NaeI endonuclease binding to pBR322 DNA induces looping

Previous work has demonstrated the existence of both resistant and cleavable NaeI sites. Cleavable sites introduced on exogenous DNA can act in trans to increase the catalysis of NaeI endonuclease cleavage at resistant sites without affecting the apparent binding affinity of the enzyme for the resistant site [Conrad, M., & Topal, M. D. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 9707-9711]. This activation suggests allosteric regulation of NaeI cleavage by distant cis- and trans-acting sites in DNAs containing both resistant and cleavable sites. Plasmid pBR322 contains four NaeI sites, at least one of which is resistant to cleavage. Electron microscopy is used here to demonstrate that NaeI endonuclease simultaneously binds to multiple recognition sites in pBR322 DNA to form loops with NaeI protein bound at the loop's base. The maximum number of loops formed with a common base suggests four binding sites per enzyme molecule. Looping was inhibited by addition of enzyme-saturating amounts of double-stranded oligonucleotide containing an NaeI site, whereas another double-strand oligonucleotide without the NaeI site had no effect. The number of loops seen was not above background when double-stranded M13 DNA, which contains only a single NaeI recognition site, was used as substrate.

Effects of bulge composition and flanking sequence on the kinking of DNA by bulged bases

We recently showed that bulged bases kink duplex DNA, with the degree of kinking increasing in roughly equal increments as the number of bases in the bulge increases from one to four [Hsieh, C.-H., & Griffith, J.D. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 4833-4837]. Here we have examined the kinking of DNA by single A, C, G, or T bulges with different neighboring base pairs. Synthetic 30 base pair (bp) duplex DNAs containing 2 single-base bulges spaced by 10 bp were ligated head to tail, and their electrophoretic behavior in highly cross-linked gels was examined. All bulge-containing DNAs showed marked electrophoretic retardations as compared to non-bulge-containing DNA. Regardless of the sequence of the flanking base pairs, purine bulges produced greater retardations than pyrimidine bulges. Furthermore, C and T bulges produced the same retardations as did G and A bulges. Bulged DNA containing different flanking base pairs showed marked differences in electrophoretic mobility. For C-bulged DNA, the greatest retardations were observed with G.C neighbors, the least with T.A neighbors, and an intermediate amount with a mixture of neighboring base pairs. For A-bulged DNA, the retardations were greatest with G.C neighbors, less with T.A neighbors, even less with a mixture of neighboring base pairs, and finally least with C.G neighbors. Thus flanking base pairs affect C-bulged DNA and A-bulged DNA differently, and G.C and C.G flanking base pairs were seen to have very different effects. These results imply an important role of base stacking in determining how neighboring base pairs influence the kinking of DNA by a single-base bulge.

Gating of auditory response in schizophrenics and normal controls. Effects of recording site and stimulation interval on the P50 wave

Auditory evoked potentials were recorded using a paired stimulus, conditioning-testing paradigm from 14 schizophrenic patients and 13 normal subjects with no family history of psychotic disorder. Previous studies of the vertex P50 wave using this paradigm have demonstrated a possible sensory gating deficit in schizophrenics, as shown by their failure to diminish the response to a test stimulus presented 500 ms after a conditioning stimulus. Recordings were made at Cz, Fz, C3, T3, C4, and T4, to compare effects at different recording sites with this paradigm. Schizophrenics had significantly poorer sensory gating than normals, with the most significant difference between the groups at Cz. In addition to the 500 ms interval, subjects were also recorded at a conditioning-testing interval of 100 ms. Most schizophrenics showed normal sensory gating at the 100 ms interval, despite their abnormalities at 500 ms. The results indicate that Cz is optimal recording site for this paradigm, and that gating abnormalities in schizophrenic subjects are limited to specific interstimulus intervals.

The reproducibility of intravascular ultrasound imaging in vitro

To determine which factors may affect the image quality when an intravascular ultrasound catheter is used in vivo, the influence of blood, temperature change, and contrast media were evaluated. In addition, to confirm the reproducibility of intravascular ultrasound imaging to measure cross-sectional lumen area, intraobserver and interobserver variability were determined. The findings indicated that ultrasound images in blood are mildly attenuated, that changes from room temperature to body temperature do not have a significant impact on the image quality, that contrast media attenuates the image intensity in a dose-dependent manner, and that the intravascular ultrasound imaging catheter provides a reproducible method for measuring arterial lumen area with excellent intraobserver and interobserver correlation.

Three-stranded paranemic joints: architecture, topological constraints and movement

The RecA and SSB proteins will catalyze the joining of two DNA molecules containing homologous sequences but lacking homologous ends in a reaction termed paranemic joining. The absence of homologous ends can be achieved by (1) pairing two circular DNAs or (2) using linear DNA(s) with ends lacking homology to the pairing partner. Here we have used electron microscopy (EM) to examine such pairings. Circular M13 single-stranded (ss) DNA enveloped by RecA protein into a presynaptic filament was paired with linear M13mp7 double-stranded (ds) DNA containing non-M13 sequences at its ends. Joint complexes were frequently seen in which the dsDNA was joined with the presynaptic filament over several kilobase (10(3) bases) lengths of the dsDNA. In this region, the presynaptic filament appeared disorganized as contrasted to the customary helical structure of the filament containing only a single strand of DNA. The same ultrastructure, but with greater detail, was observed when the samples were prepared for EM without fixation using a new method of fast-freezing and freeze-drying. EM immunogold staining demonstrated the presence of SSB protein in the disorganized region containing all three strands, but not in the regular helically arranged region. Psoralen photo-crosslinking of the DNA in the joint complexes revealed that the three DNA strands were in close proximity only over a single short (200 to 300 base-pairs) region. The joining of nicked circular M13 dsDNA and presynaptic filaments containing circular M13 ssDNA resulted in the intertwining of the dsDNA about the circular presynaptic filament. The joints produced in this case were short, as was the single region of psoralen photo-crosslinking of the three DNA strands. A model of how these long three-stranded joints form is presented involving the movement of a short "true" paranemic joint along the presynaptic filament.

