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Multidrug-resistant Acinetobacter strain HK302 was isolated from an outbreak of nosocomial infections in Switzerland in 1977. The aim of the present study was to assess whether this archive strain belongs to one of the known international clonal lineages of Acinetobacter baumannii and whether it harbours a genomic structure related to the AbaR1-like resistance islands.Multilocus sequence typing (MLST) and HindIII ribotyping were used to determine the taxonomic position of HK302 at the species and subspecies (clonal) levels. The position and structure of the putative resistance island were investigated by AbaR1-based PCR mapping followed by restriction analysis and partial sequencing of amplicons. A. baumannii AYE harbouring AbaR1 was used as a positive control for PCR mapping.The MLST allelic profile (1-1-1-1-5-1-1) and HindIII ribotype of HK302 were typical of A. baumannii European (EU) clone I. In addition, an AbaR1-related region inserted into the ATPase gene at the same position as AbaR1 was found in HK302. PCR mapping and partial sequencing revealed that this region is structurally congruent with AbaR3, a 63.4 kb island described in an A. baumannii isolate from 2004.A. baumannii HK302 belongs to EU clone I and harbours an AbaR3-like island related to resistance islands described in EU clone I strains. Our findings suggest that variants of these sophisticated genomic structures already existed in A. baumannii in the late 1970s.

Lipoprotein lipase (LPL) is a key enzyme in lipoprotein metabolism and a major candidate gene for coronary heart disease (CHD). The authors assessed associations between 7 LPL polymorphisms and lipid fractions and CHD risk in population-based cohort, case-control, and cross-sectional studies published by January 2007. Meta-analyses of 22,734 CHD cases and 50,177 controls in 89 association studies focused on the relations of the T-93G (rs1800590), D9N (rs1801177), G188E, N291S (rs268), PvuII (rs285), HindIII (rs320), and S447X (rs328) polymorphisms to high density lipoprotein cholesterol, triglycerides, myocardial infarction, or coronary stenosis. Carriers of 9N or 291S had modestly adverse lipid profiles. Carriers of the less common allele of HindIII or of 447X had modestly advantageous profiles. The combined odds ratio for CHD among carriers was 1.33 (95% confidence interval (CI): 1.14, 1.56) for 9N, 1.07 (95% CI: 0.96, 1.20) for 291S, 0.89 (95% CI: 0.81, 0.98) for the less common HindIII allele, and 0.84 (95% CI: 0.75, 0.94) for 447X. For T-93G (odds ratio (OR) = 1.22, 95% CI: 0.98, 1.52) and PvuII (OR = 0.96, 95% CI: 0.89, 1.04), there were null associations with lipid levels or CHD risk; information on G188E was limited (OR = 2.80, 95% CI: 0.88, 8.87). The study of LPL genotypes confirms the existence of close interrelations between high density lipoprotein cholesterol and triglyceride pathways. The influence of these genotypes on CHD risk warrants further investigation. Am J Epidemiol

Variations in the Y chromosome have shown significant, albeit inconsistent, associations with hypertension in men. Studies of peripubertal subjects might reveal more information on the origins of the Y chromosome's influence on blood pressure (BP). In the current study, we examined the association of a HindIII restriction site on the Y chromosome with BP in a cohort of young men.Pubertal growth-based analyses were performed in 80 unrelated males with multiple measurements spanning time points beginning before and extending to after their pubertal growth. Blood pressure, height, and weight were measured approximately every 6 months. The period of pubertal growth was used to approximate the time for puberty. The association of the HindIII restriction site to systolic and diastolic BP was determined using a mixed model ANOVA.Estimated systolic and diastolic BPs were higher in HindIII(-) males in the period before, as well as in the period after pubertal growth (systolic BP 2.6 +/- 1.3 mm Hg higher, P.05), and diastolic BP 2.3 +/- 1.2 mm Hg higher, P = .050). In addition, HindIII(-) males were younger at onset of peak height velocity (12.7 +/- 0.1 v 13.3 +/- 0.1 years, P.001). In African Americans, an earlier age of maximal height velocity was associated with a higher systolic and diastolic BP (P.05 and .02, respectively).The results suggest that variations in genes on the Y chromosome may affect BP in peripubertal males, possibly even before onset of puberty.

