Search PubMed⌕ Search

Biomedical subjects

L M Smith

Publications and source records attributed to L M Smith.

At least 127 records · Page 7Linked to original sources
PubMed1993

An adaptive, object oriented strategy for base calling in DNA sequence analysis.

An algorithm has been developed for the determination of nucleotide sequence from data produced in fluorescence-based automated DNA sequencing instruments employing the four-color strategy. This algorithm takes advantage of object oriented programming techniques for modularity and extensibility. The algorithm is adaptive in that data sets from a wide variety of instruments and sequencing conditions can be used with good results. Confidence values are provided on the base calls as an estimate of accuracy. The algorithm iteratively employs confidence determinations from several different modules, each of which examines a different feature of the data for accurate peak identification. Modules within this system can be added or removed for increased performance or for application to a different task. In comparisons with commercial software, the algorithm performed well.

Algorithms↗
PubMed1993

Nonisotopic DNA detection system employing elastase and fluorogenic rhodamine substrate.

An alternative fluorescence-based method has been developed for the direct detection of small quantities of DNA in solution. In this system, a serine protease (elastase) is coupled to a DNA oligonucleotide through a disulfide linkage. A bis-(tetraalanine)-derivatized rhodamine molecule BZTAlaR) has been synthesized for use as a substrate. BZTAlaR is nonfluorescent in its derivatized form and shows negligible hydrolysis in solution. Cleavage of the tetraalanyl groups from the rhodamine portion of the molecule restores its fluorescence. Hybridization of the elastase-oligonucleotide conjugate to its target, capture of the conjugate-target complex with streptavidin-coated magnetic beads, addition of substrate, and subsequent detection of the target by fluorescence are accomplished in solution. Hybridization is rapid and specific, with over 90% of a target sequence successfully hybridized and captured. This method exhibits low background and an amplified fluorescent signal over time, resulting in a current detection limit of 0.49 fmol of elastase alone, or 2.64 fmol of conjugate, within 2 h.

Base Sequence↗
PubMed1993

Rapid purification of double-stranded DNA by triple-helix-mediated affinity capture.

A simple and rapid method for the preparation of highly pure plasmid DNA has been developed. The DNA is directly captured from bacterial cell lysates by formation of a triple-helical structure between the plasmid dsDNA and a 20-base biotinylated oligonucleotide attached to streptavidin-coated magnetic beads and then eluted from the beads in pH 9 buffer solution. No phenol extraction, ethanol precipitation, RNase digestion, or CsCl gradient centrifugation is required. A general purpose cloning vector, pHJ19, was constructed for this application from pUC19 DNA by insertion of a 40-base sequence suitable for triple-helix formation. The approach was also found suitable for the purification of lambda bacteriophage DNA.

Bacterial Proteins↗
PubMed1993

Broadly neutralizing monoclonal antibodies to the V3 region of HIV-1 can be elicited by peptide immunization.

The third hypervariable region (V3) of the HIV-1 envelope gp120 protein contains the principal neutralizing domain. Most neutralizing antibodies directed toward this region are very type-specific. Conserved sequences do exist within this region, however, and may prove useful in developing vaccines and therapeutic monoclonal antibodies (MABs) capable of targeting diverse HIV-1 isolates. We have used synthetic peptides containing conserved V3 sequences as immunogens to produce a panel of neutralizing MABs. The characterization of these MABs is described here. In addition, a series of in vitro assays has been developed that may be useful in predicting the neutralization potential of individual antibodies.

Amino Acid Sequence↗
PubMed1993

DNA electrophoresis.

The electrophoresis of DNA is a central technology in biological and biomedical research. There is tremendous activity in the development of electrophoresis technology, extending the versatility, power, speed, resolution, and sensitivity of this already extraordinary separation tool. This review covers some of the advances that have been made in the past year.

DNA↗
PubMed1993

Early evacuation of clotted blood in hemothorax using thoracoscopy: case reports.

Hemothorax complicated by clotting of the blood is traditionally treated with thoracotomy. Successful treatment using early thoracoscopy in two patients is described. A third patient, in whom thoracoscopic evacuation failed, is also discussed. Early timing of the procedure appears to enhance the opportunity for adequate drainage of the thorax with lung re-expansion.

Adult↗
PubMed1993

Training opportunities and educational requirements for the nurse manager.

It seems inevitable that hospitals must supplement the formal education of its nurse managers. To do this most effectively, hospitals must conduct a formal needs analysis to accurately assess the training needs of the nurses. Perhaps more importantly, an adequate evaluation of all training activity should be conducted to ensure that the trainee has actually learned what is taught; the trainee is satisfied with the training; the trainee has retained the information over time; and the trainee has transferred that training to the job. Since many hospitals report investing a great deal of time and money in these programs, it would be extremely beneficial to them to carefully assess the strengths and weaknesses of their training programs. If the program is not having its intended effect, the hospitals need to know exactly where the deficiencies are and how to correct them. By doing this, nurses will receive the kind of training that will help them to manage effectively in a variety of situations.