Assessment of normal and atherosclerotic arterial wall thickness with an intravascular ultrasound imaging catheter

A prototype intravascular ultrasound imaging catheter with a 20 MHz transducer was used to obtain 59 cross-sectional images in 14 segments of human atherosclerotic arteries. Three distinct components of the arterial wall were visualized on the ultrasound images: a highly reflective intima, an echolucent media, and a moderately reflective adventitia. Images were obtained at 1 mm increments in vitro and were compared with histologic sections at the same levels. Measurements of the arterial layers showed a close correlation between ultrasound images and histologic sections for the thickness of the intimal plaque (r = 0.91), the media (r = 0.83), and the total wall thickness (r = 0.85). The ultrasound images overestimated the mean intimal and total wall thickness by 0.3 mm and 0.7 mm compared to measurements in histologic sections (p less than 0.001). Intravascular imaging with high-frequency ultrasound is an accurate method for measuring microanatomic arterial dimensions and the extent of atheromatous involvement of the arterial wall. This method could represent an important adjunct to traditional angiographic techniques for assessing the severity of atherosclerosis.

Intravascular ultrasonic imaging

Because conventional imaging methods are inadequate for evaluating human coronary arteries in vivo, an intravascular ultrasonic imaging catheter was developed that allows the arterial wall to be studied in cross-section from within the artery. The catheter incorporates a mechanically rotating 20-MHz transducer, which is designed so that the ringdown occurs within the catheter and imaging is permitted up to the catheter's surface. The device rotates at 1800-rpm within a plastic sleeve and provides real-time cross-sectional images at 30 frames/sec. Preliminary experimental and clinical studies indicate that the intravascular ultrasonic imaging catheter could play a valuable role in providing preoperative information concerning arterial wall thickness and tissue characteristics, in distinguishing normal from diseased arterial wall structures during therapeutic intervention, and in assessing the results of intervention.

Preparation for human study of pesticide applicators: sister chromatid exchanges and chromosome aberrations in cultured human lymphocytes exposed to selected fumigants

In preparation for a human study of worker exposure to grain fumigants and pesticides, we decided to screen commonly used fumigants for genotoxic effects in vitro. This research strategy was employed to test the possibility that structurally simple chemicals might have similar genotoxic properties in vivo and in vitro. As a first step, we designed our in vitro protocol to mimic to the extent possible, a single in vivo exposure of lymphocytes to fumigants. Go lymphocytes were treated with different doses of carbon tetrachloride, carbon disulfide, methyl bromide, chloropicrin, and melathion with and without addition of rat liver homogenate for 1/2 hour, washed free of toxicant, and stimulated with PHA. After culture, the prepared slides were studied for chromosome aberrations and SCEs. Malathion, methyl bromide, and chloropicrin significantly induced SCEs without S-9. Carbon disulfide alone required S-9 for significant SCE induction. Chromosome aberrations were significantly increased by malathion and methyl bromide. Carbon tetrachloride failed to induce SCEs or chromosome aberrations with or without S-9. We concluded from these preliminary studies and other comparable work that the fumigants studied here may be less likely to express genotoxicity in terms of SCEs or chromosome aberrations than ethylene oxide or phosphine given a single short-term in vivo exposure. The final design of our human study was altered to focus on seasonal worker exposure rather than on a single exposure event.

Visualization of RecA protein and its complexes with DNA by quick-freeze/deep-etch electron microscopy

Freeze-etch electron microscopy of pure RecA protein aggregates, as well as of RecA protein complexes on single-stranded and double-stranded DNA formed with various nucleotides, has permitted a clearer discrimination between the two different helical polymers that this protein forms. Both are continuous, single-start, right-handed helices; however, the form observed when ATP or non-hydrolyzable ATP analogs are present has a pitch of 9.5 nm and a diameter of 10 nm, while the other form, observed in the absence of ATP or its analogs, or in the presence of ADP, has a pitch of 6 nm and a diameter of 12 nm. The former "long pitch" helix is found only when RecA protein is bound to DNA. The latter "short pitch" helix is also observed in pure RecA protein polymers (also termed rods) and in the needle-like paracrystals of RecA protein that form in the presence of magnesium or spermidine ions, representing bundles of rods closely packed in register. Addition of ATP or non-hydrolyzable ATP analogs in the absence of DNA dissociates the pure RecA protein crystals, as well as individual helical rods, into short curvilinear chains of attached monomers. These chains typically form closed, circular rings of 7(+/- 1) protein monomers, similar in construction to a single turn of the RecA protein helix, but significantly broader in diameter. The role of ATP in interconverting the various polymeric forms of RecA protein is discussed within the context that ATP functions as a reversible allosteric effector of RecA protein, much as it mediates reversible conformational changes in other vectoral motor proteins such as myosin, dynein, kinesin and the 70,000 Mr "heat shock" ATPases. We discuss how cyclic conversions back and forth between the short- and long-pitch conformations of RecA protein could mediate in reversible single-stranded and double-stranded DNA interactions during the search for homology.

