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D C Schwartz

Publications and source records attributed to D C Schwartz.

At least 37 records · Page 2Linked to original sources
PubMed1998

A quantitative study of optical mapping surfaces by atomic force microscopy and restriction endonuclease digestion assays.

Many new techniques in biomolecular chemistry and genomic analysis require the immobilization of molecular reagents on specially prepared surfaces. However, the process of molecular fixation often interferes with or precludes the use of standard in vitro biochemical assays. Optical mapping is an emergent technology for genomic analysis which relies on the biochemical activity of DNA fixed to silanized glass surfaces. Optical mapping surfaces have been shown to be compatible with restriction endonucleases and a variety of DNA polymerases. The essential properties of biochemically active surfaces are poorly understood in most of the current technologies which utilize molecular fixation, including optical mapping. The purpose of this study is to use the powerful technique of atomic force microscopy, in combination with informative enzymatic assays, to correlate biochemical activity with microscopic surface structure. The results presented provide meaningful insight into the effect of surface preparation on the biochemical accessibility of surface-bound molecules. Novel analysis which may facilitate the automation of optical mapping is presented.

DNA↗
PubMed1998

High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping.

Large insert clone libraries have been the primary resource used for the physical mapping of the human genome. Research directions in the genome community now are shifting direction from purely mapping to large-scale sequencing, which in turn, require new standards to be met by physical maps and large insert libraries. Bacterial artificial chromosome libraries offer enormous potential as the chosen substrate for both mapping and sequencing studies. Physical mapping, however, has come under some scrutiny as being "redundant" in the age of large-scale automated sequencing. We report the development and applications of nonelectrophoretic, optical approaches for high-resolution mapping of bacterial artificial chromosome that offer the potential to complement and thereby advance large-scale sequencing projects.

Chromosome Mapping↗
PubMed1998

Mycobacterial genome structure.

Genome maps have been constructed for the mycobacterial pathogens Mycobacterium leprae and Mycobacterium tuberculosis, as well as for the attenuated vaccine strain Mycobacterium bovis BCG Pasteur. While the chromosomes of M. tuberculosis and M. bovis BCG Pasteur show extensive conservation at the gross level, comparison with M. leprae revealed a high degree of diversification, with a mosaic-like pattern apparent. The ordered libraries of M. tuberculosis and M. leprae produced during the course of these studies played a central role in the genome sequencing projects of these two bacilli, showing the utility of this approach for systematic sequencing of bacterial genomes.

Chromosome Mapping↗
PubMed1998

The large window ductus: a surgical trap.

A rare window type of patent ductus arteriosus is reported that was large (15 mm in maximal transverse dimension) but had virtually no length and hence was externally invisible. The smaller aortic isthmus (4 mm in diameter), which was intrapericardial, was mistaken for the ductus and was inadvertently clip-occluded, leading to death. After a specific diagnosis is made, the large window ductus should be patched on cardiopulmonary bypass with a transpulmonary approach.

Aorta, Thoracic↗
PubMed1998

Scanning force microscopy of DNA molecules elongated by convective fluid flow in an evaporating droplet.

Scanning force microscopy (SFM) was used to image intact, nearly fully elongated lambda bacteriophage DNA molecules, fixed onto freshly cleaved mica surfaces. Molecular elongation and fixation were accomplished using a newly characterized fixation technique, termed "fluid fixation." Here convective fluid flows generated within an evaporating droplet of DNA solution efficiently elongate DNA molecules for fixation onto suitably charged surfaces. SFM images of a very large bacteriophage genome, G, showed the presence of double-stranded bubbles. We speculate that these structures may contain putative replication forks. Overall, the experiments presented here demonstrate the viability of using fluid fixation for the preparation of DNA molecules for SFM imaging. The combination of largely automatable optically based techniques with the high-resolution SFM imaging presented here will likely produce a high-throughput system for detailed physical mapping of genomic DNA or clones.

Bacteriophage lambda↗
PubMed1998

Effect of myocardial hypertrophy on systolic and diastolic function in children: insights from the force-frequency and relaxation-frequency relationships.

