EcoRI Digestion Research Articles

The human neurokinin A (substance K) receptor. Molecular cloning of the gene, chromosome localization, and isolation of cDNA from tracheal and gastric tissues

Neurokinin A (substance K) is a peptide neurotransmitter of the tachykinin family with potential as a major mediator in human airway and gastrointestinal tissues. Neurokinin A acts via a receptor (the NK-2 receptor) believed to be localized on smooth muscle cells and pharmacologically coupled to a GTP-binding protein. To characterize the human NK-2 receptor, we prepared a partial cDNA from human tracheal RNA using the polymerase chain reaction with oligonucleotide primers derived from the bovine NK-2 receptor cDNA sequence (Masu, Y., Nakayama, K., Tamaki, H., Harada, Y., Kuno, M., Nakanishi, S. (1987) Nature 329, 836-838). This partial human NK-2 receptor cDNA was used to screen a human genomic DNA library and yielded a clone, NGNK-2, of approximately 25 kilobases. Analysis of NGNK-2 indicates that it contains the entire coding sequence of the NK-2 receptor as well as 5'- and 3'-flanking sequences. The gene is organized with five exons interrupted by four introns. The complete sequence of the exons and the intron-exon junctions was determined, as were the transcription initiation site and the 3'-polyadenylation signal. Analysis of EcoRI digests of genomic DNA from human-mouse cell hybrids indicates a single gene for the human NK-2 receptor localized to chromosome 10. Sequence analysis of exons 1 and 5, where major differences occur between the human and animal species, provided information for polymerase chain reaction primers which allowed us to prepare full-length cDNA for the human NK-2 receptor. The protein predicted from the gene sequence is extended by 14 amino acids at the COOH terminus compared to the bovine and 9 residues compared to the rat molecules. The seven membrane-spanning regions are encoded by exons 1-4 and none is interrupted by introns. These regions are highly conserved among the species studied, suggesting stringent evolutionary control over these molecules.

In vitro DNA replication by cytoplasmic extracts from cells infected with african swine fever virus

A cell-free system that catalyzes DNA replication was prepared from cytoplasmic extracts of Vero cells infected with African swine fever virus (ASFV). The cells were permeabilized with lysolecithin and disrupted by mild mechanical action and the nuclei were removed by low-speed centrifugation. Extracts prepared from infected cells at the time of maximal DNA replication incorporated [α- 32P]dTTP into acid-insoluble material that was sensitive to DNase and resistant to RNase. The reaction was inhibited by phosphonoacetic acid, an inhibitor of ASFV-specific DNA polymerase. Extracts from mock-infected cells had a negligible activity. Micrococcal nuclease-treated extracts were able to replicate added virion DNA or viral replicative DNA. An increase in the mass of DNA detected by ethidium bromide staining and by dot blot hybridization with ASFV DNA showed that the incorporation was due to true replication. Plasmid DNA was also replicated, which indicates that ASFV-specific DNA polymerase does not require a virus-specific origin of replication. The pattern of fragments generated by EcoRI digestion of the in vitro product was characteristic of viral replicative DNA. Hybridization with a recombinant plasmid containing a terminal fragment of ASFV DNA confirmed the presence of dimer terminal ASFV fragments presumably generated from concatemeric replicative intermediates.

Improving beetle karyotype analysis: restriction endonuclease banding of Tenebrio molitor chromosomes

Fixed mitotic chromosomes of Tenebrio molitor have been analysed by means of C-banding and by digestion with EcoRI and AluI restriction endonucleases. The chromosomal morphology, ambiguous after conventional staining or C-banding, is much improved by digestion with restriction endonucleases. AluI gives a banding pattern similar to that obtained by C-banding, while EcoRI induces a reverse banding pattern with respect to the previous ones. The EcoRI digestion pattern of chromosomes is probably produced by extraction of a pericentromeric and equilocated highly repeated DNA. In this species, it seems that neither the compaction of the heterochromatin nor the size of the restriction target (six base pairs (bp) for EcoRI) have any effect on the amount of removable DNA. Also, a chromosomal heteromorphism for pair number 9 due to a pericentric inversion has been found in one individual by means of EcoRI treatment, that was cryptic by the other banding techniques.