Trigeminal nerve section induces Fos-like immunoreactivity (FLI) in brainstem and decreases FLI in sensory cortex

Transecting the infraorbital nerve to the rat whiskers induced Fos-like immunoreactivity (FLI) in lamina I and II neuronal nuclei of the spinal trigeminal nucleus pars caudalis (Sp5c). The Fos-like immunostaining persisted for several weeks. The prolonged expression of FLI in Sp5c could be related to persistent activity in the sectioned nerve, or to trophic effects of injured ganglion neurons on brainstem cells. We postulate that Fos and related proteins may be involved in mediating alterations in gene expression associated with relatively long-term CNS adaptations to peripheral nerve injuries. Surprisingly, FLI decreased in contralateral sensory cortex, mainly in layers 2, 3 and 6, up to several days after the lesion. These decreases of cortical FLI may be due to decreased sensory neuronal activity, and/or to reducing the trophic influence of thalamic inputs on cortical neurons.

Biochemical and biological markers: implications for epidemiologic studies

Given that a major task for environmental epidemiology is to provide clear evidence of immediate and long-term health risks so that appropriate preventive measures can be taken, biochemical and biological markers of potentially hazardous environmental exposures are of great interest and possibly of great value. Such markers fall into two discrete classes: (1) those quantitatively related to the exposure itself, reflecting the magnitude of such exposures or the body burden of the pollutants, and (2) those markers that reflect the biological response to such exposures. In this paper we discuss the use of biochemical and biological markers in epidemiologic studies. Methods are presented for the use of markers to decrease misclassification errors in exposure studies. Relationships are derived that give minimum required values for laboratory sensitivity and specificity. Markers are also discussed in terms of some of the inherent problems in their use (e.g., ethical and legal considerations) and the likelihood of acceptance by participants in epidemiologic studies, researchers, regulators, and health professionals.

Human genotoxicity: pesticide applicators and phosphine

Fumigant applicators who, 6 weeks to 3 months earlier, were exposed to phosphine, a common grain fumigant, or to phosphine and other pesticides had significantly increased stable chromosome rearrangements, primarily translocations in G-banded lymphocytes. Less stable aberrations including chromatid deletions and gaps were significantly increased only during the application season, but not at this later time point. During fumigant application, measured exposure to phosphine exceeds accepted national standards. Because phosphine is also used as a dopant in the microchip industry and is generated in waste treatment, the possibility of more widespread exposure and long-term health sequelae must be considered.

Intravascular ultrasound cross-sectional arterial imaging before and after balloon angioplasty in vitro

A prototype ultrasound imaging catheter was evaluated in vitro using 17 human atherosclerotic artery segments before and after balloon dilatation angioplasty. The catheter was 1.2 mm in diameter and incorporated a single 20-MHz ultrasound transducer to obtain cross-sectional images of the arterial lumen. In 15 of the 17 (88%) arteries, high quality images were obtained, which demonstrated clear demarcation between the lumen and the endothelium, the atheroma plaque, the muscular media, and the adventitia. Qualitative characteristics of plaque disruption, dissection, and residual flaps were readily visible. In addition, quantitative information about cross-sectional lumen area was obtained before and after balloon dilatation. The mean cross-sectional lumen area increased from 8.7 to 15.1 mm2 (p less than 0.01) following balloon dilatation. The lumen area measured from the ultrasound images following dilatation correlated closely with the area measured from histologic sections (r = 0.88). The results from this study indicate that a small-diameter ultrasound imaging catheter can be developed that will provide high-resolution qualitative and quantitative information during peripheral and coronary angioplasty.

Antibiotic proteins of human polymorphonuclear leukocytes

Nine polypeptide peaks with antibiotic activity were resolved from human polymorphonuclear leukocyte azurophil granule membranes. All but 1 of the 12 constituent polypeptides were identified by N-terminal sequence analysis. Near quantitative recovery of protein and activity permitted an assessment of the contribution of each species to the overall respiratory-burst-independent antimicrobial capacity of the cell. Three uncharacterized polypeptides were discovered, including two broad-spectrum antibiotics. One of these, a defensin that we have designated human neutrophil antimicrobial peptide 4, was more potent than previously described defensins but represented less than 1% of the total protein. The other, named azurocidin, was abundant and comparable to bactericidal permeability-increasing factor in its contribution to the killing of Escherichia coli.

Hyperacute rejection of the transplanted mouse heart

Mouse hearts transplanted heterotopically to MHC-disparate recipients can be hyperacutely rejected (HAR) after a single or 3 sequential donor type skin grafts, or a single intradermal injection of lymphoid cells. In the combinations tested, not all hearts are HAR; most of them are rejected in accelerated fashion. Our results with transplanted rat hearts are similar, even in a genetic combination for which HAR of all hearts has been reported. However, in rats, HAR tends to occur more rapidly and to be associated with more-intense vascular changes. Transfer of serum from mice or rats sensitized by 3 sequential skin grafts likewise resulted in occasional hyperacute but never accelerated rejection. Transfer of lymph node cells from mice sensitized with a single skin graft always resulted in accelerated but never in hyperacute rejection; transfer of cells after 3 sequential skin grafts caused neither accelerated nor hyperacute rejection.

