Reassessment of breast cancers missed during routine screening mammography: a community-based study

OBJECTIVE

The purpose of this study was to have a series of screening mammograms from routine practice, including false-negative results, reviewed by peer community-based experienced radiologists to determine the percentage of these false-negative findings that might be considered detectable.

MATERIALS AND METHODS

All screening cases for 1997 and 1998 were identified from the Carolina Mammography Registry. Mammographic assessments from community mammography practices were linked with population-based cancer outcomes. The findings of four community-based radiologists who reviewed the mammograms of 339 asymptomatic women were 93 false-negatives, 180 true-negatives, and 66 false-positives. The percentage of false-negative, true-negative and false-positive findings on breast films that reviewers evaluated was determined. The findings of the reviewers were compared with the original interpreting radiologists' assessments.

RESULTS

The overall breast-specific workup rate by the reviewing radiologists was 21%. The average workup rate for the false-negative findings was 42% (range, 35-51%). Adjusting for the 13% workup rate in the cancer-free breasts, the percentage of false-negative findings that were detectable was estimated to be 29%.

CONCLUSION

This peer review of screening mammograms from a population-based screening registry estimated a missed detectable cancer rate of 29%. Thus, 71% of cancers missed at screening would not have been worked up by peers in the same community.

Placement of endovascular embolization microcoils to localize the site of breast lesions removed at stereotactic core biopsy

In 13 cases, a breast abnormality was inadvertently removed during stereotactic core biopsy, and a 0.5- or 1.0-cm-long endovascular embolization microcoil was placed to mark the biopsy site. In seven patients, the microcoils allowed successful preoperative localization of the lesion site. In six patients, 6-month follow-up mammograms showed no change in microcoil position. Placement of embolization microcoils helped localize the site of breast lesions removed during stereotactic core biopsy.

A rapid and simple procedure to detect the presence of MVM in conditioned cell fluids or culture media

During the manufacture of biopharmaceuticals, numerous adventitious agents have been detected in Master Cell Banks, end-of-production cells as well as bulk harvest fluid. Recently, a number of large-scale production bioreactors have become infected with Minute Virus of Mice (MVM) during cGMP (current good manufacturing practices) operations, and this has resulted in both the loss of product and the need for major cleaning validation procedures to be put in place. We have developed a simple DNA extraction/PCR assay to detect the presence of MVM in cell culture supernatant (conditioned cell fluids). This highly specific assay can detect 10 or fewer genome equivalents (copies) of MVM following PCR and gel electrophoresis visualization. For routine high-throughput detection, 300-100 copies could be consistently detected. The extraction procedure was shown to reliably detect MVM at a concentration of 1 TCID50/ml. The combination of the extraction/PCR procedure establishes a powerful, sensitive, specific assay that can detect the presence of MVM sequences with a 1-day turnaround time.

Image-guided core biopsy has advantages over needle localization biopsy for the diagnosis of nonpalpable breast cancer

Image-guided core biopsy (IGCB) of nonpalpable mammographic abnormalities has gained attention as an alternative to needle-localized breast biopsy (NLB). This study evaluated IGCB in the diagnostic workup of patients with nonpalpable mammographic lesions suspicious for cancer. Eighty-six patients who underwent IGCB were compared to 85 patients who underwent NLB for the diagnosis of mammographic lesions suspicious for cancer. The incidence of positive margins was less in patients who subsequently underwent needle-localized resection in the IGCB group than in the NLB group (29 and 65%; P < 0.0001). The volume of excision was greater for patients in the IGCB group than for the NLB group (106 cm3 and 52 cm3; P < 0.0001). Patients in the IGCB group averaged 1.1 operative procedures compared with patients in the NLB group, who required an average of 1.9 operative procedures. The mean charge for an IGCB was $1011 compared to $2975 for a NLB. Subset analysis of 32 spiculated masses from the IGCB group and 21 from the NLB group showed similar advantages of IGCB over NLB. The preoperative use of IGCB for mammographically suspicious lesions can reduce the incidence of positive surgical margins and the number of surgical procedures required. The use of IGCB allows for a more efficient diagnostic workup and less expense to the patient.

