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PubMed1998

Membrane-mediated sample loading for automated DNA sequencing.

A new and improved sample loading method for DNA sequencing gels using oligo/polynucleotide binding membranes is described. The labeled DNA sequencing fragments were spotted onto a membrane sample loader, which was then placed in contact with the precast polyacrylamide separation gel. In this way, the time-consuming sample well loading by the tedious pipetting procedure was avoided. The spotted DNA fragments remain immobilized on the membrane until the separation process is initiated by the application of the electric field (an active DNA release mechanism). This novel technique enables sample loading outside of the separation platform, thereby allowing full utilization of various automated sample preparation and liquid handling (robotics) systems, resulting in "real" automated DNA sequencing. The loaded membranes can be stored for more than 24 hours for later use.

Automation↗
PubMed1998

Preparative capillary zone electrophoresis in combination with off-line graphite furnace atomic absorption for the analysis of DNA complexes formed by a new aminocoumarine platinum (II) compound.

Calf thymus DNA was incubated in vitro with a new aminocoumarin platinum (II) complex in order to study its interaction with DNA. The platinated DNA was hydrolyzed enzymatically to the 5'-mononucleotide level using DNAase I and nuclease P1. Analysis of the DNA hydrolysate with capillary zone electrophoresis (CZE), using sample stacking, revealed the presence of unhydrolyzed oligonucleotides in the platinated DNA. A homemade system, using only some plastic pipet tips, was constructed to collect the oligonucleotide fraction during CZE analysis. The platinum content of this fraction was determined using graphite furnace atomic absorption with Zeeman background correction. This system proved to be a useful tool to detect platinated DNA species (with a quantifiable detection limit for the detection of platinum of 0.78 ng). Subsequent gel filtration experiments confirmed the presence of high molecular weight oligonucleotides that were platinated. This was proven by reversal of the platination using thiourea and subsequent enzymatic hydrolysis to 5'-mononucleotides.

Animals↗
PubMed2006

Ultra-slim laminated capillary array for high-speed DNA separation.

We developed a new kind of capillary array for electrophoresis by using the numerical-control (NC) wiring technique conventionally used to produce printed-circuit boards. Laminating two polyimide sheets after laying cylindrical capillaries between them according to designed geometries, we fabricated a 16-lane laminated capillary array (LCA) 9.9 cm long, 7.2 cm wide, and 0.5 mm thick in which the effective length of all capillaries was only 10.9 cm. This compact LCA thus had separation columns as short as those in capillary array electrophoresis chips fabricated by lithography techniques. Like conventional capillary arrays, it also enabled pipetting-less direct injection of analytes from sample preparation plates. Using the LCA with LIF detection and a replaceable fluid sieving matrix, we demonstrated high-speed ssDNA fragment separations. At an electric field strength of 316 V/cm, 15 fragments ranging from 50 to 500 bases were completely separated within 5.8 min in all lanes. The lane-to-lane CV of migration time was only 0.38%, and the fragment size for which the resolution per base was 0.59 was 258 +/- 15 bases (average +/-SD).

DNA, Single-Stranded↗
PubMed2004

DGGE-based whole-gene mutation scanning of the dystrophin gene in Duchenne and Becker muscular dystrophy patients.

Duchenne and Becker muscular dystrophy (DMD and BMD) are caused by mutations in the dystrophin gene. Large rearrangements in the gene are found in about two-thirds of DMD patients, with approximately 60% carrying deletions and 5-10% carrying duplications. Most of the remaining 30-35% of patients are expected to have small nucleotide substitutions, insertions, or deletions. To detect these subtle changes within the coding and splice site determining sequences of the dystrophin gene, we established a semiautomated denaturing gradient gel electrophoresis (DGGE) mutation scanning system. The DGGE scan covers the dystrophin gene with 95 amplicons, PCRed either individually or in a multiplex setup. PCR and pooling were performed semiautomatically, using a pipetting robot and 384-well plates, enabling concurrent amplification of DNA of four patients in one run. Amplification of individual fragments was performed using one PCR program. The products were pooled just before gel loading; DGGE requires only a single gel condition. Validation was performed using DNA samples harboring 39 known DMD variants, all of which could be readily detected. DGGE mutation scanning was applied to analyze 135 DMD/BMD patients and potential DMD carriers without large deletions or duplications. In DNA from 25 out of 44 DMD patients (57%) and from 5 out of 39 BMD patients (13%), we identified clear pathogenic changes. All mutations were different, with the exception of one DMD mutation, which occurred twice. In DNA from 10 out of 44 potential DMD carriers, including four obligate carriers, we detected causative changes, including one pathogenic change in every obligate carrier. In addition to these pathogenic changes, we detected 15 unique unclassified variants, i.e., changes for which a pathogenic nature is uncertain.