Cancer mortality in U.S. counties with hazardous waste sites and ground water pollution

Since the late 1950s, more than 750 million tons of toxic chemical wastes have been discarded in an estimated 30,000 to 50,000 hazardous waste sites (HWSs). Uncontrolled discarding of chemical wastes creates the potential for risks to human health. Utilizing the National Priorities Listing (NPL) of hazardous waste sites developed by the United States Environmental Protection Agency (EPA), this study identified 593 waste sites in 339 U.S. counties in 49 states with analytical evidence of contaminated ground drinking water providing a sole source water supply. For each identified county, age-adjusted, site-specific cancer mortality rates for 13 major sites for the decade 1970-1979, for white males and females, were extracted from U.S. Cancer Mortality and Trends 1950-1979. Also, HWS and non-HWS counties that showed excess numbers of deaths were enumerated for each cancer selected. Significant associations (p less than .002) between excess deaths and all HWS counties were shown for cancers of the lung, bladder, esophagus, stomach, large intestine, and rectum for white males; and for cancers of the lung, breast, bladder, stomach, large intestine, and rectum for white females when compared to all non-HWS counties. There were no consistent geographical patterns that suggested a broad distribution of gastrointestinal cancers associated with HWSs throughout the United States, although we did identify a cluster of excess gastrointestinal cancers in counties within states located in EPA Region 3 (Delaware, Maryland, Pennsylvania, Virginia, West Virginia).(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular cloning, characterization, and expression of a human 14-kDa lectin

Full length cDNAs coding for a 14-kDa beta-galactoside binding lectin have been isolated from HL-60 cells and human placenta. Oligonucleotide probes based on a pentapeptide present in several partial sequences of homologous human lectins were used to screen a lambda GT10 HL-60 cDNA library. The HL-60 cDNA clones that were isolated were used to design a synthetic primer representing the 3'-untranslated region of the HL-60 lectin. This primer was then used to synthesize a lambda GT10 human placenta cDNA library, and restriction fragments of the HL-60 cDNA clones were used to screen the library. The cDNA clones for both HL-60 and placenta lectin had identical sequences with short 5'- and 3'-untranslated regions and coded for a 135-amino acid protein which lacks a hydrophobic signal peptide sequence. Biochemical data show that, despite the presence of a possible N-linked glycosylation site, the protein is not glycosylated. Northern and Southern blot analyses indicate that the 14-kDa lectin is encoded for by a single gene. The lectin cDNA was expressed in Escherichia coli and biologically active protein was purified from cell lysates by affinity chromatography.

Gap formation is associated with methyl-directed mismatch correction under conditions of restricted DNA synthesis

A covalently closed, circular heteroduplex containing a G-T mismatch and a single hemimethylated d(GATC) site is subject to efficient methyl-directed mismatch correction in Escherichia coli extracts when repair DNA synthesis is severely restricted by limiting the concentration of exogenously supplied deoxyribonucleoside-5'-triphosphates or by supplementing reactions with chain-terminating 2',3'-dideoxynucleoside triphosphates. However, repair under these conditions results in formation of a single-strand gap in the region of the molecule containing the mismatch and the d(GATC) site. These findings indicate that repair DNA synthesis required for methyl-directed correction can initiate in the vicinity of the mispair, and they are most consistent with a repair reaction involving 3'----5' excision (or strand displacement) from the d(GATC) site followed by 5'----3' repair DNA synthesis initiating in the vicinity of the mismatch.

Isolation of a complementary DNA clone encoding a precursor to human eosinophil major basic protein

A 14-kD protein was purified from human PMNs and its NH2-terminal sequence was determined. Comparison of a portion of the NH2-terminal sequence of this protein to the recently reported NH2-terminal sequence of eosinophil major basic protein (MBP) showed them to be identical. To aid further characterization of the structural and functional properties of this molecule, we isolated from an HL-60 cDNA library a single class of cDNA clones whose sequence matched exactly the NH2-terminal amino acid sequence of the 14-kD polypeptide. Northern analysis of HL-60 cells suggests that MBP is constitutively expressed in HL-60 cells and is highly transcribed from a single copy gene. The sequence of the full-length cDNA clones predicts that MBP is synthesized as a 23-kD precursor form (pro-MBP) which is subsequently cleaved to release the mature 14-kD MBP. The putative pro-MBP has a predicted pI of 6.0, but both the charged and the hydrophobic residues are asymmetrically distributed, creating a bipolar molecule. The NH2-terminal half has a predicted pI of 3.7 and is hydrophilic, while the COOH-terminal half (corresponding to mature MBP) has a predicted pI of 11.1 and is hydrophobic.

Evidence for structural deformation of the DNA helix by a psoralen diadduct but not by a monoadduct

We have investigated the structural change in a double-stranded DNA helix caused by covalent addition of a psoralen. A synthetic double-stranded DNA was constructed to contain either a psoralen furan-side monoadduct or an interstrand diadduct at a specific site. When the unmodified and psoralen modified DNAs were examined by electron microscopy in the presence of distamycin, which stiffens the DNA helix, the DNA containing the psoralen interstrand diadduct appeared bent (or kinked), whereas the furan-side monoadducted DNA appeared similar to the unmodified DNA. RecA protein from E. coli has been shown to preferentially bind UV (ultra violet) irradiated DNA presumably due to alterations in the normal DNA helical structure. Using a nitrocellulose filter binding assay, we have found that the psoralen interstrand diadduct enhances the binding of recA protein to the double-stranded DNA, whereas a furan-side monoadduct has little effect. Thus both the recA protein binding and the electron microscopic data suggest that a psoralen diadduct causes deformation of a DNA helix, most likely by kinking the helix, and that a monoadduct has little effect on the DNA helix structure.