Development of an improved product enhanced reverse transcriptase assay

A PCR based reverse transcriptase (RT) assay was developed that has 10(4)-fold higher sensitivity than conventional nucleotide incorporation assays and allows discrimination between false positive results generated by cellular polymerases and positives resulting from authentic RT activity. Recently, several reverse transcriptase (RT) assays have been developed where a reverse transcriptase reaction is performed on an RNA template/DNA primer combination. A specific region of the cDNA product is then amplified by the polymerase chain reaction to increase the sensitivity of cDNA detection. These reverse transcriptase assays up to 10(6)-fold more sensitive at detecting retroviruses than conventional methods. The drawback to these assays with increased sensitivity is the increased incidence of false positive results generated by cellular polymerases that can reverse transcribe. The MS2 bacteriophage RNA template and primers from one of the recently developed assays were used as the basis to develop the assay. A simple high resolution agarose gel was used as the endpoint for the assay without compromising sensitivity. In addition, the pH of the RT reaction was lowered to pH 5.5, the RT incubation was 1 h, and protease inhibitors were added to the RT reaction components. These modifications yield an assay that can discriminate between authentic RT activity and contaminating cellular polymerases.

Results of MDR-1 vector modification trial indicate that granulocyte/macrophage colony-forming unit cells do not contribute to posttransplant hematopoietic recovery following intensive systemic therapy

To formally test the hypothesis that the granulocyte/macrophage colony-forming unit (GM-CFU) cells can contribute to early hematopoietic reconstitution immediately after transplant, the frequency of genetically modified GM-CFU after retroviral vector transduction was measured by a quantitative in situ polymerase chain reaction (PCR), which is specific for the multidrug resistance-1 (MDR-1) vector, and by a quantitative GM-CFU methylcellulose plating assay. The results of this analysis showed no difference between the transduction frequency in the products of two different transduction protocols: "suspension transduction" and "stromal growth factor transduction." However, when an analysis of the frequency of cells positive for the retroviral MDR-1 vector posttransplantation was carried out, 0 of 10 patients transplanted with cells transduced by the suspension method were positive for the vector MDR-1 posttransplant, whereas 5 of 8 patients transplanted with the cells transduced by the stromal growth factor method were positive for the MDR-1 vector transcription unit by in situ or in solution PCR assay (a difference that is significant at the P = 0.0065 level by the Fisher exact test). These data suggest that only very small subsets of the GM-CFU fraction of myeloid cells, if any, contribute to the repopulation of the hematopoietic tissues that occurs following intensive systemic therapy and transplantation of autologous hematopoietic cells.

Preclinical testing of an anti-erbB-2 recombinant toxin

The performance of OLX-209 indicates it should enter phase I clinical testing. OLX-209 is a recombinant toxin targeting the erbB-2 oncoprotein. The design of OLX-209 takes advantage of improvements in immunotoxin technology to produce a molecule that is smaller and more potent than a conventional chemically linked antibody-toxin conjugate. The targeting portion of OLX-209 is a single chain antibody structure derived from the anti-erbB-2 hybridoma, e23. This antibody has unusual specificity in that it does not bind to most normal tissue including peripheral nerve or kidney tissue. Preclinical testing shows in vitro activity against breast cancer cell lines in the pM range. Efficacy testing in five models of human cancer indicates that a dose of 43 micrograms/kg causes reproducible tumor regressions. Efficacy can be achieved on a variety of schedules of administration. The effective dose results in no measurable change in serum liver enzymes when delivered to mice or primates. The LD10 is over twice the effective dose in mice. The pharmacokinetics indicate a t 1/2 of 50 minutes for both mice and cynomolgus monkeys. Serum concentrations of more than ten times those observed at the effective dose can be achieved in monkeys with no evidence of toxicity. Antigenicity of OLX-209 is surprisingly low. These results form the basis for the clinical testing phase for OLX-209.

Critical pathways in analyzing breast calcifications

Screening-detected microcalcifications are responsible for more benign biopsy results than any other mammographic lesion. The management of these lesions comes at a large cost in terms of morbidity and dollars spent. Both costs and morbidity could be reduced by decreasing the number of surgical biopsies. This could be accomplished by increasing the positive biopsy rate and by substituting core needle biopsy for surgical biopsy when appropriate. To increase the positive biopsy rate, we need to improve the preoperative evaluation of microcalcifications. A scheme is presented for the mammographic evaluation of these microcalcifications and for the appropriate use of core biopsy in the management of these lesions.