A cloned chromosomal DNA fragment which differentiates Yersinia pestis from Yersinia pseudotuberculosis and Yersinia enterocolitica

Chromosomal DNA from reference Yersinia strains was digested individually with 9 restriction endonucleases. DNA fragments were separated and analyzed by electrophoresis through agarose gels. The clearest fragment patterns were obtained when EcoRI was employed. the Y. pestis fragment pattern obtained after the use of this enzyme showed the presence of a unique DNA fragment with molecular mass 1400 bp. This DNA fragment was cloned, purified, labeled with 32P and then used to probe EcoRI digests of all three Yersinia species. A strong hybridization signal was obtained with Y. pestis strain. No such signal was found with Y. pseudotuberculosis or Y. enterocolitica. These results indicate that the DNA fragment is species specific and could be used as a diagnostic DNA probe for Y. pestis.

Restriction fragment length polymorphism of mitochondrial DNA in subantarctic mussels

Mitochondrial DNA (mtDNA) variation in samples of the marine mussel Mytilus desolationis Lamy 1936, from two localities in the Kerguelen Islands are analysed by the restriction fragment length polymorphism (RFLP) method to test for panmixia among the genetic regions previously established with enzyme polymorphism data. The results of Eco RI digestions and the reduced level of DNA polymorphism inside of the archipelago compared to oceanic coasts give evidence for the absence of panmixia. Genetic data are related to the hydrology of the archipelago. It is proposed that larvae from external oceanic coasts cannot enter the Gulf of Morbihan. In the particular context of isolation from continental masses of the Kerguelen archipelago, these results provide an opportunity to combine estimations of migration rate to those of natural selection in an island model.

Extrahepatic Hepatitis B Virus Dna Sequences in Patients With Acute Hepatitis B Infection

Recent studies have demonstrated the presence of hepadnavirus-related nucleic acids in extrahepatic tissues in various animal models. The prevalence and biological significance of extrahepatic infection in humans remains undetermined. To characterize the tissue distribution and physical state of extrahepatic hepatitis B virus nucleic acids in acute hepatitis infection, we examined serum, liver and multiple extrahepatic tissues obtained at autopsy from two patients with fulminant hepatitis and one patient with resolving hepatitis who died of an unrelated cause. Southern-blot hybridization analysis was used to analyze the physical state of hepatitis B virus-related DNA. Hepatitis B virus-related RNA sequences were examined by slot-blotting total RNA extracted from corresponding tissues. Hepatitis B virus nucleic acids were demonstrated in lymph nodes, spleen, gonads, thyroid gland, kidneys, pancreas and adrenal glands. The most intense signal of hybridization was obtained with DNA extracted from lymph nodes. In general, the levels of hepatitis B virus RNA correlated with the amount of viral DNA. Fast-migrating DNA sequences resembling replicative intermediates and ranging in size from 1 to 3.2 kb were detected in EcoRI digests. Faint high-molecular-weight smears suggesting random integration also were observed. Remarkably, little or no hepatitis B virus nucleic acid was detected in the serum or liver. In control specimens obtained from hepatitis B virus carriers, most hybridizable hepatitis B virus nucleic acid was present in liver, but hepatitis B virus DNA was also detected in extrahepatic tissues. Finally, no specific histological changes were observed in extrahepatic tissues harboring hepatitis B virus.(ABSTRACT TRUNCATED AT 250 WORDS)

Candida albicans in Patients with the Acquired Immunodeficiency Syndrome: Absence of a Novel or Hypervirulent Strain

To determine whether Candida albicans in patients with AIDS represents a unique strain, C. albicans isolated from 24 patients with AIDS was compared with Candida isolated from 23 healthy adults. Resistance to 5-fluorocytosine, synthesis of amino acids and nucleotides, sugar use, and enzyme activity patterns were similar among isolates from the two groups. Molecular analysis revealed similar banding patterns of EcoRI restriction fragments of DNA between 2.5-3 and 6-7 kb. In addition, the frequency of a dimorphic 3.7-versus 4.2-kb band, identified by agarose gel electrophoresis and by probing Southern transfers of EcoRI digests with a cloned fragment of C. albicans DNA encoding 25S ribosomal RNA, was not significantly different between the AIDS-derived and control C. albicans. C. albicans isolated at different time points in the course of disease and from different sites in individual patients showed identical DNA fingerprints. The similarity in isolates of C. albicans that cause disease in AIDS patients and those present in healthy subjects suggests that the candidiasis associated with AIDS is not due to the presence of a unique or particularly virulent strain but is likely the consequence of a defect in host defense mechanisms.