Direct visualization of RecA protein binding to and unwinding duplex DNA following the D-loop cycle

The RecA protein of Escherichia coli will promote the plectonemic joining of a linear single-stranded DNA molecule with a homologous supertwisted double-stranded (ds) DNA molecule. As shown by others, this reaction is characterized by a single cycle of joint formation and dissociation, termed the D-loop cycle. The released DNA products appear by electron microscopy to be topologically identical to the reactant DNAs, yet a second cycle of joining is not observed. This implies that either the RecA protein-single-stranded DNA filament or the dsDNA must be altered during the pairing reaction such that further joint formation is inhibited. Shibata et al. (Shibata, T., DasGupta, C., Cunningham, R. P., Williams, J. K. G., Osber, L., and Radding, C. M. (1982) J. Biol. Chem. 256, 7565-7572) proposed that the dsDNA was inactivated due to the binding of RecA protein following the D-loop cycle, but were unable to describe the structure of the putative RecA-protein-dsDNA complex. Here we have extended those studies to show that if fresh dsDNA is added to a reaction mixture following completion of the D-loop cycle, joint formation is stimulated, but only with the freshly added dsDNA. Following completion of the D-loop cycle, a labile RecA protein-dsDNA complex, in which the dsDNA is partially unwound can be preserved by glutaraldehyde fixation and visualized by electron microscopy. This result provides direct evidence that the block to a second cycle of joining is due to the presence of RecA protein remaining bound to the released dsDNA.

Successful single lung transplantation

We have presented a successful case of lung transplantation in a man with pulmonary fibrosis. We believe it is the first successful attempt in the United States, following demonstration of its feasibility in Toronto, Canada. Twenty years after the first lung transplantation, several factors have evolved that help to secure a successful outcome, including a strong, dynamic organ procurement system; static, hypothermic lung preservation; omental wrapping of the bronchial anastomosis; improved immunosuppressive agents; and improved postoperative care.

Purification and visualization of native spliceosomes

Mammalian spliceosomes were purified in preparative amounts by gel filtration chromatography and shown to be functional by in vitro complementation experiments. The column fractions containing spliceosomes are enriched in the snRNAs U1, U2, U4, U5, and U6 and a subset of proteins present in the nuclear extract. Splicing intermediates, the entire set of snRNAs, and the enriched proteins can be immunoprecipitated with three different monoclonal antibodies that recognize snRNP determinants. At least one U1 snRNP is present in each spliceosome since the particles are quantitatively immunoprecipitated by an anti-U1 snRNP monoclonal antibody. Examination of the spliceosome fractions by EM revealed a relatively homogeneous population of 40-60 nm particles with a striking morphology. Evidence that these particles are spliceosomes is their sensitivity to micrococcal nuclease, their ATP-dependent assembly, and their immunoprecipitation with a trimethyl cap monoclonal antibody. In addition, pre-mRNA was visualized in the particles by EM.

Thymine dimers bend DNA

A 32-base-pair DNA fragment containing a thymine photodimer was constructed and ligated head-to-tail to obtain multimers of this sequence in which thymine dimers were in phase with the helix screw axis (approximately equal to 3 turns apart). The ligation products were analyzed by one- and two-dimensional gel electrophoresis and quantitative electron microscopy. These analyses show that the thymine photodimer introduces a bend of approximately equal to 30 degrees in DNA, which causes anomalously slow migration of DNA fragments in polyacrylamide gels and facilitates the formation of small covalent circles. Repair of thymine dimers by DNA photolyase abolishes the anomalous migration.

Electron microscopic visualization of the RecA protein-mediated pairing and branch migration phases of DNA strand exchange

The RecA protein of Escherichia coli will drive the pairing and exchange of strands between homologous DNA molecules in a reaction stimulated by single-stranded binding protein. Here, reactions utilizing three homologous DNA pairs which can undergo both paranemic and plectonemic joining were examined by electron microscopy: supertwisted double-stranded (ds) DNA and linear single-stranded (ss) DNA, linear dsDNA and circular ssDNA, and linear dsDNA and colinear ssDNA. Several major observations were: (i) with RecA protein bound to the DNA, plectonemic joints were ultrastructurally indistinguishable from paranemic joints; (ii) complexes which appeared to be joined both paranemically and plectonemically were present in these reactions in roughly equal numbers; and (iii) in complexes undergoing strand exchange, both DNA partners were often enveloped within a RecA protein filament consisting of hundreds of RecA protein monomers and several kilobases of DNA. These observations suggest that, following RecA protein-ssDNA filament formation, strand exchange proceeds by a pathway that can be divided structurally into three phases: pairing, envelopment/exchange, and release of the products.