In vitro and in vivo activity of a recombinant toxin, OLX-209, which targets the erbB-2 oncoprotein

OLX-209 has readily measurable activity, is safe in experimental animals, and is efficacious in model systems. These results support the concept of OLX-209 and provide groundwork for further development of this oncoprotein targeted agent.

Type IV collagenase(s) and TIMPs modulate endothelial cell morphogenesis in vitro

It has been proposed that proteases are important in endothelial cell behavior. We examined the contribution of the gelatinase/type IV collagenase system in an in vitro model of endothelial differentiation. Human umbilical vein endothelial cells rapidly align and form networks of tubes when cultured on a basement membrane preparation, Matrigel. Zymograms of culture supernates demonstrate a 72-kD and a 92-kD gelatinase activity; the cells produce most of the 72-kD gelatinase, whereas the 92-kD activity is derived entirely from the Matrigel. Addition of antibodies against type IV gelatinase/collagenase decreases the area of the tube network. Both tissue inhibitors of metalloproteinases, TIMP-1 and TIMP-2, similarly decrease tube formation when added to cultures. Conversely, exogenous recombinant 72-kD gelatinase increases tube-forming activity. The effects of the anti-gelatinase antibodies and the TIMPs are not additive. Inhibition by either antibodies or TIMPs is greatest when they are added at culture initiation, suggesting that the protease activity is important in the early steps of morphogenesis. However, culture of the cells on Matrigel does not increase early expression of mRNA for the 72-kD gelatinase. Expression of message for the enzyme actually decreases during the course of the assay, while transcription of mRNAs for TIMPs increases, further supporting the concept that collagenases facilitate an early event in tube formation. These data demonstrate that gelatinase/type IV collagenase activity is important in endothelial cell morphogenesis on Matrigel, and suggest a role for collagenases in formation of new capillaries in vivo.

Expression of human recombinant 72 kDa gelatinase and tissue inhibitor of metalloproteinase-2 (TIMP-2): characterization of complex and free enzyme

The human 72 kDa gelatinase/type IV collagenase is a metalloproteinase that is thought to play a role in metastasis and angiogenesis. The 72 kDa progelatinase can be isolated from conditioned media as a complex with the tissue inhibitor of metalloproteinase-2 (TIMP-2). To investigate 72 kDa gelatinase-TIMP-2 interactions and to compare the activity of the complex versus that of the free enzyme, we have expressed and purified human 72 kDa progelatinase and TIMP-2 as single proteins in a recombinant vaccinia virus mammalian cell expression system. The recombinant 72 kDa progelatinase was able to bind TIMP-2, and it digested gelatin and collagen type IV after activation by p-aminophenylmercuric acid (APMA). The specific activity of the recombinant free enzyme was 20-fold higher than the activity of an APMA-treated stoichiometric complex of recombinant 72 kDa progelatinase and TIMP-2. Also, TIMP-2 caused an 86% inhibition of activity when added to the activated enzyme at a 1:1 molar ratio. Activation of the free recombinant 72 kDa progelatinase yielded the 62 kDa species and two fragments of 46 and 35 kDa that cross-reacted with monoclonal antibodies to the 72 kDa proenzyme. TIMP-2 inhibited the conversion of the recombinant proenzyme to the 62 kDa species and the appearance of the 45 and 35 kDa bands. These results suggest that TIMP-2 is not only a potent inhibitor of the activated enzyme but also prevents the generation of low-molecular-mass species and full enzymic activity from the zymogen.

Analysis of cancers missed at screening mammography

Analysis of 320 cancers found in a screened population between August 1985 and May 1990 revealed 77 cancers that were "missed" at screening mammography. The missed lesions consisted of cancers incorrectly diagnosed after mammography (false-negative results) but visible in retrospect (n = 19); cancers correctly diagnosed after mammography but visible in retrospect on an earlier mammogram (n = 47); and cancers that went undetected by the first of two readers (n = 11). Missed lesions were categorized according to type of miss, reason for the miss, breast density, lesion features, and lesion location. The missed lesion were compared with 121 cancers that were correctly diagnosed at screening mammography. The missed cancers occurred in women with denser breasts (P = .046), were less likely to demonstrate malignant microcalcifications, and were more likely to demonstrate a developing opacity as an indication of cancer (P = .005). An understanding of the characteristics of missed lesions may be a valuable aid in increasing the sensitivity of screening mammography.