An iridescent virus from Simulium vittatum (Diptera: Simuliidae) in Saskatchewan

An iridescent virus was isolated from larvae of the black fly, Simulium vittatum, collected from the South Saskatchewan River. Infected larvae displayed a brilliant blue-green iridescence. The virions occurred in paracrystalline arrays in the cytoplasm of fat body and epithelial cells. The apex-apex diameter of the icosahedral virions measured 127.7 ± 0.9 nm in negatively stained preparations. Characterization of virion structural polypeptides on SDS-polyacrylamide gels resolved 26 polypeptides ranging from 12.7 to 205.8 kDa. Analysis of EcoRI, HindIII, and PstI restriction endonuclease digests of purified viral DNA indicated that the genome had an approximate size of 153 kbp. On the basis of the restriction endonuclease profiles, this iridescent virus is a new isolate from black flies.

Differences in the organization and chromosomal allocation of satellite DNA between the European long tailed house miceMus domesticus andMus musculus

We compared the organization of satellite DNA (stDNA) and its chromosomal allocation in Mus domesticus and in Mus musculus. The two stDNAs show similar restriction fragment profiles after digestion (probed with M. domesticus stDNA) with some endonucleases of which restriction sequences are present in the 230-240 bp repetitive unit of the M. domesticus stDNA. In contrast, EcoRI digestion reveals that M. musculus stDNA lacks most of the GAATTC restriction sites, particularly at the level of the half-monomer. The chromosome distribution of stDNA (revealed by an M. domesticus stDNA probe) shows different patterns in the M. domesticus and M. musculus karyotypes, with about 60% of M. domesticus stDNA retained in the M. musculus genome. It is particularly noteworthy that the pericentromeric regions of M. musculus chromosomes 1 and X are totally devoid of M. domesticus stDNA sequences. In both groups, the differences in energy transfer between the stDNA-bound fluorochromes Hoechst 33258 and propidium iodide suggest that AT-rich repeated sequences have a much more clustered array in the M. domesticus stDNA, as if they are organized in tandem repeats longer than those of M. musculus. Considering the data as a whole, it seems likely that the evolutionary paths of the two stDNAs diverged after the generation of the ancestral 230-240 bp stDNA repetitive unit through the amplification, in the M. domesticus genome, of a family repeat which included the EcoRI GAATTC restriction sequence.

Isolation and nucleotide sequence of an autonomously replicating sequence (ARS) element functional in Candida albicans and Saccharomyces cerevisiae

An 8.6-kb fragment was isolated from an EcoRI digest of Candida albicans ATCC 10261 genomic DNA which conferred the property of autonomous replication in Saccharomyces cervisiae on the otherwise non-replicative plasmid pMK155 (5.6 kb). The DNA responsible for the replicative function was subcloned as a 1.2-kb fragment onto a non-replicative plasmid (pRC3915) containing the C. albicans URA3 and LEU2 genes to form plasmid pRC3920. This plasmid was capable of autonomous replication in both S. cerevisiae and C. albicans and transformed S. cerevisiae AH22 (leu2-) to Leu+ at a frequency of 2.15 x 10(3) transformants per microgram DNA, and transformed C. albicans SGY-243 (delta ura3) to Ura+ at a frequency of 1.91 x 10(3) transformants per microgram DNA. Sequence analysis of the cloned DNA revealed the presence of two identical regions of eleven base pairs (5'TTTTATGTTTT3') which agreed with the consensus of autonomously replicating sequence (ARS) cores functional in S. cerevisiae. In addition there were two 10/11 and numerous 9/11 matches to the core consensus. The two 11/11 matches to the consensus, CaARS1 and CaARS2, were located on opposite strands in a non-coding AT-rich region and were separated by 107 bp. Also present on the C. albicans DNA, 538 bp from the ARS cores, was a gene for 5S rRNA which showed sequence homology with several other yeast 5S rRNA genes.(ABSTRACT TRUNCATED AT 250 WORDS)