Streptococcus iniae (junior synonym S. shiloi) isolated from tilapia and trout in Israel and in the United States were subtyped by restriction length polymorphism (RFLP) based on PCR amplified 16S rDNA and by ribotyping. 16S rDNA RFLP discriminated between S. iniae and other fish pathogens but not between S. iniae strains. HindIII and EcoRI ribotypes of S. iniae discriminated American from Israeli strains rejecting the possibility of an epidemiological link between S. iniae infections in the two countries. Israeli strains isolated from tilapia and trout could not be completely differentiated. The S. iniae ATCC 29178T (T = Type strain) strain, isolated from a freshwater dolphin belonged to a ribotype different from those of all the fish isolates.

BACKGROUND: Women with recurrent pregnancy loss (RPL) and T-helper (Th)1-type immunity to trophoblast antigens have an increased frequency of the IL1B-511*1 promoter variant. Since CD46 gene products also regulate maternal immune responses including Th1 immunity, we investigated whether CD46 gene polymorphisms are also associated with RPL in women with and without Th1 immunity to trophoblast, and the possibility of a synergistic effect with the IL1B-511*1 promoter variant. METHODS: A case-controlled study was performed to document HindIII site polymorphism in intron 1 of the CD46 gene in 131 women with RPL and 72 fertile controls. Clinical information, Th1-type immune responsiveness to trophoblast in women with RPL history, and IL1B promoter allelo-types for this cohort were documented in a previous study. RESULTS: The frequency of the CD46H*2 allele and CD46H*2 homozygosity were significantly increased in women with RPL compared with fertile controls (P

More than 3000 type II restriction endonucleases have been discovered. They recognize short, usually palindromic, sequences of 4–8 bp and, in the presence of Mg2+, cleave the DNA within or in close proximity to the recognition sequence. The orthodox type II enzymes are homodimers which recognize palindromic sites. Depending on particular features subtypes are classified. All structures of restriction enzymes show a common structural core comprising four β-strands and one α-helix. Furthermore, two families of enzymes can be distinguished which are structurally very similar (EcoRI-like enzymes and EcoRV-like enzymes). Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone. In contrast, specific binding is characterized by an intimate interplay between direct (interaction with the bases) and indirect (interaction with the backbone) readout. Typically ∼15–20 hydrogen bonds are formed between a dimeric restriction enzyme and the bases of the recognition sequence, in addition to numerous van der Waals contacts to the bases and hydrogen bonds to the backbone, which may also be water mediated. The recognition process triggers large conformational changes of the enzyme and the DNA, which lead to the activation of the catalytic centers. In many restriction enzymes the catalytic centers, one in each subunit, are represented by the PD . . . D/EXK motif, in which the two carboxylates are responsible for Mg2+ binding, the essential cofactor for the great majority of enzymes. The precise mechanism of cleavage has not yet been established for any enzyme, the main uncertainty concerns the number of Mg2+ ions directly involved in cleavage. Cleavage in the two strands usually occurs in a concerted fashion and leads to inversion of configuration at the phosphorus. The products of the reaction are DNA fragments with a 3′-OH and a 5′-phosphate.

Seven Enterococcus moraviensis and 16 Enterococcus haemoperoxidus as well as nine reference cultures of other enterococcal species obtained from the Czech Collection of Microorganisms were characterized using ribotyping with EcoRI and HindIII in the present work. The ribopatterns obtained by both restriction enzymes clearly distinguished all E. moraviensis and E. haemoperoxidus strains from the other enterococci (E. faecalis, E. faecium, E. avium, E. raffinosus, E. pseudoavium, E. malodoratus) and they differentiated both species from each other as well. Although all strains were isolated from different sampling sites, many strains shared the same band patterns. E. moraviensis formed four ribogroups using EcoRI and two ribogroups using HindIII restriction enzyme. E. haemoperoxidus gave six different patterns with EcoRI and five using the HindIII restriction enzyme.

We have performed mutational analyses of restriction endonuclease HindIII in order to identify the amino acid residues responsible for enzyme activity. Four of the seven HindIII mutants, which had His-tag sequences at the N-termini, were expressed in Escherichia coli, and purified to homogeneity. The His-tag sequence did not affect enzyme activity, whereas it hindered binding of the DNA probe in gel retardation assays. A mutant E86K in which Lys was substituted for Glu at residue 86 exhibited high endonuclease activity. Gel retardation assays showed high affinity of this mutant to the DNA probe. Surprisingly, in the presence of a transition metal, Mo(2+) or Mn(2+), the E86K mutant cleaved substrate DNA at a site other than HindIII. Substitution of Glu for Val at residue 106 (V106E), and Asn for Lys at residue 125 (K125N) resulted in a decrease in both endonucleolytic and DNA binding activities of the enzyme. Furthermore, substitution of Leu for Asp at residue 108 (D108L) abolished both HindIII endonuclease and DNA binding activities. CD spectra of the wild type and the two mutants, E86K and D108L, were similar to each other, suggesting that there was little change in conformation as a result of the mutations. These results account for the notion that Asp108 could be directly involved in HindIII catalytic function, and that the substitution at residue 86 may bring about new interactions between DNA and cations.