DNA Mutational Analysis↗
PubMed1994

A robotics-assisted procedure for large scale cystic fibrosis mutation analysis.

We describe a convenient, efficient, semiautomated protocol for assaying large numbers of DNA samples for over 20 mutations causing cystic fibrosis. The protocol uses the following: (1) a programmable robotic workstation to perform rapid pipetting and dot-blotting operations, (2) an allele-specific oligonucleotide hybridization in a single water bath without correcting for G+C content of oligonucleotides, and (3) a combinatorial system that allows direct determination of the genotype for more frequent mutations. We have used this system routinely for 16 months for carrier detection and for diagnosis of cystic fibrosis. The method can be readily applied to any combination of allele-specific oligonucleotide assays whether for multiple alleles at one locus or for a few alleles at multiple loci.

Base Sequence↗
PubMed1984

A general method for preparing intact nuclear DNA.

Naked nuclear DNA is easily sheared. Two general methods are described for preparing intact DNA in a stable form that can be pipetted without breaking it. Cells are encapsulated in agarose microbeads and then lysed in a non-ionic detergent (i.e., Triton X-100) and 2 M NaCl or an ionic detergent (e.g., sodium or lithium dodecyl sulphate) in low salt. Most cellular protein and RNA then diffuse out through pores in the beads to leave encapsulated and naked DNA which is nevertheless accessible to enzymes and other probes. Remarkably, considerable structure is preserved since the DNA is supercoiled and chromosomes retain their shape.

Cell Nucleus↗
PubMed1995

Cadaverine induces closing of E. coli porins.

We have used the electrophysiological technique of patch-clamp to study the modulation of Escherichia coli porins by cadaverine. Porin channels typically have a very high probability to be open, and were not known to be inhibited by specific compounds until the present study. Experiments performed on patches of outer membrane reconstituted in liposomes reveal that cadaverine applied to the periplasmic side increases the frequency of channel closures in a concentration-dependent fashion, and thereby decreases the total amount of ion flux through a porin-containing membrane. The positive charge on cadaverine is important for inhibition, because the effect is relieved at higher pH where fewer polyamine molecules are charged. Modulation is observed only at negative pipet voltages, and therefore confers voltage dependence to porin activity. Cadaverine increases the number and duration of cooperative closures of more than one channel, suggesting that it does not merely block the pore but exerts its kinetic effect allosterically. As a biological assay of porin inhibition, E. coli behavior in chemotaxis swarm plates was tested and found to be impaired in the presence of cadaverine. Polyamines are naturally found associated with the outer membrane of E.coli, but are lost upon fractionation. We postulate that cadaverine might be a natural regulator of porin activity.

Bacterial Outer Membrane Proteins↗
PubMedDate not supplied

Standardized methods for semen evaluation in a multicenter research study.

Semen evaluation methodology is complex and difficult to standardize. Rigorously standardized laboratory protocols and strict quality control (QC) are essential for meaningful comparison of data from multiple sites. We describe the methods used for determination of semen volume, sperm concentration, and percent sperm motility in the Study for Future Families, a multicenter study of semen quality in the United States. Each of these 3 semen parameters was assessed using 2 techniques, which provided the opportunity to compare precision and assess suitability for multicenter studies. Detailed protocols were used, and technicians were centrally trained. A total of 509 semen evaluations were performed. Semen volume measured by weight was greater (P <.0001) than that determined by pipetting (3.7 +/- 1.6 mL vs 3.2 +/- 1.6 mL). Sperm concentration determined using hemacytometer chambers was consistently higher (P <.001) than that using disposable MicroCell chambers (81.0 x 10(6)/mL vs 65.9 x 10(6)/mL). Precision was slightly greater for the MicroCell chamber. The percentage of motile sperm was assessed by a simple counting technique as well as by the World Health Organization categorical method that assigns individual motile sperm to "a," "b," and "c" categories on the basis of progression. When these 3 categories were collapsed, the methods provided values that were not statistically different (P >.05), although the collapsed values tended to be higher (58.1% vs 51.6%) and less precise (CV 7.7% vs 4.1%) for the categorical method than for motility determined using the simple method. The data obtained in this study demonstrate the critical need for rigorous standardization of protocols and techniques for multicenter studies.