Phenotypic variation of Staphylococcus epidermidis in infection of transvenous endocardial pacemaker electrodes

Coagulase-negative staphylococci isolated from a patient with a pacemaker electrode infection were extensively evaluated by phenotypic and genotypic characterization. Findings from this evaluation were striking because different colony morphologic subtypes were recovered from blood and resected pacemaker electrodes. Staphylococci from each colony subtype (LBL, LBV, LBP, LBS) were identified as slime-producing strains of Staphylococcus epidermidis sensu stricto. Direct plating of isolates from a restricted electrode revealed a mixture of colony phenotypes when examined on a high-salt, low-glucose medium, Memphis agar. Bacteriophage typing employing 17 different phages and plasmid profile analysis were largely unsuccessful in further characterizing bacterial cells of each of the four colony morphotypes. On the other hand, restriction endonuclease analysis by EcoRI digestion of the chromosomal DNA demonstrated the probable common clonal origin of the four colony phenotypes.

Unmethylated regions in the intergenic spacer of maize and teosinte ribosomal RNA genes

The restriction endonucleases Hpa II and Msp I were used to examine cytosine methylation in the ribosomal RNA genes (rDNA) of inbred lines of maize and species of teosinte. In all of the rDNAs examined, Msp I (not sensitive to mCpG) digestion yielded a distribution of lower molecular weight fragments indicative of multiple recognition sites. The majority of the rDNA arrays in an individual were inaccessible to Hpa II (sensitive to mCpG) cleavage, but a significant fraction (10-25%) was cleaved at least once by Hpa II into repeat unit length fragments (9.1 kbp). In some maize inbred lines, one or two additional fragment populations (less than 9.1 kbp in length) were also produced by Hpa II digestion. All of the unmethylated Hpa II sites mapped to the intergenic spacer (IGS), and the major unmethylated site was located approximately 800 bp 5' to the start of the 18S RNA coding sequence. An Eco RI polymorphism, present in the 26S gene of certain inbred lines and hybrids, was utilized to investigate the organization of unmethylated repeat units in the rDNA array. In double digest experiments with Hpa II/Eco RI, the fragments from repeat units with two Eco RI sites were sensitive to Hpa II digestion, whereas, the fragments from repeat units with a single Eco RI site were almost completely resistant to Hpa II digestion. Similar digestion patterns were also observed in Eco RII (sensitive to mCNG)/Eco RI digests. These results suggest that unmethylated and Eco RI polymorphic sites occur in the same repeat units.

Cloning and nucleotide sequence analysis of the human β-microseminoprotein gene

β-microseminoprotein (MSP) is a small protein (94 amino acids) synthesized by the epithelial cells of the prostate gland and secreted into the seminal plasma. Restriction endonuclease mapping of human genomic DNA with a human MSP cDNA probe identified a 19 kilobase (Kb) hybridizing band in both EcoRI and BamHI digestions. Subsequently, the 19 Kb EcoRI fragment of human genomic DNA containing the MSP gene was isolated and cloned into an EMBL4 phage vector. Screening of the recombinant phages resulted in the isolation of one clone containing the MSP gene. Restriction endonuclease mapping and sequence analysis of this clone revealed the human MSP gene of approximately 15 Kb in length. The gene contains four exons and three large introns of approximately 6, 1, and 7 Kb.

A highly repeated retropseudogene-like sequence in DNA of the redbreasted merganser ( Mergus serrator)

Two highly repeated nucleotide sequences (RBMI and RBMII) cloned from an EcoRI digest of DNA of the redbreasted merganser ( Mergus serrator) account for approx. 5 to 10% of the DNA of M. serrator and the closely related Mergus merganser. Complete DNA digestion of seven members of the Mergini with EcoRI produces distinct, relatively species-specific patterns of a few high-M r (>1.5 kb) fragments of RBMI-like material. In such digests RBMII forms ladder-type patterns with monomers of approx. 200 bp. The sequence of a cloned 2.6-kb RBMI fragment from M. serrator contains several extended (up to 70 bp) and modified poly(dA) sequences, two open reading frames in opposite orientation to the longest poly(dA) sequence and two direct 10-bp repeats suggesting that RBMI is a rearranged retropseudogene-like element.