Domain structure of human 72-kDa gelatinase/type IV collagenase. Characterization of proteolytic activity and identification of the tissue inhibitor of metalloproteinase-2 (TIMP-2) binding regions

The 72-kDa gelatinase/type IV collagenase, a metalloproteinase thought to play a role in metastasis and in angiogenesis, forms a noncovalent stoichiometric complex with the tissue inhibitor of metalloproteinase-2 (TIMP-2), a potent inhibitor of enzyme activity. To define the regions of the 72-kDa gelatinase responsible for TIMP-2 binding, a series of NH2- and COOH-terminal deletions of the enzyme were constructed using the polymerase chain reaction technique. The full-length and the truncated enzymes were expressed in a recombinant vaccinia virus mammalian cell expression system (Vac/T7). Two truncated enzymes ending at residues 425 (delta 426-631) and 454 (delta 455-631) were purified. Like the full-length recombinant 72-kDa gelatinase, both COOH-terminally truncated enzymes were activated with organomercurial and digested gelatin and native collagen type IV. In contrast to the full-length enzyme, delta 426-631 and delta 455-631 enzymes were less sensitive to TIMP-2 inhibition requiring 10 mol of TIMP-2/mol of enzyme to achieve maximal inhibition of enzymatic activity. The activated but not the latent forms of the delta 426-631 and delta 455-631 proteins formed a complex with TIMP-2 only when excess molar concentrations of inhibitor were used. We also expressed the 205-amino acid COOH-terminal fragment, delta 1-426, and found that it binds TIMP-2. In addition, a truncated version of the 72-kDa gelatinase lacking the NH2-terminal 78 amino acids (delta 1-78) of the proenzyme retained the ability to bind TIMP-2. These studies demonstrate that 72-kDa gelatinases lacking the COOH-terminal domain retain full enzymatic activity but acquire a reduced sensitivity to TIMP-2 inhibition. These data suggest that both the active site and the COOH-terminal tail of the 72-kDa gelatinase independently and cooperatively participate in TIMP-2 binding.

Recombinant anti-erbB2 immunotoxins containing Pseudomonas exotoxin

Immunotoxins were made using five different murine monoclonal antibodies to the human erbB2 gene product and LysPE40, a 40-kDa recombinant form of Pseudomonas exotoxin (PE) lacking its cell-binding domain. All five conjugates were specifically cytotoxic to cancer cell lines overexpressing erbB2 protein. The most active conjugate was e23-LysPE40, generated by chemical crosslinking of anti-erbB2 monoclonal antibody e23 to LysPE40. In addition, a recombinant immunotoxin, e23(Fv)PE40, was constructed that consists of the light-chain variable domain of e23 connected through a peptide linker to its heavy-chain variable domain, which in turn is fused to PE40. The recombinant protein was made in Escherichia coli, purified to near homogeneity, and shown to selectively kill cells expressing the erbB2 protooncogene. To improve the cytotoxic activity of e23(Fv)PE40, PE40 was replaced with a variant, PE38KDEL, in which the carboxyl end of PE is changed from Arg-Glu-Asp-Leu-Lys to Lys-Asp-Glu-Leu and amino acids 365-380 of PE are deleted. The e23(Fv)PE38KDEL protein inhibits the growth of tumors formed by the human gastric cancer cell line N87 in immunodeficient mice.

A successful breast cancer screening program

A private, low-cost mammography screening program in Charlotte, North Carolina, has grown from one to four fixed sites in the past 6 years and now screens more than 25,000 women annually. An ongoing medical audit of the program shows that the percentage of patients with breast cancer with positive lymph nodes has decreased from 29% to 13%, and the percentage of minimal cancers found has increased from 31% to 52%. Compliance for regular screening has remained at approximately 50% for the past 2 years. Means of increasing compliance to desired levels are discussed.