OBJECTIVE: The objective of this study was to evaluate the effect of myocardial hypertrophy on systolic and diastolic properties of the left ventricle in children. BACKGROUND: In children with myocardial hypertrophy, ejection phase indices are invariably increased. However, indices of force-generation, e.g., end-systolic elastance and invasive indices of diastolic properties, have been studied infrequently in children with myocardial hypertrophy. METHODS: We studied 10 children with congenital aortic stenosis or coarctation of aorta and nine control patients. Systolic properties were assessed from shortening fraction, end-systolic fiber elastance (Ef(es)) measured at resting heart rates, and force-frequency relationship measured at heart rates increasing from 110 to 160 beats per minute. Diastolic properties were assessed from time constant of relaxation (tau) at matched heart rates, chamber stiffness constant, myocardial stiffness constant, and relaxation-frequency relationship measured at gradually increasing heart rates. RESULTS: Ef(es) remained unchanged by myocardial hypertrophy, however, tau was prolonged (tauL: 27.3+/-2.3 vs. 21.8+/-2.2 ms, p < 0.001; and tauD: 43.2+/-3.1 vs. 34.3+/-3.3 ms, p < 0.001). Both chamber and myocardial stiffness constants remained unchanged. Incremental increases in heart rate produced incremental improvement in both contraction and relaxation. Slopes of force-frequency and relaxation-frequency relationships remained unchanged in the experimental group. However, the relaxation-frequency relationship manifested a parallel shift upward. CONCLUSIONS: In conscious, sedated children with myocardial hypertrophy, systolic function assessed by an index of force generation remains unchanged. However, relaxation is prolonged but passive diastolic properties remain unaffected. The combined effect of hypertrophy and heart rate does not alter the force-frequency and relaxation-frequency relationships.

Aortic Coarctation↗
PubMed1997

Is echocardiography or magnetic resonance imaging superior for precoarctation angioplasty evaluation?

We compared the dimensions of the aorta obtained by two-dimensional transthoracic echocardiography (echo) (median, 2.5 mo preangioplasty) and magnetic resonance imaging (MRI) (median, 4.2 mo preangioplasty) to those obtained by angiography (cath) in 13 patients (age, 7.7 +/- 1.6 yr; mean +/- SEM) who underwent evaluation for coarctation balloon angioplasty between April 1993-January 1996. Echo measurements were obtained from the suprasternal and subcostal sagittal planes, MRI measurements from axial and sagittal oblique views, and cath measurements from the straight lateral or oblique views. Measurements of the diameters of the aortic isthmus, coarctation, descending aorta at the diaphragm, and isthmus length were made by all three modalities. Presence of aorto-aortic collaterals was determined, and the coarctation length was delineated. Investigators were blinded to other measurement data prior to statistical analysis. Data analysis by repeated analysis of variance (ANOVA) and Student-Newman-Keuls testing revealed no statistically significant difference between systolic pressure gradient by clinical examination (32.2 +/- 5.9 mm Hg), peak instantaneous Doppler evaluation (37.5 +/- 2.9 mm Hg), or preangioplasty systolic pressure gradient (32.1 +/- 3.3 mm Hg). With the exception of measurements of the descending aorta (echo, 11.7 +/- 0.9 mm vs. MRI, 13.3 +/- 0.8 mm vs. cath, 14.0 +/- 1.3 mm; P = 0.04), there was no statistically significant difference in dimensions of the aortic isthmus (9.2 +/- 0.6 mm vs. 10.5 +/- 0.9 mm vs. 10.8 +/- 0.9 mm), coarctation site diameter (4.8 +/- 0.6 mm vs. 5.6 +/- 0.9 mm vs. 5.3 +/- 0.8 mm), or isthmus length (12.4 +/- 2.1 mm vs. 12.1 +/- 2.2 mm vs. 10.9 +/- 1.7 mm). The correlation coefficients derived from comparisons of MRI vs. cath to echo vs. cath were similar for all dimensions except for isthmus length (P < 0.01). MRI demonstrated aorto-aortic collaterals more frequently than echo, while echocardiography better demonstrated cardiac function and intracardiac anomalies. Both modalities detected the single patient with a long segment coarctation. We conclude that echocardiography and MRI provide similar definition of the coarcted thoracic aorta, and either test may be individually advantageous in specific clinical situations.

Adolescent↗
PubMed1997

Optical mapping approaches to molecular genomics.

A variety of physical mapping methods exist for the analysis of nucleic acids or genomes, including hybridization, sequence tagged site mapping, restriction enzyme fingerprinting, radiation hybrid mapping and optical mapping. Single-molecule approaches offer numerous advantages, including very high resolution, small sample size requirements, and parallel sample processing. The convergence of recent advances in new single molecule techniques, surface chemistry and machine vision technology has contributed to novel approaches to genome analysis.

Biotechnology↗
PubMed1997

Genomics via optical mapping. II: Ordered restriction maps.

In this paper, we describe our algorithmic approach to constructing ordered restriction maps based on the data created from the images of population of individual DNA molecules (clones) digested by restriction enzymes. The goal is to devise map-making algorithms capable of producing high-resolution, high-accuracy maps rapidly and in a scalable manner. The resulting software is a key component of our optical mapping automation tools and has been used routinely to map cosmid, lambda and BAC clones. The experimental results appear highly promising.