Background: Lipoprotein lipase (LPL) is the rate-limiting enzyme in the hydrolysis of core triglycerides in chylomicrons and VLDL.Methods: We investigated the association between the HindIII polymorphism of the LPL gene and fasting glucose, lipid, and lipoprotein concentrations in 683 Caucasians. We first stabilized the study subjects, using an 8-day diet and exercise intervention program before obtaining blood samples. The use of this standardization period reduced the variance of all glucose and lipid concentrations.Results: In our study, the HindIII allele frequencies for females and males were 0.29 and 0.34 for H− and 0.71 and 0.66 for H+, respectively. We found in females, but not in males, a significant association between the HindIII genotype and total cholesterol (P = 0.007) and LDL-cholesterol (P = 0.018), with females homozygous for the rare H− allele having the lowest, heterozygotes (H−/+) having intermediate, and women homozygous for the common H+ allele having the highest of each of these lipid traits. With regard to triglycerides, HDL-cholesterol, and glucose, no significant effect of the HindIII genotype was noted in either gender.Conclusions: These results suggest that in a gender-specific manner, the rare LPLHindIII H− allele has a cholesterol-lowering and, therefore, potentially cardioprotective effect compared with the common H+ allele.

Site-directed mutagenesis by inverse PCR was done on the HindIII gene. Target residues to be mutated were chosen according to (i) the fact that a mutant obtained by sodium nitrite treatment showed almost no HindIII activity, where Asp-123 was replaced with Asn, and (ii) the model proposed by Stahl et al. (Stahl, F., Wende, W., Jeltsch, A. and Pingoud, A. Biol. Chem. 379, 467-473 (1998)). Seven kinds of mutants were obtained by the PCR, and their enzymatic and biochemical properties were examined. Three mutants, P50S, D108L, and D123N, showed fairly low HindIII activity. On the other hand, the other four, P84Q, E86K, V106E, and K125N, retained the activity. In particular, E86K showed higher activity than the wild enzyme. This fact was confirmed when activities of the purified wild and E86K enzymes were assayed. These results coincided fairly well with data using E. coli strains that carry the respective mutant plasmids, on their resistance to phage T7 and on growth rate. We conclude that the PE motif at residues 50 and 51, and DXK motif at residues 108-110, are responsible for the enzymic reaction of HindIII.

Successful amplification of the whole intergenic spacer region of the nuclear ribosomal repeat (IGS) in Pyrenophora graminea was obtained with a PCR-based assay. Single amplification products showed length differences. Depending on the length of the IGS-PCR product, ca. 3.8 or 4.4 kb, two groups of isolates could be identified. The RFLP patterns of isolates obtained with the 6-base cutting enzymes Apal, BglII, DraI, EcoRV, HindIII and SacI were similar within each group and different between the two groups. Restriction patterns of IGS-PCR products digested with the 4-base cutting enzyme AluI were polymorphic among isolates in spite of their IGS-PCR product length. In order to characterize the long and short IGS-PCR products the restriction map is shown. The long product shows an additional HindIII site and a BglII site that is lacking in the short product. However, the latter shows a SacI site that is not present in the long IGS-PCR product. Therefore, the described PCR-RFLP analysis of the IGS appears to be a useful tool to resolve genetic variation between P. graminea isolates.

A genomic clone spanning 16 kb of the GH receptor gene was mapped and used as a probe for identifying restriction fragment length polymorphisms (RFLPs) in chickens. Several strains of meat-type and egg laying chickens were found to segregate for an HindIII RFLP located in the intron preceding exon 4. The polymorphic HindIII site overlapped with a poly(A) signal. Association of the HindIII RFLP with traits was analyzed in a random-bred White Leghorn strain in three generations using either selective or random genotyping. Both methods revealed significant association of the HindIII+ allele (presence of the poly(A) signal) with an increased juvenile body weight (130 days of age). In two meat-type strains divergently selected for size of the abdominal fat pad, the HindIII+ allele was coselected with leanness. The results indicate the presence of a genetic variant of the GH receptor gene which affects growth and abdominal fat deposition and which is relatively frequent in egg laying as well as in meat-type chickens.