Cloning and sequencing of mammalian glutathione reductase cDNA

The molecular cloning of a partial cDNA to mouse glutathione reductase mRNA and of a full-length cDNA to the mRNA of the human enzyme is described. An initial cDNA clone designated lambda GRM-B11 was isolated by plaque-screening of an induced mouse cDNA expression library in the lambda gt11 vector with a rabbit antibody probe to human glutathione reductase. 125Iodine-labelled whole anti-rabbit immunoglobulin was used as second antibody. EcoRI digestion of the lambda GRM-B11 clone released a 720-bp fragment which was identified as a partial mouse glutathione reductase cDNA by the following techniques. (a) Escherichia coli Y1089 lysogenized with lambda GRM-B11 could be induced to synthesize a recombinant polypeptide whose antigenicity to anti-(glutathione reductase) serum was established by SDS/polyacrylamide gel electrophoresis and subsequent immunoblotting. (b) The GRM-B11 sequence, recloned in the Bluescript vector to give the plasmid pGRM-B11, was found to code for a polypeptide consisting of 242 amino acid residues exhibiting 82% identities with the known amino acid sequence of the human glutathione reductase from position 77 to 318. The insert of the pGRM-B11 plasmid was used as a bona fide nucleic acid probe to screen mouse and human cDNA libraries prepared in the lambda gt11 or in the lambda gt10 vector. The first full-length cDNA clone (lambda GRH-Mev10) was identified in a human cDNA library based on RNA of human placental cells. Its insert was composed of three EcoRI fragments of 720, 613 and 336 bp. The three fragments were recloned in the Bluescript vector and sequenced. The largest fragment (pGRH-B) is colinear with the mouse sequence cloned in the pGRM-B11 plasmid. The fragment of intermediate size (pGRH-CT) comprises the 3' end of the mRNA and the poly(A) tail while the short fragment (pGRH-NT) corresponds to the 5' region of the mRNA. The amino acid sequence deduced from the nucleotide sequences of the three subclones is identical with the known sequence of the mature glutathione reductase from human erythrocytes in all 478 positions.

Regulation of Elastin Gene Expression: Evidence for Functional Promoter Activity in the 5′-Flanking Region of the Human Gene

Analysis of nucleotide sequences in the 5'-flanking region of the human elastin gene has revealed several unusual features, suggesting that regulation of elastin gene expression is complex. To identify any cis-acting regulatory promoter elements, a 35-kb fragment of DNA (CosE) was isolated from a human genomic cosmid library by hybridizations with a human elastin cDNA. Southern blots of EcoRI digests of CosE DNA, utilizing a 5'-end labeled 21-mer oligonucleotide corresponding to the signal sequence of elastin, revealed the presence of a single 7.8-kb genomic fragment. Partial dideoxynucleotide sequencing of this EcoRI genomic subclone revealed that it extended approximately 2.5 kb 3' of the translation initiation site (ATG), encompassing exon 1 and a portion of the first intron, while the remaining DNA encompassed the 5'-flanking region. Exonuclease III digestion (3'----5') was performed to remove sequences of the first intron and first exon, including the ATG site. One clone, approximately 5 kb in size, had the 3' end located 14 bp upstream of the ATG site. A 462-bp 3' portion of this 5-kb fragment was subcloned into a Bluescript/CAT chimeric plasmid (pBS0CAT) to generate an elastin gene promoter/CAT reporter gene construct (pEP6CAT). Transient transfection experiments with pEP6CAT using human skin fibroblasts, human HT-1080, mouse NIH-3T3, or freshly isolated neonatal rat aortic smooth muscle cells revealed significant CAT activity in each cell line. These results suggest that the 5'-flanking region of the elastin gene contains the cis-acting regulatory elements necessary for transcription. The chimeric plasmid pEP6CAT provides a means to study the transcriptional control of elastin gene expression by exogenous affector molecules, as well as in human dermatologic diseases.