Algorithms↗
PubMed1996

Predictors of successful pulmonary balloon valvuloplasty: 10-year experience.

At our institution, 55 infants and children (ages 0.3-21 yr, median 2.5 yr) underwent pulmonary balloon valvuloplasty between August 1983 and May 1993. Systolic pressure gradients fell acutely following balloon valvuloplasty from 63.5 +/- 24.8 mmHg (mean +/- standard deviation) to 26.7 +/- 12.9 mmHg (P < 0.001) with a decrease in systolic pressure ratio from 0.81 +/- 0.25 to 0.42 +/- 0.12 (P < 0.0001). Fifty of the 55 patients had long-term echocardiographic evaluation performed > 2 yr following balloon valvuloplasty. Thirty-four of the 50 patients (Group A; 68%) were classified as having successful (residual systolic gradients < 25 mmHg, ventricular systolic pressure ratios < 0.6) long-term outcomes. Their peak systolic gradients fell acutely from 58.8 +/- 16.6 mmHg to 22.7 +/- 11.2 mmHg (P < 0.001). At 4.6 +/- 2.3 yr postvalvuloplasty, peak instantaneous pressure gradients were 17.8 +/- 5.7 mmHg (P = ns vs. acute postvalvuloplasty). Fifteen of the 50 patients (Group B; 30%) had unsuccessful (residual systolic gradients > or = 25 mmHg and/or ventricular systolic pressure ratios > 0.6) long-term outcomes. Their peak instantaneous systolic gradients fell acutely from 76.5 +/- 33.1 mmHg to 36.6 +/- 11.4 mmHg (P < 0.05). At 3.8 +/- 1.7 yr postvalvuloplasty, peak instantaneous pressure gradients were 35.1 +/- 9.1 mmHg (P = ns vs. acute postvalvuloplasty). One 3-yr-old patient (Group C, 2%) required repeat balloon valvuloplasty on two separate occasions for recurrent stenosis. There was no significant prevalvuloplasty difference between Groups A and B with regard to age, weight, or Z scores of the pulmonary annuli or balloon/annulus ratio; however, patients in Group A had significantly lower prevalvuloplasty gradients and lower systolic pressure ratios than patients in Group B. Total systolic gradient reduction between patients with successful and unsuccessful outcomes was not significantly different (Group A: 36.1 +/- 16.6 mmHg; Group B: 41 +/- 22.3 mmHg). At long-term follow-up, patients in Group A had fewer symptoms and a significantly lower rate of electrocardiographic right ventricular hypertrophy than Group B patients. Successful outcomes defined by our criteria following balloon valvuloplasty were achieved in 68% of patients with greatest long-term success in patients with prevalvuloplasty systolic gradients < 60 mmHg and systolic pressure ratios < 0.8. Intervention at lesser systolic gradients (40-60 mmHg) appears indicated to achieve lower long-term gradients and fewer symptoms as total systolic gradient reduction by this technique is limited.

Adolescent↗
PubMed1996

New polyacrylamide gel-based methods of sample preparation for optical microscopy: immobilization of DNA molecules for optical mapping.

New methods have been developed for rapid immobilization of biological macromolecules and other microscopic objects from aqueous solution at gel/gel, gel/solid and gel/solution interfaces using thin polyacrylamide gels covalently bound to glass surfaces. When quickly spread over a dry gel, an aqueous sample loses most of its water and low-molecular-weight solutes due to migration of these components into the gel. All optically observable objects thus become concentrated at the gel surface and may be easily located by light microscopy. Based on this, a procedure for binding DNA at a positively charged gel/solution interface was developed. A mild immobilization of the DNA molecules was obtained, allowing 'all in focus' observations of DNA digestion by restriction endonucleases with an apparent rate close to that in solution.

Acrylamides↗
PubMed1996

Inhibition of restriction endonuclease activity by DNA binding fluorochromes.