We compared the classifications of strains obtained by analysis of several genetic markers to demonstrate the panmictic structure of Helicobacter pylori, previously suggested by the study of multilocus enzyme electrophoresis. A series of 39 strains, including 37 clinical isolates from patients with gastritis or ulcers from two regions of France, reference strain CIP 101260 and the Sydney strain (strain SS1), were used. They were studied by restriction fragment length polymorphism analysis of ribosomal DNA (ribotyping) using HindIII and HaeIII, by polymorphism analysis of the ureA-ureB and flaA genes by PCRRFLP using HaeIII and MboI, by vacA genotyping and by the presence or absence of the cagA gene and of the insertion sequence IS605 detected by PCR. There was a high level of genetic polymorphism over the studied strains, with 38 ribotypes, 38 restriction profiles for the ureA-ureB gene, 19 restriction profiles for the flaA gene and five combinations of the signal and midregion sequences of the vacA gene. Factorial analysis of correspondence and hierarchical clustering performed using each marker revealed that the different classifications of the strains were not correlated. This suggests there is much genetic recombination between strains and supports the hypothesis of a panmictic structure for the H. pylori species. z 1998 Published by Elsevier Science B.V.

In a collaborative study by three laboratories, arbitrarily primed polymerase chain reaction (AP-PCR), HindIII restriction enzyme analysis (REA), and pulsed-field gel electrophoresis (PFGE) using SmaI were compared for typing of Clostridium difficile. The study included 30 isolates from nosocomial outbreaks in six geographically disparate hospitals and 15 isolates from sporadic cases of C. difficile diarrhea. REA distinguished a total of 23 types representing 10 groups; AP-PCR performed at Deaconess Hospital resolved 19 types; AP-PCR performed at the Centers for Disease Control resolved 15 types. Thirty isolates exhibited degradation of larger sized fragments during processing and therefore were nontypeable by PFGE; among the remaining 15 isolates, PFGE resolved 11 types. Outbreak isolates in five different hospitals represented REA group J and constituted a single AP-PCR strain. In summary, nosocomial outbreaks of C. difficile diarrhea in five hospitals were associated with a single genetic lineage as resolved by multiple strain typing systems.

Strains (107) of L. monocytogenes were tested with a PCR-restriction enzyme analysis with two new original primers. A segment of 1395 bp containing the entire iap gene in L. monocytogenes was amplified by the PCR technique. The PCR product was cleaved with the restriction enzymes HindIII and RsaI, and the fragments generated were separated by gel electrophoresis. Two groups of serovars were obtained: one group contained serovars 1/2a and 1/2c, the other group contained serovars 1/2b, 3b and 4b. The PCR-restriction enzyme analysis method described in this paper could be a useful tool for the unambiguous division of L. monocytogenes into two serovar groups, and it could be used to study the evolution of different serotypes and groups of serotypes in foods produced in the same processing plant and processed during the same month. The RE-PCR method used can give a rapid confirm at the subgroup level in the laboratory of an epidemiological association between human disease and suspected sources of contaminated food.

UDP-glucose pyrophosphorylase (UGPase) was cloned from six American and nine European potato (Solanum tuberosum L.) cultivars. Restriction mapping of the different UGPase-cDNAs with BamHI, HindIII, and EcoRI revealed that at least two mRNA populations were present in most cultivars. Staining for UGPase activity in nondenaturing gels of proteins extracted from developing potato tubers yielded two major isozymes that were highly active and appeared to be dimeric in nature. Following sodium dodecyl sulfate-polyacrylamide gel electrophoresis, all isozymes were disassociated into a single subunit with a molecular mass of 53 kD. Since UGPase has been demonstrated to be a single-copy gene in the haploid genome of potato (A.Y. Borovkov, P.E. McClean, J.R. Sowokinos, S.H. Ruud, G.A. Secor [1995] J Plant Physiol 147: 644–652), there must be allelic differences at the UGPase locus (chromosome 11). The two alleles, designated ugpA and ugpB, were identified by the absence and presence of a BamHI site, respectively. The relative band intensities of the two cDNA populations following polymerase chain reaction amplification and agarose gel electrophoresis were related to a potato cultivar's ability to resist sweetening when exposed to cold temperatures.