Fertility↗
PubMed2002

Cytotoxicity of modern dentin adhesives--in vitro testing on gingival fibroblasts.

The present investigation was designed to test cellular toxicity of modern dentin adhesives. With the use of the products Ariston Liner, Etch & Prime 3.0, Optibond Solo, Prime & Bond NT, Scotchbond 1, and Syntac Sprint, test specimens were prepared according to the manufacturers' instructions and transferred into a culture medium. Eluates were obtained and pipetted onto fibroblast cultures, incubated, and subsequently stained. The respective cell densities and the numbers of normal, altered, and dead cells were determined and compared with control cell cultures. Statistical analysis of the data showed that all materials caused cytotoxic effects. Scotchbond 1 displayed the highest number of dead cells. The difference was statistically significant compared to Etch" 3.0, Optibond Solo, Prime&Bond NT, and the control. The lowest cell density was found for Scotchbond 1 and Ariston Liner. The difference was also statistically significant in comparison with Etch" 3.0, Optibond Solo, Prime&Bond NT, and the control. To conclude, all tested dentin adhesives caused cytotoxic reactions. Taking the limitations of an in vitro experiment into consideration, Prime&Bond NT, Optibond Solo, and Etch" 3.0 appear to be the most recommendable products, and Scotchbond 1 and Ariston Liner the least.

Acrylates↗
PubMed1978

Hydraulic permeability of hollow-fiber membranes.

Two experimental methods have been developed to characterize the pressure-driven flow of a liquid through the walls of single hollow-fiber membranes. In one method, the permeation rate is measured directly by following the air-water interface in a pressurized pipet connected to a hollow fiber which is sealed at one end. With the second method, the permeation rate is determined by tracking the decent of an air bubble inside a pressurized hollow fiber sealed at one end. Results obtained by the two experimental methods are in good agreement. Darcy's law is used to analyze the experimental data because the Darcy permeability constant, k is an intrinsic property of the material. The membrane dimensions and the Darcy permeability constant for reconstituted collagen hollow fibers are shown to be quite sensitive to hydrogen ion concentration and ionic strength. A conceptual link between the Darcy permeability constant and the membrane microstructure is obtained by combining the the aligned-rod structural model for reconstituted collagen proposed by Kramer with a hydrodynamic calculation due to Happel and electrical double-layer theory. On the average, the predictions of this model for volume fraction solids and microstructure dimensions are in reasonable agreement with experimental observations.

Collagen↗
PubMed2007

Mechanical stimulation induces morphological and phenotypic changes in bone marrow-derived progenitor cells within a three-dimensional fibrin matrix.

One of the major limitations in tissue engineering is cell sourcing. Multipotent progenitor cells appear to have many promising features for that purpose. Mechanical stimulation is known to play an important role in determining cell phenotype. The aim of this work was to investigate the effects of cyclic stretch on rat bone marrow derived progenitor cell (BMPC) morphology and smooth muscle-directed differentiation within a three-dimensional fibrin matrix. BMPCs were suspended in a fibrin gel, pipetted into the trough of Flexcell Tissue-Train plates, and stimulated with 10% longitudinal cyclic stretch at 1 Hz for 6 days. Unconstrained (stress- and strain-free) and static anchored (constrained but not stretched) samples were used as controls. Stress filament area per cell was increased in the stretched samples compared to static anchored and free-float controls. Cells in the free float controls were randomly aligned, while they aligned parallel to the direction of the stress or strain in the other groups. Immunofluorescence suggested an increased expression of smooth muscle markers (smooth muscle alpha actin and h1-calponin) in both stretched and constrained control samples, but not in unconstrained controls. Qualitative assessment suggested that collagen production was increased in both mechanically stimulated samples. Proliferation was inhibited in stretched samples compared to the constrained controls. This work suggests an ability of rat BMPCs to differentiate toward a smooth-muscle-cell-like lineage when exposed to biomechanical stimulation in a three-dimensional model. The observation that the constrained samples induced changes in BMPCs suggests that stress alone may be stimulatory, but addition of cyclic stretch appears to augment the responses.

Animals↗
PubMed2007

Photocatalytic antibacterial effect of TiO(2) film formed on Ti and TiAg exposed to Lactobacillus acidophilus.