Activity of type II restriction endonuclease is affected by many common factors including buffer composition and sequences flanking the recognition site (Brabec et al., Eur.J. Biochem. 216, 183, 1993). The successful development of Optical Mapping (Schwartz et al., Science, 262, 110, 1993; Meng et al., Nature Genet. 9, 432, 1995; Wang and Schwartz, PNAS, 1995 Cai et al., PNAS, 92, 5164, 1995) relied on optimization of light microscope-based imaging of fluorescently labeled DNA molecules during restriction endonuclease digestion. Little was known about the effects of commonly used DNA-fluorochromes on restriction endonuclease activity. Thus, we developed an enzyme activity assay using lambda bacteriophage DNA or adenovirus-2 DNA to evaluate the effects of five DNA binding fluorochromes (4'-6-daimidine-2-phenylindole (DAPI), ethidium bromide (EtdBr), ethidium bromide homodimer (EthD-1), bis-benzimide (H33258) and benzothiazolium-4-quinolinium dimer (TOTO-1)) on the enzymatic activities of eleven type II restriction endonucleases (Asc I, Csp I, Dra I, EcoR I, Hha I, Hind III, Not I, Rsr II, Sfi I, SgrA I and Sma I). We found that the minor groove binding fluorochrome, DAPI, did not measurably inhibit activity of this group, with the exception of Dra I. Similarly, another minor groove binding fluorochrome H33258 inhibited Dra I and Not I (slightly). The three intercalating fluorochromes EtdBr, EthD-1 and TOTO-1, however, variably inhibited the other enzymes. Since Beta-mercaptoethanol (Beta-ME) is used to discourage photodamage of stained DNA molecules, we also assessed its effect on restriction endonuclease activity. Interestingly, Dra I, Hind III, Sfi I and Sma I retained full activities at high concentration of Beta-ME (5%), but Asc I, Csp I, Not I, Rsr II and SgrA I showed varying sensitivities to the Beta-ME. Isoschizomers Csp I and Rsr II behaved differently to both fluorochromes and Beta-ME. The results presented here should provide a basis for further development of new Optical Mapping-based techniques requiring fluorescence labeling of other actively imaged enzymatic reactions.

Binding Sites↗
PubMed1995

Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces.

We have developed a surface mounting technology for the rapid construction of ordered restriction maps from individual DNA molecules. Optical restriction maps constructed from yeast artificial chromosome DNA molecules mounted on specially derivatized glass surfaces are accurate and reproducible, and the technology is amenable to automation. The mounting procedures described here should also be useful for fluorescence in situ hybridization studies. We believe these improvements to optical mapping will further stimulate the development of nonelectrophoretic approaches to genome analysis.

Automation↗
PubMed1995

Optical mapping of site-directed cleavages on single DNA molecules by the RecA-assisted restriction endonuclease technique.

Fluorescence in situ hybridization (FISH) resolution has advanced because newer techniques use increasingly decondensed chromatin. FISH cannot analyze restriction enzyme cutting sites due to limitations of the hybridization and detection technologies. The RecA-assisted restriction endonuclease (RARE) technique cleaves chromosomal DNA at a single EcoRI site within a given gene or selected sequence. We recently described a mapping technique, optical mapping, which uses fluorescence microscopy to produce high-resolution restriction maps rapidly by directly imaging restriction digestion cleavage events occurring on single deproteinized DNA molecules. Ordered maps are then constructed by noting fragment order and size, using several optically based techniques. Since we also wanted to map arbitrary sequences and gene locations, we combined RARE with optical mapping to produce site-specific visible EcoRI restriction cleavage sites on single DNA molecules. Here we describe this combined method, named optical RARE, and its initial application to mapping gene locations on yeast chromosomes.

Base Sequence↗
PubMed1995

Optical mapping of lambda bacteriophage clones using restriction endonucleases.

Optical mapping is an emerging single molecule approach for the rapid generation of ordered restriction maps, using fluorescence microscopy. We have improved the size resolution of optical mapping by imaging individual DNA molecules elongated and fixed onto derivatized glass surfaces. Averaged fluorescence intensity and apparent length measurements accurately determined the mass of restriction fragments 800 basepairs long. We have used optical mapping to create ordered restriction maps for lambda clones derived from the mouse pygmy locus.

Animals↗
PubMed1993

Effect of tamoxifen on serum cholesterol and lipoproteins during chemohormonal therapy.

The effect of tamoxifen on serum cholesterol, high density lipoprotein cholesterol (HDL-cholesterol), low density lipoprotein cholesterol (LDL-cholesterol) and the ratio of LDL-cholesterol to HDL-cholesterol (LDL-C/HDL-C) was investigated in breast cancer patients undergoing therapy for advanced disease. Longitudinal studies in 24 patients treated with tamoxifen (10 mg, twice daily) indicated average decreases in total serum cholesterol (17%) and LDL-cholesterol (27%), whereas the effect of tamoxifen on HDL-cholesterol varied with the individual patient. There was a significant decrease in the LDL-C/HDL-C ratio (33%) consistent with a decreased risk for coronary artery disease. This beneficial influence of tamoxifen on risk factors associated with cardiovascular disease was evident in both premenopausal and postmenopausal patients whether tamoxifen was administered alone or in combination with cytotoxic chemotherapy.

Antineoplastic Combined Chemotherapy Protocols↗