A phosphate group at the cos ends of phage lambda DNA is not a prerequisite for in vitro packaging: an alternative method for constructing genomic libraries using a new phasmid vector, λpGY97

It is shown here that the phosphate groups at the cos ends of phage λ DNA are not a prerequisite for in vitro packaging. Molecules with phosphatase-treated cos ends are packaged in vitro as efficiently as native λ DNA. This observation can be used for an alternative strategy to improve the efficiency of gene library construction, since cos-cos ligation decreases in vitro encapsidation and infectivity. Dephosphorylated cos ends and a new phasmid vector λpGY97 have been used to construct a representative gene bank of alfalfa in a Mcr − (5-methylcytosine resstriction deficient) Escherichia coli host strain. These recombinant clones can be propagated as phages or more conveniently as plasmids in recA − E. coli , to prevent possible homologous recombination events between repetitive sequences of the insert that would otherwise interfere with clone stability. The 5–19-kb inserts can be easily recloned as plasmids from the recombinant phasmids with simple EcoRI digestion and re-ligation. This observation also implies that the construction of gene libraries in cosmid vectors can be made more efficient if cos-cos ligates were cleaved by λ terminase just before in vitro packaging.

Diversity and stability of restriction enzyme profiles of plasmid DNA from methicillin-resistant Staphylococcus aureus

Nosocomial infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a significant epidemiological problem. Detecting the sources of epidemic strains and preventing their access to patients, however, depend upon the availability of techniques to reliably distinguish among MRSA strains. We evaluated restriction enzyme analysis of plasmid DNA for use as an epidemiological marker of MRSA strains. The diversity of plasmid types was assessed by examining 120 clinical and environmental MRSA isolates from five southern California hospitals and from the American Type Culture Collection. Thirty-seven distinctive EcoRI digestion patterns were observed. We characterized each strain by the number of plasmids it contained and the sizes of the fragments that were generated by EcoRI. Very few of the isolates (4.2%) lacked plasmids, and some (6.7%) contained DNA that was not digested by EcoRI. Several isolates (12.5%) contained two or more plasmids. We were able to assess the stability of MRSA plasmid types by tracking epidemic strains over a 2-year period. We also examined successive isolates from 10 individual patients during their hospitalization. In all but one case, the patient's plasmid profiles remained unchanged. We conclude that the diversity and stability of MRSA plasmid types make them excellent epidemiological markers. In support of this conclusion, we found that our data provided significant epidemiological insights. Two epidemic strains, accounting for more than half of the infections, were identified in the five hospitals. The remaining cases were sporadic, caused by MRSA strains that appeared very infrequently and that may have originated from sources outside the hospitals.

ラットのアクチン遺伝子関連配列に検出された多型性

Southern blot hybridization of EcoRI digests of DNAs from 13 rat strains using human cardiac actin gene as a probe revealed polymorphisms in actin-related sequences of rats. EcoRI fragments of 11 kb, 7 kb, 6 kb, 5 kb, 4.5 kb and 4 kb detected in several strains were absent in the remaining strains. The presence of these fragments was suggested to be due to presence of extra sequences homologous to the actin genes, such as processed pseudogenes, in the particular strains. The 13 strains were assigned to each of 7 specific patterns of the polymorphic EcoRI fragments. It was concluded that the polymorphisms of actin-related sequences should be useful for genetic monitoring of laboratory rats.

Neoplastic angioendotheliosis: demonstration of immunoglobulin gene rearrangements by the Southern blot hybridization technique

Using the Southern blot hybridization technique, two cases of 'neoplastic angioendotheliosis' (NAE) were examined for immunoglobulin gene rearrangements. For DNA analysis, frozen kidney (Case 1) and lung (Case 2) tissue, in which intravascular neoplastic cells were abundant, were used. In each case rearrangements were observed in both heavy and light chain genes. On examination of the heavy chain gene, the JH DNA probe detected one rearranged band in Case 1 and two in Case 2 after EcoRI digestion. On examination of the light chain genes, the C kappa DNA probe revealed one rearranged band in Case 1 and two in Case 2 after BamHI digestion, while the C lambda 2 DNA probe revealed only germline configurations after EcoRI digestion in each case. Thus, B-lymphocytic differentiation at the gene level was demonstrated in neoplastic cells in both cases. Since no more than two rearrangements were detected in each immunoglobulin gene, the intravascular neoplastic cells were considered to be monoclonal in nature.