When irradiated under near-ultraviolet (UV) light, TiO(2) exhibits strong bactericidal activity. The TiO(2) photocatalyst would be effective on orthodontic appliances after its antibacterial effect on the carcinogenic microorganism Lactobacillus acidophilus is evaluated. To compare the antibacterial effect of two crystalline forms of TiO(2), rutile and anatase, thermal oxidation and anodic oxidation were employed to form each structure, respectively. The antibacterial effect of TiO(2) film on TiAg was also compared with that on Ti. Bacterial solutions were pipetted onto the TiO(2)-coated specimen and illuminated with UVA (2 x 15 W, black light, 356 nm) up to 100 min and the reaction solutions were incubated to count the colony-forming units. The antibacterial activity of the coated specimens was similar to that of the uncoated group. The antibacterial activity of the coated specimens of TiAg was not different from that of Ti. TiO(2) coatings formed on both Ti and TiAg specimens did not exhibit cytotoxicity on the L-929 cells of mice.

Alloys↗
PubMed1989

Cholesterol assays in the Seralyzer instrument.

We evaluated the Seralyzer instrument for the assay of serum cholesterol and compared it to the Kodak Ektachem method. The Seralyzer showed good accuracy in the analysis of cholesterol in Abell-Kendall-verified serum pools, and the bias from the expected value was small in all cases but one. The Seralyzer exhibited CVs of less than 5% in all cases and good comparison with the Ektachem method. The Seralyzer is easy to use; however, some training in the proper pipetting technique is necessary. The Seralyzer meets medical needs criteria of total error greater than 5% from the true cholesterol value.

Blood Chemical Analysis↗
PubMed1995

Evaluation of an automated urine chemistry reagent-strip analyzer.

We evaluated the Miles Inc., Clinitek Atlas Automated Urine Chemistry Analyzer for 11 tests: bilirubin, color, glucose, ketones, leukocyte esterase, nitrite, occult blood, pH, protein, specific gravity, and urobilinogen. The instrument uses a roll of reagent strips affixed to a clear plastic support; urine specimens are automatically pipetted onto these strips. The instrument measures the pads' color using reflectance colorimetry. Specific gravity is measured using a fiberoptic refractive index method. Four hospitals participated in the evaluation, and tests were performed only on fresh urine samples. We found the instrument easy to use; it has walk-away capability with up to 40-specimen loading capacity plus spaces for STATs, calibrators and controls. We found good comparability with chemical tests and other nonreagent strip procedures, as well as good agreement with the Miles Inc. Clinitek 200+ urine chemistry analyzer and visual reading of the Miles Inc. Multistix Reagent Strips. The Clinitek Atlas is rugged and reliable, and is suitable for a high-volume urinalysis laboratory.

Automation↗
PubMed1989

Rapid deformation of "passive" polymorphonuclear leukocytes: the effects of pentoxifylline.

Entry times for spherical (no pseudopods) polymorphonuclear leukocytes (PMNs) into a 4 microns micropipet have been measured as a function of pipet suction pressure (2,500-20,000 dyn/cm2) and concentration of the drug pentoxifylline (PTX, 0.1-10.0 mM). For control cells (0 mM PTX), entry rates (reciprocal entry times) increased almost linearly with increasing suction pressure, indicating a Newtonian-like behavior. With incubation in PTX solutions, entry rate vs. suction pressure became increasingly non-linear, suggesting a shear-thinning effect for the dissipative structure. At a given suction pressure the rate of entry showed a dose-dependent increase with increasing PTX concentration, the effect being most pronounced at high suction pressures (20,000 dyn/cm2). Also, with increasing PTX concentration two other effects were observed: i) there was a decreased incidence of cells that displayed pseudopodia, and ii) there was an increased incidence of cells forming hernias and an increased streaming of cell cytoplasm during aspiration. The first observation points to a down-regulation of the cell's functional ability to "activate" in response to surface/chemical stimuli, and the second indicates that both the cortical and cytoskeletal networks are weakened either by disruption and/or reduction in density of the protein polymers. These observations are in line with other recently published experiments which suggest that the rheological effects of pentoxifylline on PMNs may be associated with the state of actin.

Actins↗
PubMed2006

Wound-induced p38MAPK-dependent histone H3 phosphorylation correlates with increased COX-2 expression in enterocytes.