Analysis of Variance↗
PubMed1993

Evaluating the flow characteristics of artificial pumping devices using nuclear scintigraphy.

The design and development of artificial blood pumps require qualitative and quantitative data relative to pump filling, ejection, and wall motion in order to optimize the design and maximize the pattern of blood flow through the pump. To assist in the development of an artificial heart, we utilized radionuclide scintigraphy and a high-resolution gamma camera to evaluate the flow patterns through the pump. We performed a comparative analysis of the flow patterns in a pneumatically driven ventricular assist device (Sarns/3M VAD) and the electrically driven Milwaukee Heart. These analyses disclose some significant differences between the two devices with regard to the blood sac compression patterns and ejection as well as valvular regurgitation. On the basis of these findings, nuclear scintigraphy for analyzing fluid shear stress and flow dynamics seems a useful technique for evaluating blood flow through artificial blood pumps. Because the procedure does not require a translucent casing or direct contact with the device being studied, it would be especially useful in evaluating artificial blood pumps implanted in patients with heart failure.

Coronary Circulation↗
PubMed1993

Solid phase purification in automated DNA sequencing.

A solid phase purification method has been utilized to investigate the effect of template DNA and other contaminants present in enzymatic DNA sequencing reactions upon data quality in automated DNA sequence analysis. The primer oligonucleotide is prepared with an internal biotin group and one of four fluorescent tags at the 5' terminus. The fluorescently labeled DNA fragments produced in the sequencing reactions are separated from other reaction components, including template DNA, using superparamagnetic streptavidin beads. Template DNA and other reaction components may then be added back to the purified material to assess their effect upon sequence data. It is found that band intensity and base calling accuracy are decreased by the presence of the template DNA and other reaction components.

Animals↗
PubMed1992

Solid-phase method for the purification of DNA sequencing reactions.

A solid-phase method for the purification of the single-stranded DNA molecules produced in enzymatic sequencing reactions has been developed. A primer oligonucleotide is synthesized containing a biotin moiety at an internal position. This primer is utilized in enzymatic extension reactions, and the resulting products are bound to streptavidin-coated magnetic beads. Contaminating species such as protein, salts, template DNA, and unincorporated or degraded deoxy and dideoxy nucleotide triphosphates may be removed by washing the beads after immobilizing them in the sample tube with a fixed magnet. The resulting pure single-stranded DNA fragments are removed from the solid support by heating in 10 mM EDTA, 95% formamide, loading dye at 90 degrees C, and may then be directly loaded onto a polyacrylamide gel for sequence analysis. This method was used to investigate the effect of various contaminants upon DNA sequence data.

Base Sequence↗
PubMed1992

Rapid shotgun cloning utilizing the two base recognition endonuclease CviJI.

A new approach has been developed for the rapid fragmentation and fractionation of DNA into a size suitable for shotgun cloning and sequencing. The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions which alter the specificity of this enzyme (CviJI**) yield a quasi-random distribution of DNA fragments from the small molecule pUC19 (2686 base pairs). To quantitatively evaluate the randomness of this fragmentation strategy, a CviJI** digest of pUC19 was size fractionated by a rapid gel filtration method and directly ligated, without end repair, to a lacZ minus M13 cloning vector. Sequence analysis of 76 clones showed that CviJI** restricts PyGCPy and PuGCPu, in addition to PuGCPy sites, and that new sequence data is accumulated at a rate consistent with random fragmentation. Advantages of this approach compared to sonication and agarose gel fractionation include: smaller amounts of DNA are required (0.2-0.5 micrograms instead of 2-5 micrograms), fewer steps are involved (no preligation, end repair, chemical extraction, or agarose gel electrophoresis and elution are needed), and higher cloning efficiencies are obtained (CviJI** digested and column fractionated DNA transforms 3-16 times more efficiently than sonicated, end-repaired, and agarose fractionated DNA).

Bacteriophage lambda↗
PubMed1992

Inhibition of factor X, factor V and prothrombin activation by the bis(lactobionic acid amide) LW10082.

The minimum concentrations of heparin, dermatan sulfate, hirudin, and D-Phe-Pro-ArgCH2Cl required to delay the onset of prothrombin activation in contact-activated plasma also prolong the lag phases associated with both factor X and factor V activation. Heparin and dermatan sulfate prolong the lag phases associated with the activation of the three proteins by catalyzing the inhibition of endogenously generated thrombin. Thrombin usually activates factor V and factor VIII during coagulation. The smallest fragment of heparin able to catalyze thrombin inhibition by antithrombin III is an octadecasaccharide with high affinity for antithrombin III. In contrast, a dermatan sulfate hexasaccharide with high affinity for heparin cofactor II can catalyze thrombin inhibition by heparin cofactor II. A highly sulfated bis(lactobionic acid amide), LW10082 (Mr 2288), which catalyzes thrombin inhibition by heparin cofactor II and has both antithrombotic and anticoagulant activities, has been synthesized. In this study, we determined how the minimum concentration of LW10082 required to delay the onset of intrinsic prothrombin activation achieved this effect. We demonstrate that, like heparin and dermatan sulfate, LW10082 delays the onset of intrinsic prothrombin activation by prolonging the lag phase associated with both factor X and factor V activation. In addition, LW10082 is approximately 25% as effective as heparin and 10 times as effective as dermatan sulfate in its ability to delay the onset of prothrombin activation. The strong anticoagulant action of LW10082 is consistent with previous reports which show that the degree of sulfation is an important parameter for the catalytic effectiveness of sulfated polysaccharides on thrombin inhibition.