Visualization of the homologous pairing of DNA catalyzed by the bacteriophage T4 UvsX protein

The uvsX gene product is essential for DNA repair and general recombination in T4 bacteriophage. The ability of UvsX protein to catalyze the homologous pairing of single-stranded DNA (ssDNA) with double-stranded DNA (dsDNA) in vitro was examined by electron microscopic (EM), nitrocellulose filter binding, and gel electrophoretic methods. Optimal joining was observed at ratios of UvsX protein:ssDNA of 2 nucleotides/protein monomer. At this level, the ssDNA was fully covered by UvsX protein as seen by EM, while the dsDNA appeared protein-free. Using this stoichiometry, the pairing of circular ssDNA with homologous supertwisted dsDNA was found to produce a high frequency of complexes in which a supertwisted dsDNA molecule was joined to a UvsX protein-ssDNA filament over a distance of less than 100 base pairs. These joints were labile to deproteinization and must have been paranemic. Pairing of linear ssDNA containing buried homology to the dsDNA produced identical structures. Pairing of fully homologous linear ssDNA and supertwisted dsDNA yielded D-loop joints (plectonemic) as seen by EM following deproteinization. Both the paranemic and the plectonemic joints were at sites of homology, as demonstrated by restriction cleavage of the complexes. Visualization of the joined complexes prior to deproteinization showed that 50% of the joints had the architecture of the paranemic joints, whereas in the remainder, a topologically relaxed dsDNA circle merged with the UvsX protein-ssDNA filament for a distance of 450 base pairs. The structure of the filament was not visibly altered in this region. These observations are similar, but not identical, to findings in parallel studies utilizing the RecA protein of Escherichia coli.

Visualization of the bent helix in kinetoplast DNA by electron microscopy

Kinetoplast DNA minicircles from the trypanosomatid Crithidia fasciculata contain a segment of approximately 200 bp which is probably more highly bent than any other DNA previously studied. Electron microscopy (EM) of relaxed minicircles (2.5 kb) revealed 200-300 bp loops within the larger circles, and the loops could also be detected on full-length linear molecules. Examination by EM of a 219 bp cloned fragment which contains the bent helix revealed that up to 70% of the molecules appeared circular whether or not the ends were cohesive. In contrast, a 207 bp fragment from pBR322 showed no circles and the fragments in general appeared much straighter than the kinetoplast fragments. Treatment of the 219 bp bent kinetoplast fragment with the drug distamycin caused a striking reduction in curvature.

DNA loops induced by cooperative binding of lambda repressor

It has been shown by Hochschild and Ptashne that lambda repressors bind cooperatively to operator sites separated by five or six turns of the helix. Cooperative binding is not observed if the sites are separated by a nonintegral number of turns, unless a four-nucleotide gap is introduced into one of the strands between the two sites. These and other facts suggested that repressors at the separated sites touch each other, the DNA bending smoothly so as to accommodate the protein-protein interaction. Here we use electron microscopy to visualize the predicted protein-DNA complexes.

A gross morphologic, histologic, hematologic, and blood chemistry study of adult and neonatal mice chronically exposed to high magnetic fields

Six sets of Charles River CD-1 mice (3 sets of adults and 3 sets of offspring: 156 mice total) were raised for varying times (360 h over 1 month to 624 h over 3 months) in a 1.89-T magnetic field. Each set was divided into 3 groups: control group raised in the animal facility (Control); control group raised in the magnet room but not in the magnet (Magnet-Controls); experimental group raised in the magnet (Magnet). At the end of each predefined exposure period, the mice were euthanized and studied. Body and organ weights were lower in 3 of 6 sets in the Magnet groups when compared to Control groups, but they were not significantly different from age matched, sex matched Magnet-Controls. This seems to indicate that the decreased growth of mice was due to the laboratory environment surrounding the magnet, when compared to the animal facility environment, rather than to magnetic field effects. No consistent differences were found in gross and microscopic morphology, hematocrit and white blood cell counts, plasma creatine phosphokinase, lactic dehydrogenase, cholesterol, triglyceride, or protein concentrations in Magnet groups compared to the two control groups.

Visualization of the paranemic joining of homologous DNA molecules catalyzed by the RecA protein of Escherichia coli

In reactions catalyzed by the RecA protein of Escherichia coli, synapsis between two DNA molecules is believed to occur even in the absence of free homologous DNA ends and to involve a metastable interaction termed paranemic joining. We have used electron microscopic methods to visualize synapse formation between supertwisted M13 double-stranded DNA (dsDNA) and linear M13 mp7 single-stranded DNA (ssDNA) with non-M13 sequences at its ends. These non-M13 sequences block strand invasion and make this pairing equivalent to the joining of two fully circular molecules. We observed a high frequency of joining when the ssDNA was initially assembled into presynaptic filaments with RecA protein. Cleavage of the dsDNA in the joined complexes by Hpa I revealed that the joint was at a site of homology. In these joints, the dsDNA entered the presynaptic filament over a length of 360 +/- 80 base pairs, not visibly altering its ultrastructure, and then dissociated from the filament. Although the dsDNA in the complexes appeared topologically relaxed, deproteinization released supertwisted dsDNA, indicating that the dsDNA was unwound by 34 degrees per base pair in the paranemic joint. When supertwisted M13 dsDNA was paired with circular M13 ssDNA, similar joints were observed and both DNA circles appeared topologically relaxed.

Comparison of plasma cholinesterase depression among workers occupationally exposed to organophosphorus pesticides as reported by various studies

A number of studies have reported on the inhibitory effects of organophosphorus pesticides (OPs) on the enzyme cholinesterase (ChE) among agricultural workers. With the increasing use of OPs, surveys of blood ChE activity on exposed workers may help to identify workers at greatest risk and to provide insight into the use history--e.g., mixing, loading, application, and harvesting--that might lead to a hazardous situation. Although it does appear that measurements of ChE activity are valuable in worker surveillance programs, it is difficult to interpret findings from various studies since they are dependent on the method of assay and the emphasis is usually placed on statistical tests (i.e., p values) that depend on the number of subjects studied. In the present paper a method is presented to compare ChE values reported in several studies utilizing various methods and units of measurement, and to assess the impact of OP exposure as a percentage of subjects with ChE values depressed below normal limits.

