient use of the apoAI-CIII-AIV gene cluster polymorphisms, based on the evaluation of their individual and cumulative heterozygosities, is presented.

Carrier Detection of Partial Hypoxanthine-Guanine Phosphoribosyltransferase Deficiency by Analysis with BamHI Restriction Fragment Length Polymorphisms and Oligonucleotide Probes

Hyperuricemic nephropathy can progress to the permanent renal damage even in infancy in partial hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency. We have encountered two unrelated patients with partial HPRT deficiency, and found that early detection of the disease and long-term management for hyperuricemia were necessary to prevent renal impairment. The HPRT gene is situated in the q26-27 region of the long arm of the X-chromosome, and females with mutant HPRT alleles are heterozygous for the disease, and they develop gout after menopause. We undertook the investigation of carriers in the two patients' families, using BamHI restriction fragment length polymorphisms and oligonucleotide probes that recognized the specific mutations within the HPRT gene. We also demonstrated that the allele frequencies of BamHI restriction fragment length polymorphisms in 62 Japanese females were 0.36 for the 22-kb/25-kb allele, 0.41 for the 12-kb/25-kb allele, and 0.23 for the 22-kb/18-kb allele, resulting in a heterozygous state in 66% of females.

Analysis of proto-oncogenes in acute myeloid leukemia: loss of heterozygosity for the Ha-ras gene

At least 13 of 34 patients with acute myeloid leukemia (AML) of varying FAB types were heterozygous for a BamHI restriction fragment length polymorphism (RFLP) of the Ha-ras gene on chromosome 11. In 4 of these 13 patients, one allele of the Ha-ras gene was deleted. Two of these cases had an informative heterozygosity for an RFLP on the long arm of chromosome 11. Analysis of these cases indicated that loss of genes from chromosome 11 was restricted to the short arm. In three cases with loss of one Ha-ras gene, the remaining gene had no mutations in critical areas of exons 1 and 2. With the exception of one AML case with amplification of MYC, no gross structural abnormalities in 12 other oncogenes were detected.

Analysis of Proto-Oncogenes in Acute Myeloid Leukemia: Loss of Heterozygosity for the Ha-ras Gene

Abstract At least 13 of 34 patients with acute myeloid leukemia (AML) of varying FAB types were heterozygous for a BamHI restriction fragment length polymorphism (RFLP) of the Ha-ras gene on chromosome 11. In 4 of these 13 patients, one allele of the Ha-ras gene was deleted. Two of these cases had an informative heterozygosity for an RFLP on the long arm of chromosome 11. Analysis of these cases indicated that loss of genes from chromosome 11 was restricted to the short arm. In three cases with loss of one Ha-ras gene, the remaining gene had no mutations in critical areas of exons 1 and 2. With the exception of one AML case with amplification of MYC, no gross structural abnormalities in 12 other oncogenes were detected.