Conformational stability, folding, and ligand-binding affinity of single-chain Fv immunoglobulin fragments expressed in Escherichia coli

A fluorescein-binding single-chain Fv (scFv) was chosen as a model for the study of the physicochemical parameters associated with synthetic IgG fragments. Three such scFv proteins were designed from the primary sequences of one anti-fluorescyl monoclonal antibody (Mab 4.4.20). These were constructed with varying-length interdomain peptide linkers of between 12 and 25 residues, expressed in Escherichia coli, and the protein folding, stability, and antigen-binding characteristics were assessed. Efficient renaturation could be accomplished in vitro to yield approximately 26 mg of active scFv/L of fermentation. Scatchard analysis for fluorescein ligand binding revealed that the scFv designs come within 2-fold of the Ka = 1.99 (+/- 0.18) x 10(9) observed for the parental 4.4.20 Fab and have identical stoichiometries (n approximately 0.99). Reversible solvent denaturation studies demonstrated that the unfolding/refolding equilibria for the scFv proteins can be fit to a simple two-state model and that two of the scFv designs were found to be slightly more stable than single IgG domains (VL and CL) when assessed in terms of the free energy of unfolding, delta Gon-u, or nearly identical to other multiple domain immunoglobulin proteins such as light chains and Fab's when relative transition midpoints, Cm, are compared. Linkers which conferred conformational flexibility beyond the minimally required length of 12 residues were found to have a stabilizing effect. By these criteria of ligand-binding function and protein stability, the scFv proteins were found to be bona fide minimal replicas of their parental IgG molecules.

Single chain antibody variable regions

The use of antibodies or antibody fragments for targeting tumors (either for tumor imaging or as carriers for drugs or toxins), has encountered problems of clearance, and non-specific or inefficient binding in clinical trials. A novel approach, linking two antibody variable fragments (Fvs), with a short peptide to generate a continuous polypeptide chain, may be able to overcome some of these problems. Since these single chain antibody variable regions (scFvs), are transcribed from constructed 'genes', large-scale production in, for example, E. coli, should be straightforward.

Low-cost screening mammography: report on finances and review of 21,716 consecutive cases

A review of the results of 21,716 mammograms obtained at a low-cost screening center is presented, along with a report on the finances of that center. A total of 142 cancers were discovered, 12 of which gave false-negative results at mammography. The sensitivity was 91.5% and the specificity 90%. The positive predictive value for lesions categorized as "suspicious for malignancy" was 54%. Thirty-one percent of the cancers were "minimal," in other words, in situ or less than 1 cm in diameter and with no tumor-positive lymph nodes. An average of 42 examinations were performed each day at a cost of +28 each. Nonphysician expenses were +16 for each examination, leaving +12 per examination as professional revenue. This project demonstrates that high-quality, low-cost screening mammography can be provided if the volume is adequate and if there is sufficient attention to detail.

Single-chain antigen-binding proteins

Single-chain antigen-binding proteins are novel recombinant polypeptides, composed of an antibody variable light-chain amino acid sequence (VL) tethered to a variable heavy-chain sequence (VH) by a designed peptide that links the carboxyl terminus of the VL sequence to the amino terminus of the VH sequence. These proteins have the same specificities and affinities for their antigens as the monoclonal antibodies whose VL and VH sequences were used to construct the recombinant genes that were expressed in Escherichia coli. Three of these proteins, one derived from the sequence for a monoclonal antibody to growth hormone and two derived from the sequences of two different monoclonal antibodies to fluorescein, were designed, constructed, synthesized, purified, and assayed. These proteins are expected to have significant advantages over monoclonal antibodies in a number of applications.

Synthesis of biologically active deletion mutants of human factor VIII:C

The recent cloning and sequence analysis of human factor VIII:C (antihaemophilic factor) revealed a domain structure for the protein which can be presented as A1-A2-B-A3-C1-C2. In this report we describe the construction of two altered factor VIII:C cDNAs coding for molecules in which a part (amino acids 816 to 1598) or all of the B domain (amino acids 741 to 1689) was removed. In the latter mutant a new thrombin cleavage site has been created, which does not exist in wild-type factor VIII:C. The mutated cDNAs were cloned into eucaryotic expression vectors based on regulatory sequences of the virus SV40 and transfected into two different mammalian cell lines. Both truncated recombinant factor VIII:C molecules were secreted into the culture medium, showed full biological activity and could be activated by thrombin.