We examined the role of common genetic variation in determining the consistency and magnitude of change in plasma total cholesterol (TC) levels in response to two separate changes from a high-saturated (SFA) to a low-saturated/high-polyunsaturated-fat (PUFA) diet, in a group of free-living healthy men and women. Consistent responders were defined as those whose mean difference in the change in TC was within one SD of the mean for all participants, and the remainder were defined as variable responders. DNA was obtained from 55 individuals and genotype determined at the apolipoprotein (apo) B locus (signal peptide, SP), apoCIII (C1100-T) and lipoprotein lipase (LPL) gene loci (HindIII). In the 38 consistent responders, the apoBSP24 allele was significantly more common than in the 17 individuals with a variable response (0.29 vs. 0.12; p < 0.05). No other polymorphism showed a significant frequency difference between groups. In the group as a whole, the correlation between the change in TC level in response to the first and second dietary change was 0.28 (p = 0.05), but those with one or more apoB SP24 alleles and those with the apoCIII genotype CC had a significantly higher correlation than those with other genotypes (0.46 (p = 0.05) vs. 0.12 (NS) and 0.31 (p = 0.05) vs. 0.02 (NS), respectively). In the group as a whole, mean response left TC 10% higher on the SFA than on the PUFA diet, and neither apoB nor apoCIII genotypes affected the magnitude of this response. However, individuals with the LPL HindIII genotype H+ H+ had a significantly smaller change in mean TC in response to diet than those with one or more H- allele (9.3% vs. 14.4%; p = 0.03). Thus variation at the apoB and apoCIII loci affects the consistency of response to change in dietary fat content, while variation at the LPL gene locus affects magnitude of response.

To evaluate the genetic homogeneity of Trichophyton mentagrophytes var. interdigitale, restriction enzyme analysis of mitochondrial(mt) DNA was performed on 29 isolates of T. mentagrophytes var. interdigitale isolated from Belgian or Indian patients with dermatophytosis. The restriction enzyme profiles of these mtDNAs were compared with those of the teleomorphic members composing the T. mentagrophytes complex. Using the restriction enzymes MspI, HaeIII, HindIII and BglII the restriction profiles of all the examined clinical isolates showed the same profiles as those of Arthroderma vanbreuseghemii. T. mentagrophytes var. interdigitale isolates found in Japan have been shown to have the same profiles as those of A. vanbreuseghemii. Therefore, T. mentagrophytes var. interdigitale is considered to be a highly homogeneous taxon phylogenetically related to A. vanbreuseghemii.

Desiccation by vacuum-drying inactivates the restriction endonuclease HindIII completely. However, when dried in the presence of a disaccharide such as trehalose, maltose, or sucrose, the endonuclease retains its lambda DNA-cleaving activity and produces the same digestive fragments as does the intact enzyme. Thus, the disaccharides are effective in protecting the restriction enzyme in terms of both recognition and accurate cleavage of the substrate. Among the disaccharides, trehalose protects the enzyme most effectively; and it also stabilizes the enzyme during dilution in aqueous solution. The restriction enzyme dried with trehalose maintains its activity without detectable loss for at least 4 days at 37 degrees C, but it shows reduced activity after 30-day storage at either 4 degrees C or room temperature. Trehalose also protects other restriction endonucleases, EcoRI and BamHI, from inactivation during vacuum-drying, whereas drying them alone leads to severe loss of their activity. The restriction endonucleases dried with trehalose retain their activities for at least 20 days at 4 degrees C and for 7 days at room temperature.

The GmENOD40-2 gene was isolated from a soybean genomic library and the nucleotide sequence of a 3 kb EcoRI/HindIII fragment was determined. A 1.7 kb fragment of the GmENOD40-2 promoter region was used in a transcriptional fusion construct with GUS. In transgenic Vicia nodules containing this construct, β-glucuronidase activity was detected in the pericycle of the nodule vascular bundles as well as in the root pericycle at the attachment point of the nodule

Restriction endonuclease HindIII was purified from Haemophilus influenzae Rd. Two active fractions, P1 and P2, were obtained in phosphocellulose chromatography. HindIII could be purified completely from the first fraction, P1, by subsequent DEAE-cellulose chromatography. The second fraction, P2, showed HindIII activity higher than that of P1, though it was still contaminated with some minor proteins. The HindIII in P2 fraction showed differences in stability, binding to substrate DNA, electrophoretic mobility, etc., from the HindIII in P1 fraction. It is likely that there are two forms of HindIII in the bacterial cell. The endonuclease HindIII in P2 fraction was finally purified by DNA-cellulose chromatography, though considerable loss of enzymatic activity resulted. Upon infection of the cells with phage T4, the P2 fraction in phosphocellulose chromatography almost disappeared. The presence of two forms of HindIII may be related to bacterial defense against viral infection.