The direction of RecA protein assembly onto single strand DNA is the same as the direction of strand assimilation during strand exchange

The RecA protein of Escherichia coli optimally promotes DNA strand exchange reactions in the presence of the single strand DNA-binding protein of E. coli (SSB protein). Under these conditions, assembly of RecA protein onto single-stranded DNA (ssDNA) occurs in three steps. First, the ssDNA is rapidly covered by SSB protein. The binding of RecA protein is then initiated by nucleation of a short tract of RecA protein onto the ssDNA. Finally, cooperative polymerization of additional RecA protein accompanied by displacement of SSB protein results in a ssDNA-RecA protein filament (Griffith, J. D., Harris, L. D., and Register, J. C. (1984) Cold Spring Harbor Symp. Quant. Biol. 49, 553-559). We report here that RecA protein assembly onto circular ssDNA yields RecA protein-covered circles in which greater than 85% are completely covered by RecA protein with no remaining SSB protein-covered segments (as detected by electron microscopy). However, when linear ssDNA is used, 90% of the filaments contain a short segment at one end complexed with SSB protein. This suggests that RecA protein assembly is unidirectional. Visualization of the assembly of RecA protein onto either long ssDNA tails (containing either 5' or 3' termini) or ssDNA gaps generated in double strand DNA allowed us to determine that the RecA protein polymerizes in the 5' to 3' direction on ssDNA and preferentially nucleates at ssDNA-double strand DNA junctions containing 5' termini.

New data from the Addiction Severity Index. Reliability and validity in three centers

The Addiction Severity Index (ASI) is a clinical/research instrument which has been in wide use during the past 6 years to assess the treatment problems found in alcohol- and drug-abusing patients. In a study of male veterans, a preliminary evaluation of the ASI has indicated reliability and validity. The present report presents an expanded examination of these issues; 181 subjects from three treatment centers were studied. Results of concurrent reliability studies indicate that trained technicians can estimate the severity of patients' treatment problems with an average concordance of .89. Test-retest studies show that the information obtained from the ASI is consistent over a 3-day interval, even with different interviewers. Comparisons of the ASI severity ratings and composite measures with a battery of previously validated tests indicate evidence of concurrent and discriminant validity. The reliability and validity results were consistent across subgroups of patients categorized by age, race, sex, primary drug problem, and treatment center. The authors discuss the strengths and limitations of the instrument based upon 5 years of use. The overall conclusion is that the ASI is a reliable and valid instrument that has a wide range of clinical and research applications, and that it may offer advantages in the examination of important issues such as the prediction of treatment outcome, the comparison of different forms of treatment, and the "matching" of patients to treatments.

The uvsX protein of bacteriophage T4 arranges single-stranded and double-stranded DNA into similar helical nucleoprotein filaments

The bacteriophage T4 uvsX gene codes for a DNA-binding protein that is important for genetic recombination in T4-infected cells. This protein is a DNA-dependent ATPase that resembles the Escherichia coli recA protein in many of its properties. We have examined the binding of purified uvsX protein to single-stranded DNA (ssDNA) and to double-stranded DNA (dsDNA) using electron microscopy to visualize the complexes that are formed and double label analysis to measure their protein content. We find that the uvsX protein binds cooperatively to dsDNA, forming filaments 14 nm in diameter with an apparently helical axial repeat of 12 nm. Each repeat contains about 42 base pairs and 9-12 uvsX protein monomers. In solutions containing Mg2+, the uvsX protein also binds cooperatively to ssDNA. The filaments that result are 14 nm in diameter, show a 12-nm axial repeat, and they are nearly identical in appearance to the filaments that contain dsDNA. In the filaments formed along ssDNA, each axial repeat contains about 49 DNA bases and 9-12 uvsX monomers. Both the filaments formed on the ssDNA and dsDNA show a strong tendency to align side-by-side. T4 gene 32 protein also binds cooperatively to ssDNA and interacts both physically and functionally with uvsX protein. However, when gene 32 and uvsX proteins were added to ssDNA together, no interaction between the two proteins was detected.

RecA protein rapidly crystallizes in the presence of spermidine: a valuable step in its purification and physical characterization

The RecA protein of Escherichia coli, whether pure or in a crude cell lysate, will rapidly form small crystals (microcrystals) in the presence of low concentrations of spermidine. We describe the conditions of time, pH, and polyamine concentration over which crystallization occurs. Microcrystal formation is inhibited by concentrations of chloride over 25 mM and concentrations of phosphate or sulfate ions as low as 2 mM. Crystallization is not inhibited by high concentrations of other proteins, and the RecA protein microcrystals are easily collected by brief centrifugation. This provides a powerful purification step with high yield. Using this novel property, we prepared over 200 mg of RecA protein at least 95% pure with a single-strand DNA-dependent ATPase activity of 98% from 65 g of cells in 2-3 days. Spermidine was easily removed from the RecA protein by dialysis.