Gastrointestinal epithelial cell damage triggers an important biological response called restitution, a process aimed at re-epithelializing the wounded areas. Unfortunately, little is known about the intrinsic molecular signaling events implicated in this host response. We hypothesized that wounding intestinal epithelial cells activates signaling pathways leading to chromatin modification and COX-2 upregulation during restitution. Confluent rat IEC18 cells were mechanically wounded by multiple parallel scratches using a pipet tip. NF-kappaB(Ser536), p38, and histone H3(Ser10) (H3S10) phosphorylation were determined by Western blot using specific phospho-antibodies. COX-2 gene expression was evaluated by RT-PCR, Western Blot, and ELISA. Association of phosphorylated H3, RelA (NF-kappaB), and RNA polymerase II to the COX-2 gene promoter was evaluated by chromatin immunoprecipitation (ChIP). The specific inhibitors Bay11-7082 and SB239063 as well as Ad5IkappaB-superrepressor (Ad5IkappaBAA) and Ad5dnp38 were used to block NF-kappaB- and p38-signaling pathways, respectively. Wounding induced a rapid and sustained (24 h) phosphorylation of RelAS536, H3S10, and p38MAPK in enterocytes. ChIP analysis of the COX-2 gene promoter demonstrated the presence of phospho-H3S10 and recruitment of RelA and RNA polymerase II, a process blocked by SB239063. Finally, molecular blockade of NF-kappaB (Ad5IkappaBAA) or p38MAPK (Ad5dnp38) signaling strongly inhibited enterocyte restitution. p38MAPK-dependent histone 3 phosphorylation is an important component of the intestinal wound-healing response. Targeting-signaling pathways selectively involved in healing/restitution may provide a novel means to maintain or re-establish host intestinal barrier integrity.

Animals↗
PubMed2004

Methods for determining the composition of nasal fluid by X-ray microanalysis.

The nasal fluid is an easily accessible form of airway surface liquid. The objective of this study was to find a technically easy and reproducible method for sampling and analysis of this fluid. In a pilot study, several methods to carry out X-ray microanalysis of sub-microliter droplets were compared. Acceptable results were obtained with several of these methods (pipeting on filter paper or analysis of frozen-hydrated droplets at low temperature). Nasal fluid was collected from the inferior turbinate with a micropipette after occlusion of a nostril for 5-10 minutes. Ion concentrations in nasal fluid from six control subjects were (in mM, mean +/- standard error): sodium (Na) 127 +/- 6, chloride (Cl) 140 +/- 7, potassium (K) 27 +/- 3, and calcium (Ca) 5 +/- 1. This sampling method proved difficult to apply to cystic fibrosis (CF) patients because of the viscous quality of their nasal secretion. Therefore, an alternative method was devised. Sephadex G-25, ion exchange beads were mounted on double-sided tape, which was stuck on a filter paper as support. The filter paper was applied for 10 minutes to the nostril of a subject, and kept loosely in place. During the exposure period, the nasal fluid equilibrates with the beads. After removal of the filter paper with the beads from the nostril, the beads were rinsed with a hydrophobic volatile silicone oil to remove excess nasal fluid, dried, and analyzed. This method of collection is not cumbersome for the subject and gives results similar to those obtained by the direct collection method: Na 142 +/- 28 mM, Cl 150 +/- 36 mM, K 43 +/- 10 mM (mean and standard error of four determinations). Small differences between the filter method and the bead method can be explained by the fact that the filter method measured total nasal fluid, whereas the bead method measures predominantly the fluid component. Subjects suffering from mild respiratory illness or rhinitis had higher values for Na, K, and Cl in their nasal fluid.

Adult↗
PubMed1986

Effect of cutting the zona pellucida on the pronuclear transplantation in the mouse.

A new and reliable pronuclear transplantation procedure for the mouse egg has been developed by McGrath and Solter ('83). To overcome the technical difficulties of such a procedure, especially in uniformly preparing enucleation pipettes and in reducing damages during micromanipulation, we have examined the effect of cutting the zona pellucida of the eggs. By making a slit in the zona of an egg, the time for pipetting and exchange of pronuclei between eggs was shortened because the sharp tip of the pipette was not necessary. Although the proportion of pregnant recipients and young obtained after transfer of pronuclear transplanted eggs cultured for 1 day or 3 days was quite low, it was significantly increased (70% for pregnancy rate and 32% for the young) following transfer of eggs cultured for 4 days. These values were comparable with those after transfer of unoperated eggs cultured to morulae and blastocysts.

Animals↗