To determine which of the N-acetyltransferase (NAT) alleles [monomorphic (NAT1) or polymorphic (NAT2)] are expressed in the target cells for arylamine carcinogenesis, namely normal human uroepithelial cells, cDNA was prepared from cellular RNA and amplified by polymerase chain reaction (PCR), using upstream primer 1 comprising the 5' end (nt 47-68) and either downstream primers 2 (nt 908-889) or 3 (nt 953-931) corresponding with the 3' end. With primers 1 and 2, selective for NAT1, a characteristic 861 bp DNA fragment was obtained, whereas with primers 1 and 3, selective for NAT2, a characteristic 907 bp fragment was formed. Similarly, the PCR-amplified cDNA products from the SV40-immortalized human uroepithelial cell line were also found to contain both NAT1 and NAT2. Restriction fragment length polymorphism (RFLP) analysis with HincII (digesting NAT2 to produce 659 bp and 248 bp fragments) and HindIII (digesting NAT1 to produce a 786 bp fragment) further confirmed the authenticity of the NAT alleles. Furthermore, the NAT genotypes of 38 individuals were determined by PCR amplification of lymphocyte DNA and subsequent RFLP analysis using TaqI, KpnI and BamHI. The genotypes were compared to their in vivo acetylator phenotypes which were determined by measuring 5-acetylamino-6-formylamino-3-methyluracil and 1-methylxanthine in urine following administration of caffeine. A good correlation between the genotype and phenotype was obtained in the study population and the frequency of NAT2 allele distribution was M1 > wild-type > M2 > M3. These results suggest that susceptibility to arylamine-induced bladder cancer might be influenced by both hepatic and bladder NAT and that the NAT genotype might be a useful biomarker for screening high risk individuals for bladder cancer resulting from exposure to arylamines.

Using the restriction endonucleases, Bam HI, Bgl II, Hind III and EcoRI, the alpha-gene arrangements were investigated in heterozygotes and homozygotes for the sickle cell haemoglobin (Hb S). In the heterozygotes (Hb AS) group the Hb S level showed a trimodal distribution due to presence of the normal alpha-globin genes (alpha alpha/alpha alpha) or of one (-alpha/alpha alpha) or two (-alpha/-alpha) alpha-genes deletions. The haematological analytes inversely correlated with the associated alpha-thalassaemia (alpha-thal.) genes. In the Hb S homozygotes (Hb SS), associated alpha-thalassaemia was found to ameliorate the clinical manifestations and improved the haematological values. Co-existing triple alpha-gene arrangement, alpha alpha alpha anti 3.7/, with Hb AS did not influence the haematological analytes. In Hb SS, presence of alpha alpha alpha anti 3.7/ resulted in a severe sickle cell anaemia (SCA) with a high severity index (> 11) and with frequent crises, transfusion requirements and hospitalizations. It is suggested that reduced level of alpha-chain ameliorates SCA while excess of alpha-globin chain production gives rise to a severe form of SCA.

We have examined the stability of the tandemly repeated genes that encode the ribosomal RNA in Coprinus cinereus. These genes are contained within two linked HindIII fragments in a 3.0-Mb chromosome. We monitored the size of these fragments in both mitotic and meiotic segregants using the contour-clamped homogeneous electric field (CHEF) method. No length changes were observed in the smaller HindIII fragment (100 kb; 10 repeats) among the DNAs prepared from 46 asexual spore derivatives (oidia) or 128 meiotic segregants (basidiospores from 32 tetrads). However, the larger HindIII fragment (1100 kb; 120 repeats) did exhibit variability. Substantial changes, involving up to 40% of the larger HindIII fragment were recorded in 7 of 46 oidial isolates (including 4 of 22 transformed derivatives). To learn if the changes were confined to the vegetative portion of the life cycle, we examined transmission of HindIII variants through three crosses. In the first two crosses (16 tetrads total), no changes were observed in the large HindIII fragment. However, in the third cross (16 tetrads), each tetrad showed at least one alteration. In half of the tetrads from the third cross, the altered patterns segregated 2:2, suggesting that the changes occurred after mating but prior to premeiotic DNA replication. We conclude that breakage and rejoining reactions within the rDNA are frequent and are not confined to any particular stage of the life cycle. It also appears that certain repeats are sheltered from these events. Finally, marked differences in rDNA stability were observed in the cross analyzed.