How to initiate and operate a low-cost screening mammography center

An in-depth "how-to" report on initiating and operating a low-cost screening mammography facility is presented. It is based on a successful program of this type in Charlotte, North Carolina, and includes information on feasibility determination, financial analysis, site selection and preparation, equipment, public relations, promotion, and operational details. The authors believe that use of such a model, with modification as necessary, should result in a successful program and a valuable community service.

Accumulation of ColE1 early replicative intermediates catalyzed by extracts of Escherichia coli dnaG mutant strains

To investigate the events occurring at the replication forks during DNA synthesis, we studied the replication of plasmid ColE1 DNA in vivo and in vitro, using strains of Escherichia coli carrying either the dnaG3(Ts) or dnaG308(Ts) mutation. Extracts of both mutant strains supported in vitro DNA synthesis, but the amount of [3H]TMP incorporated into DNA was always less for mutant extracts than for extracts of revertant strains, which were able to grow at 42 degrees C. Sucrose gradient analysis, Southern blot analysis, and electron microscopy showed that mutant extracts synthesize a large number of early replicative intermediates containing one or two (one on each template strand) fragments at the origin of replication and some completed molecules, either open circles or covalently closed circles. The revertant extracts synthesized more completed molecules although the fraction of templates used was about the same, 0.27 for mutant extracts and 0.21 for revertant extracts. Our results show that a mutation in dnaG causes a block in the synthesis of both leading and lagging strands after initiation, which results in the accumulation of early replicative intermediates. The average size of the newly replicated region in the early replicative intermediates is 730 bases as measured from electron micrographs of early replicative intermediates. We conclude that the DnaG protein functions in lagging strand synthesis and may be necessary for the continuation of leading strand synthesis as well.

Ectopic pro-opiolipomelanocortin: sequence of cDNA coding for beta-melanocyte-stimulating hormone and beta-endorphin

A recombinant bacterial plasmid, pMS1, was constructed that contains 318 nucleotides complementary to a portion of pro-opiolipomelanocortin (proOLMC) messenger RNA from an ectopic adrenocorticotropin-producing tumor. The cloned complementary DNA insert, which contains the sequence that codes for all of the beta-melanocyte-stimulating hormone and beta-endorphin portions of proOLMC, as well as the 3' nontranslated section, is identical to the genomic sequence. Hybridization of tumor proOLMC complementary DNA to RNA subjected to electrophoresis and transferred to a nitrocellulose filter revealed two proOLMC messenger RNA species in the tumor polyadenylated RNA, but only one in pituitary polyadenylated RNA. At least one of the tumor proOLMC messenger RNA's is similar, if not identical, to human pituitary proOLMC messenger RNA.

Solar spectral measurements in the terrestrial environment

Calibrated terrestrial solar spectra are presented from measurements made with a new instrument under diverse atmospheric conditions. The atmospheric turbidity and the amount of cloud cover were recorded simultaneously with the spectra. The two main objectives of this paper are: to provide spectral data of high enough resolution and on a broad enough wavelength scale to make the data useful for studies where spectral position and bandwidth are critical factors; and to provide in one location sets of spectra that illustrate several atmospheric effects on the solar spectrum. Interpretation of the spectra is primarily left to the reader. Direct normal, diffuse, and global spectra are illustrated.

Homology between Escherichia coli plasmids ColE1 and p15A

The location and extent of the homology between plasmids ColE1 and p15A were determined by analysis of heteroduplexes formed between them as well as with a related plasmid, pBR322, and by hybridization of radioactive deoxyribonucleic acids to restriction fragments of p15A and ColE1. The homology between the plasmids contained the entire region of ColE1 required for its replication as well as an additional 400 base pairs downstream from the origin of replication. This region on p15A, which was 980 +/- 43 base pairs, started at 0.1 of the molecular length from one end formed by cleavage with the restriction endonuclease BglI and extended to 0.54 of the molecular length from the same end. Restriction cleavage maps for the enzymes BglI, HpaI, HaeII, HaeIII, and HincII are also presented.