Antithrombin III↗
PubMed1992

Preservative-free artificial tear preparations. Assessment of corneal epithelial toxic effects.

Scanning electron microscopy was used to evaluate the corneal epithelium of rabbit eyes after administration of two preservative-free ocular lubricants, preservative-free artificial tear-1 (Hypotears PF) and preservative-free artificial tear-2 (Refresh), and 0.02% benzalkonium chloride. Animals were randomly assigned to either mild or exaggerated use regimens. A quantitative rating system was used to assess epithelial damage. With mild use, scanning electron microscopy revealed normal epithelial morphologic characteristics for both preservative-free artificial tear solutions (mean relative damage score, solution 1, 0.75 +/- 0.16; solution 2, 1.02 +/- 0.23), which were not significantly different from eyes treated with phosphate-buffered saline (1.38 +/- 0.38) or a mild dosage regimen of 0.02% benzalkonium chloride (1.20 +/- 0.12). Exaggerated use with preservative-free artificial tear solutions (solution 1, 1.31 +/- 0.21; solution 2, 1.35 +/- 0.08) induced minimal damage that was not different from control eyes treated with phosphate-buffered saline (1.26 +/- 0.13). Compared with an exaggerated use of 0.02% benzalkonium chloride (4.0 +/- 0.16), both preservative-free artificial tear solutions induced significantly less epithelial damage (P = .0001). These results suggest that with frequent-dosage regimens, preservation-free artificial tear solutions-1 and -2 are free of the toxic effects associated with preserved solutions.

Animals↗
PubMed1992

Temporal and spatial regulation of a novel gene in barley embryos.

The temporal and spatial pattern of expression of a novel barley gene is described. The gene has been identified through the differential screening of a cDNA library constructed to poly(A)+ RNA of zygotic embryos. Transcripts corresponding to the cDNA, pZE40, become abundant in the non-axial tissues of the developing embryo within 8-10 days after anthesis, when steady-state levels are high in the scutellum, coleoptile and coleorhiza, with the exception of the scutellar epithelium. This expression pattern is maintained throughout maturation of the embryo until levels eventually decline as the grain desiccates. On germination, there is a transient re-appearance of mRNA to pZE40, with accumulation specifically restricted to the scutellum of the seedling. In situ hybridization has enabled the detection of transcripts elsewhere in the barley plant, in highly localized groups of cells. The timing and cell specificity of expression suggests the gene product is involved in the synthesis and/or transport of metabolites.

Base Sequence↗
PubMed1992

The frequency of translocations after treatment for Hodgkin's disease.

We studied the frequency of translocations in peripheral blood lymphocytes of patients with Hodgkin's disease to determine the extent of chromosome changes induced by radiation or radiation and chemotherapy. Comparisons were made to patients with second cancers to determine if this population is more susceptible to the effects of treatment. Group one included six patients with newly diagnosed Hodgkin's disease who were treated with radiation only. Group two included Hodgkin's disease patients who were treated 12-24 years previously and have been continuously free of disease. Five of these patients were treated with radiation only and five patients received radiation and mechlorethaminehydrochloride, oncovin, procarbazine, prednisone (MOPP) chemotherapy for six cycles. Group three included three patients who developed a second cancer after successful treatment for Hodgkin's disease. Two of these patients had a sarcoma within the radiation field and one had breast cancer. Metaphase spreads were obtained from cultured lymphocytes and hybridized with a chromosome 4 specific probe. After fluorescein staining, approximately 1000 metaphases were scored per patient. In group one only one patient in six demonstrated translocations in chromosome 4 before treatment for a mean frequency of .0009. After treatment the frequency of translocations increased to a mean of .016 (p = .036) (range .006-.034). Group two patients treated with radiation only had a mean translocation frequency of .012 (range .004-.022) in comparison to the radiation/mechlorethaminehydrochloride, oncovin, procarbazine, prednisone chemotherapy treated patients who demonstrated a mean frequency of .016 (p = .425) (range .0009-.023). The third group of second cancer patients showed inconsistent translocation frequencies of .002, .020, and .035. Of these patients, the one who demonstrated the greatest frequency of translocations (.035) was treated with mechlorethaminehydrochloride, oncovin, procarbazine, prednisone/adriamycin, bleomycin, vinblastine, decadron) and radiation. Our data demonstrates a statistically significant increase in translocations detected after radiation. When compared to combined modality therapy a greater mean frequency of translocations is observed over radiation alone; however, this was not statistically significant. In the three patients who developed second cancers in our series we saw no consistent increase in translocation frequency compared to Hodgkin's disease patients who did not develop a second cancer.

Antineoplastic Combined Chemotherapy Protocols↗