In Saudi Arabia two major forms of sickle cell anaemia (SCA) have been identified, a benign SCA is reported mainly in the Eastern province and a severe form is reported in other parts of the country. Multiple factors including associated alpha-thalassaemia, elevated Hb F and glucose-6-phosphate dehydrogenase (G-6PD) deficiency have often been reported as modifying the clinical presentation of the disease. However, these factors do not completely explain the amelioration in the clinical manifestations in SCA. More recently interest has been directed toward the investigations of the regions surrounding the beta-globin genes. Using restriction endonucleases extensive polymorphism has been identified and different haplotypes have been encountered. We initiated studies in the different regions of Saudi Arabia. Our studies on the Saudi population from different regions of the country using Hinc II and Hind III showed that the beta-globin gene haplotype ++-++ is associated with a mild sickle cell anaemia, while ----+ is associated with the severe form of the disease. Xmn I polymorphic site 5' to the G gamma gene and 7.6 kb Hpa I fragments 3' to the beta-globin gene are also associated mainly with the mild disease. This paper presents and compares the two major forms of SCA in Saudi population and relates it to the genetic heterogeneity.

We have investigated the ability of a large number of restriction enzymes to digest non-canonically hemimethylated DNA at high enzyme-to-substrate ratios. A single-stranded unmethylated phagemid was used as a template to complete synthesis of the second strand using 5-methyl-dCTP to substitute for all the deoxycytosine residues. A fragment of this double-stranded hemimethylated DNA which contains the multiple cloning site region was used as a substrate. For all the enzymes tested, at least some degree of protection from digestion is observed. Sites completely protected from digestion by their cognate enzymes are SalI, BstXI, SacI, SacII, SmaI, SstI, XhoI, PstI, HinfI, BamHI and AccI. Sites partially protected from digestion by their cognate enzymes are XbaI, HindIII, KpnI, SpeI, ClaI, EcoRI and PvuII. Knowledge of the sensitivity of commonly used restriction enzymes to hemimethylated substrates is useful for several applications, which will be discussed.

Fourteen strains of Shigella dysenteriae type 1 (Shiga bacillus) isolated from people in diverse locations from 1940 to 1987 were studied. Southern hybridization with three cloned Escherichia coli genes, Shiga-like toxin I (SLTI), frd, and ompF, was used to determine restriction fragment length polymorphism (RFLP) of the genomic DNA of these strains. Digestion with each of four restriction endonucleases generated fragments of identical size to which the frd and ompF hybridized for each of the 14 strains, indicating the conservation of these genes and their flanking sequences. In contrast, after digestion with HindIII, EcoRV, and ClaI and probing with SLTI, there were RFLP among the strains. The results showed three clones of the Shiga bacillus, and suggested that dissemination of a single clone may continue for decades within a wide geographical area.

We examined the progesterone receptor (PgR) gene in tissue from both primary human breast tumors and normal placentas, detecting restriction fragment length polymorphisms (RFLPs) with the restriction endonucleases Pst I/Sst I and HindIII. There was a general agreement of the Pst I and Sst I polymorphisms in any individual tumor, suggesting that they define two alleles in the human PgR locus, one being characterized by a deletion of about 300 base pairs with respect to the other. Both primary human breast tumor specimens (n = 36) and human term placentas (n = 48) displayed similar allele frequencies and typical mendelian distribution of these Pst I/Sst I alleles. The previously reported HindIII PgR RFLP was also investigated in 132 breast tumors. The HindIII PgR gene RFLP did not display typical mendelian distribution in the breast tumors; the factors affecting the HindIII allele frequencies are presently unknown. Neither the HindIII RFLP nor the deletion defined by Pst I and Sst I correlated with PgR expression as determined by a ligand-binding assay, suggesting that neither is related to the heterogeneity of PgR expression seen in breast tumors.