Cell specific antiserum to chromosome scaffold proteins

Antiserum has been raised to a chromosomal protein fraction specific for Hela cells. The immunoactivity is located in the transcriptionally inactive regions of log phase chromatin. Digestion of metaphase chromosomes results in the purification of the immunoactivity in the scaffold region of the chromosomes. Extensive nuclease digestion of the scaffolds results in loss of activity. The data suggest that some of the proteins in the scaffold area are both tight binding and cell specific and may therefore play a sophisticated role in gene expression.

Origin of replication of colicin E1 plasmid DNA

Cleavage maps of colicin E1 plasmid DNA and its smaller derivative, pNT1 DNA, were constructed by using restriction endonucleases. The nucleotide sequence of a region that contains the orgin of replication was determined. The site of the nucleotide from which DNA replication is initiated was determined with 6S L-fragments, the DNA fragment first made on colicin E1 plasmid DNA. The fragments were labeled with [gamma-32P]ATP and polynucleotide 5'-hydroxyl-kinase (ATP:5'-dephosphopolynucleotide 5'-phosphotransferase, EC 2.7.1.78) at the 5'-OH groups which were uncovered by alkali treatment. The site is one of three consecutive nucleotides, dA, dA, and dC, located at a unique position. One or a few rA residues were found to be attached to some of the DNA molecules. The transition from the primer RNA to DNA occurs in a region consisting of a segment of five A residues. Both sides of this segment are rich in G and C.

Suppression of an Escherichia coli dnaA mutation by the integrated R factor R.100.1: Change of chromosome replication origin in synchronized cultures

We have followed, by deoxyribonucleic acid-deoxyribonucleic acid hybridization, the order of replication of three chromosomal markers during a synchronous round of replication in three strains of Escherichia coli carrying a dnaAts mutation: one strain in which the F-like R factor R.100.1 was established as a plasmid and two strains in which the dnaA mutation was suppressed by the integration of R.100.1 into the chromosome. In the R+ strain at 30C, replication of the plasmid took place simultaneously with the initiation of chromosome replication at the normal origin. In the integratively suppressed Hfr strains, at 42.5 C, chromosome replication was initiated preferentially from the integrated plasmid; little or no initiation occurred at the normal origin. Similar results were obtained for the one strain tested at 30 C. For both Hfr strains at 42.5 C, the data suggest that at least part of the population replicated bidirectionally. This conclusion had been confirmed using an autoradiographic procedure. Both types of experiment indicate a wide variation in the rate of travel of individual replication forks within the population.

More precise mapping of the replication origin in Escherichia coli K-12

The origin of replication in Escherichia coli K-12 was mapped by determining the rate of marker replication during a synchronous round of replication. Four isogenic strains were made lysogenic for lambdaind(-) and for phage Mu-1, with Mu-1 integrated into a different chromosomal location in each strain. Cultures were starved for amino acids to allow completion of chromosome replication cycles and then starved for thymine in the presence of amino acids, and a synchronous cycle of replication was initiated by the addition of thymine. Samples were exposed to radioactive thymidine at intervals, deoxyribonucleic acid was extracted, and the rate of marker replication was determined by deoxyribonucleic acid-deoxyribonucleic acid hybridization to filters containing Mu-1, lambda, and E. coli deoxyribonucleic acid. The results confirm that the origin of replication is near ilv. The travel times of the replication forks, calculated from the data obtained for cultures with doubling times of approximately 40 and 61 min, are 40 and 52 min, respectively.

Size distribution and molecular polarity of newly replicated DNA in Escherichia coli

Newly synthesized DNA, in E. coli lysogenic for the phage lambda, was labeled by short pulses of [(3)H]-thymidine, isolated, and separated on the basis of size by alkaline sucrose density gradient centrifugation. The molecular polarity of this DNA was determined by hybridization with each of the separated strands of lambda DNA. The results show that, in the 3' to 5' direction, replication proceeds by synthesis of short chains that are subsequently joined to long DNA. This is true for both a polA(+) and a polA(-) strain. (The polA locus codes for DNA polymerase I.) In the 5' to 3' direction, replication proceeds continuously, by addition of nucleotides to long DNA, for the polA(+) strain. In the polA(-) strain, however, replication in the 5' to 3' direction is also discontinuous, but the discontinuities are 1-40 times less frequent than in the other direction.