Monitoring study of urinary metabolites and selected symptomatology among Florida citrus workers

A cross-sectional monitoring study was made of citrus fieldworkers employed during an entire citrus growing season in Florida. A survey questionnaire was administered to 1811 fieldworkers employed as applicators, mixers, loaders, tractor drivers, general combination workers, and pickers on 436 citrus groves throughout Florida. The study was designed to evaluate exposure to organophosphorus pesticides by analyzing the urine of citrus fieldworkers for dimethyl phosphate (DMP), dimethyl thiophosphate (DMTP), dimethyl dithiophosphate (DMDTP), diethyl phosphate (DEP), diethyl thiophosphate (DEPT), and diethyl dithiophosphate (DEDTP), and to relate the findings to the reported occurrence of selected health symptoms associated with pesticide intoxication. Urine samples were collected for analysis from 332 spray-season workers and 265 harvest-season workers. Measurable DEP residue values were found in 68% of the spray season workers and 43% of the harvesters. However, with the exception of DEP and DETP values in the urine of spray-season workers, metabolite residues were low, often at, or just above, detection limits (which were usually 0.02 ppm but occasionally rose higher, with a few at 0.03 ppm and a very few at 0.04 ppm). Although there was clearly exposure to organophosphates among the citrus fieldworkers, there was no apparent association between the reported health symptoms and the relatively low levels of organophosphate metabolites found in the urine of the workers.

A community survey of psychological impairment among Anglo- and Mexican Americans and its relationship to service utilization

Discussions of Mexican American mental health need have been limited to analyses of service utilization statistics, most of which have shown Mexican Americans to use mental health services proportionally less than other racial/ethnic groups. Consequently, Mexican Americans have been viewed as a group having greater unmet mental health needs. Yet, these utilization-based needs assessments make an implicit and untested assumption: that the proportion of the psychologically impaired is comparable across racial/ethnic groups. The purpose of the present investigation was, first, to contribute to a baseline measurement of psychological impairment among Mexican Americans in order to assess what utilization should be for this group and, second, to determine relationships between impairment symptomatology and sociodemographic characteristics which are unique to the Mexican American population. Anglo- and Mexican Americans (n = 515) living in one of three suburban communities in Southern California were selected by way of a random-digit, multistage cluster telephone sampling procedure. Respondents gave responses to a standardized measurement of psychological impairment. Results showed that Anglo- and Mexican Americans did not differ in anxiety, psychosocial dysfunction, and depressive symptoms. Mexican Americans in the three communities, however, were found to use mental health services proportionally less than Anglos. Relationships between age and psychosocial dysfunction symptoms, and between income and anxiety problems were different for Mexican Americans than those for Anglos. Issues related to what constitutes mental health need and the use of self-report measures of impairment to estimate mental health need across culturally diverse groups are discussed.

Association of M13 I-forms and spheroids with lipid vesicles

Electron microscopy and density gradient centrifugation were used to demonstrate that the coat protein of M13 I-forms and spheroids, but not of filaments, can form some type of association with lipid vesicles in vitro. The association was detected only when the phage particles were incubated with dilauroylphosphatidylcholine (DLPC) or dimyristoylphosphatidylcholine (DMPC) small unilamellar vesicles (SUV) above the phase transition temperature of the lipid. Under these conditions the I-form coat protein was resistant to proteolytic digestion, and the viral DNA was also associated with the vesicles.

Nelson's syndrome after Cushing's disease in childhood: a continuing problem

Nelson's syndrome--progressive cutaneous hyperpigmentation with x-ray film evidence of an expanding pituitary tumor--is now a well-recognized sequela of bilateral adrenalectomy for Cushing's disease. It is estimated to occur in 8% to 38% of adults. Because Cushing's disease is rare in children, a higher incidence of Nelson's syndrome has not been suggested until recently. Although transsphenoidal operation is now the treatment of choice for Cushing's disease, children who have undergone bilateral adrenalectomy remain at risk for the development of Nelson's syndrome. A review of our experience and the literature indicates that the incidence of Nelson's syndrome after the treatment of Cushing's disease is higher in children than in adults. In our six children who underwent adrenalectomy between 8 and 17 years of age, four developed Nelson's syndrome at 2, 6, 10, and 12 years after adrenalectomy. Two of these patients remain well at 6 and 9 years after treatment with external irradiation. One patient treated with external irradiation developed recurrence at 5 years and required total hypophysectomy. The fourth patient required total hypophysectomy followed by external irradiation. Of the 37 patients reviewed and analyzed, the mean age at diagnosis of Cushing's disease was 12 years, with a mean interval of 8.4 years between adrenalectomy and Nelson's syndrome. Information regarding treatment for Nelson's syndrome was known in 24 patients and included pituitary irradiation (four patients), pituitary operation (11 patients), pituitary irradiation followed by operation (six patients), and pituitary operation followed by irradiation (three patients).

Electron microscopy can be used to measure DNA supertwisting

We have examined the use of electron microscopy (EM) to measure the degree of supertwisting of covalently closed circular fd and pBR322 DNAs. Band counting agarose gel electrophoresis was used to quantitate the number of twists in these DNAs. DNA species having moderate-to-low superhelical densities were prepared by treatment of the DNA with Drosophila topoisomerase 1 in the presence of ethidium bromide (EtBr) followed by isolation of discrete DNA topoisomers from preparative gels. These DNAs were then examined by EM using a direct mounting method employing a buffer containing spermidine. The crossovers in individual DNA molecules were counted and compared to the supertwist values obtained from gel studies. The results show that EM can provide a reliable estimate of the number of supertwists in DNAs having low-to-moderate superhelical densities.

Procedure development. A simplified approach

A step-by-step guide for writing procedures/protocols in an easy-to-read, standardized format is presented. The guidelines emphasize clarity, accessibility, and directness to provide an efficient method of producing finished and effective procedures that enhance performance.