Twenty-two Bacillus licheniformis strains, freshly isolated from pasture-land, were studied for the presence of plasmid DNA. Among these strains, 14 were shown to harbor one or more plasmids of different size. Southern-hybridization experiments showed a high homology between all plasmids investigated and a 2.2-kb PvuII/HindIII fragment of pBL1, a B. licheniformis plasmid previously isolated. Three fragments of pBL1, including the 2.2-kb PvuII/HindIII region, were cloned into pJH101 vector. The resulting chimeras were able to transform Bacillus subtilis. The fragment with high homology probably contains the region with the replicative functions of plasmids from B. licheniformis species.

Biotype, genome, protein and plasmid profile diversitu amongst 40 epidemiologically unrelated strains of Helicobacter pylori was studied. Strains were API Zym biotypes II, III and IV but most (87%) were biotype II. Four subsets of strains were defined on a combination of motility (56% positive) and cytotoxin production (44% positive). A close association ( P = 0.45) between these two features was observed for 69% of strains. Each strain of H. pylori had a unique DNA type defined by either Hae III or Hind III total digest patterns and by ribopatterns, except for DNA of the rare strains not cut by these endonucleases. Strain diversity was confirmed by one-dimensional SDS-PAGE electrophoretic protein patterns. No consistent associations between cytotoxin activity and overall ribopattern or band subsets within a ribopattern were detected. Some strains (39%) contained a plasmid but the presence of plasmids was not consistently associated with either cytotoxin activity, biotype, motility or ribopattern. We conclude that the cytotoxin-producing strains of H. pylori were genomically as diverse as the non-cytotoxin producing strains.

We constructed a new vector containing the promoter and the signal sequence of E. coli phoA gene, the structural gene for the periplasmic alkaline phosphatase. One of the most useful characteristics of this vector is the unique HindIII restriction site located just at the end of the phoA signal sequence. This restriction site was generated by oligonucleotide-directed site-specific mutagenesis without changing the amino acid sequence of the signal peptide. Any kind of foreign structural gene can be easily inserted into the HindIII site by using synthetic oligonucleotides to construct a hybrid gene which has neither an extra sequence nor a deletion between the phoA signal sequence and the foreign structural gene. Human alpha-interferon gene was inserted into this HindIII site. When this hybrid gene was expressed under the control of the phoA promoter region, a low but significant activity was recovered in the cold water wash of the cells after an osmotic shock procedure.

Yeast ribosomal DNA (rDNA) was digested with the restriction endonuclease EcoRI. Eight distinct fragments were obtained with a molecular weight of 4.35 (1), 1.75 (2), 1.45 (3), 1.07 (4), 0.42 (5), 0.37 (6), 0.26 (7) and 0.22 x 10(6) (8) daltons, respectively. Except for fragment 1 with a molecular weight of 4.35 x 10(6) daltons, all fragments are derived from the multiple ribosomal transcription units. The 'spacer' sequences, on the other hand, gave rise to digestion products which are very heterogeneous in size. By analysis of the partial digestion products which are very heterogeneous in size. By analysis of the partial digestion products, together with the data obtained by digestion with a combination of two restriction enzymes (EcoRI and Hind II or Hind III) and redigestion of the Hind II-and Hind III-fragments with EcoRI, the physical map of the EcoRI cleavage sites in the ribosomal transcription unit could be established.

A screening of plasmids in 25 nonpathogenic coryneform bacteria was carried out. 11 Strains showed at least one plasmid, ranging in size from 4.2 to 55 kb. These plasmids did not encode bacteriocin production or resistance to a number of antibiotics or to ions such as arsenite, mercury(II) and cobalt(II). A detailed study of plasmid pBL100 from Brevibacterium linens is presented. pBL100 has a size of 7.75 kb, and contains single sites for the endonucleases: HindIII; PstI, BglII, EcoRI and BamHI. B. linens is easily and efficiently transformed with vectors derived from pBL1 isolated from Brevibacterium lactofermentum.

The ribosomal DNA (rDNA) of Cucurbita pepo L. has been found to consist of tandemly arrayed repeat units, most of which are 10 kilobases in length. Thirty-six repeat units, cloned into the HindIII site of pACYC 177, fall into seven classes which differ from each other in length and/or nucleotide sequence. Most of the heterogeneity occurs in noncoding portions of the repeat unit although there is some nucleotide sequence variation in the coding portion as well. Heterogeneity of base modification was observed in genomic rDNA of which two examples are: (a) all of the repeat units have three BamHI sites, one of which is unavailable for restriction in about half of the units and (b) all of the CCGG sites except one are methylated at the internal cytidine in many of the units; a second site is unmethylated in some of the units and in a very few units a third site remains unmethylated.