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PubMed1993

The Pearson product-moment correlation coefficient is better suited for identification of DNA fingerprint profiles than band matching algorithms.

A database of DNA fingerprint profiles from permanently established human and animal cell lines was prepared with a computer program originally designed for numerical taxonomy of bacteria. Identifications of cell line DNA profiles were performed, both by the Pearson product-moment correlation coefficient and by band matching. Under the conditions used the Pearson product-moment correlation coefficient was consistently more reliable.

Algorithms↗

PubMed1995

Parallel genome analysis by one- and two-dimensional DNA fingerprinting in human gliomas.

The detection of DNA variation in cancers is an important step in elucidating the mechanism of tumorigenesis. Using the strategy of multipoint genome analysis we detected many differences between glioma-derived and constitutional DNA by customary DNA fingerprinting with simple repetitive oligonucleotide probes. Amplification of the epidermal growth factor receptor (EGFR) gene has been found to be easily detectable as new or highly intensified bands in one-dimensional (1-D) DNA fingerprints of glioblastoma DNA generated with probes (GTG)5 or (GT)8. However, in most low-grade astrocytomas, 1-D DNA fingerprinting has failed to reveal any genomic abnormalities. In these cases a two-dimensional (2-D) technique was successfully employed that is based on size separation in neutral gels followed by sequence-dependent separation in denaturing gradient gels and hybridization with several mini- and microsatellite core probes. The hundreds of spots visualized with this technique were used to detect subtle changes probably occurring as the initial steps of tumorigenesis in human gliomas. On average, five of the approximately 580 spots generated by probes CAC and 33.6 were found to be altered in tumor DNA; 80% of the alterations were spot losses, the rest being spot gains or amplifications. Computer-based image analysis using an external lambda marker provided a stringent way to compare spot patterns generated by 2-D DNA fingerprinting. In comparisons performed between typing patterns generated on the same gel, 99% of truly identical spots were confirmed by the software. In intergel comparisons 84% of identical spots were matched on the basis of the marker information alone.

Base Sequence↗

PubMed1996

Use of internally controlled reverse transcriptase-polymerase chain reaction for absolute quantitation of individual multidrug resistant gene transcripts in tissue samples.

Research into the relative importance of P-glycoprotein (pgp) overexpression, in comparison to other mechanisms of multidrug resistance (mdr) phenotype development, has been hampered by difficulties of measurement in clinical samples. The small size, heterogeneity and often poor quality of clinical specimens renders the quantitation of mdr mRNA species by Northern analysis or RNAse protection difficult. The reverse transcriptase-polymerase chain reaction (RT-PCR) assay has both the sensitivity and specificity to make it suitable for the analysis of mdr mRNA levels in clinical samples. It also has a significant speed advantage over Northern and RNAse protection analysis. Unfortunately the variable nature of the reactions involved have made it difficult to obtain accurate and reproducible quantitative data. To overcome this difficulty we constructed internal RNA standards to each human and rat mdr mRNA species. When included in the RT-PCR reaction these internal standards allow both comparative and absolute quantitation of individual mdr family mRNA levels.

Animals↗

PubMed1997

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.

Comparative protein modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative protein modeling that consists of SWISS-MODEL, a server for automated comparative protein modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-MODEL, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-MODEL Repository, a database containing more than 3500 automatically generated protein models. By making such tools freely available to the scientific community, we hope to increase the use of protein structures and models in the process of experiment design.

Amino Acid Sequence↗

PubMed2005

Rapid differentiation of Fusarium oxysporum isolates using PCR-SSCP with the combination of pH-variable electrophoretic medium and low temperature.

Differentiation of Fusarium oxysporum is significantly important for unraveling the pathogenetic mechanism of Fusaria wilts. In this study, isolates of F. oxysporum were screened from the soils in the rhizosphere of watermelon plant by Komada medium and differentiated by SSCP approach with the combination of pH-variable electrophoretic medium (Tris-MES-EDTA (TME), pH 6.1) and low temperature (9 degrees C). We found that TME was a good electrophoretic medium and its pH value was variable over the course of electrophoresis in our apparatus. The pH-variable electrophoretic medium made more contribution for the better differentiation of F. oxysporum isolates than low temperature. The combination of TME pH 6.1 and low temperature showed an improved effect on resolution of ssDNAs. Leaving partial nondenatured dsDNA for SSCP was advantageous for differentiation of F. oxysporum isolates. The SSCP patterns of F. oxysporum isolates proved to be highly reproducible. Sequencing data confirmed that this SSCP method could detect one single base change within the 550 bp PCR fragment from the ribosomal internal transcribed spacer region of F. oxysporum.

Base Sequence↗

PubMed2006

A precise mRNA quantification method using CE-based SSCP.

Even though mRNA quantification provides significant information for biological analysis, current methods such as Northern blot analysis and real-time PCR are known to be laborious and lacking in precision. In this study, we demonstrate a new precise mRNA quantification method using CE based on SSCP (CE-SSCP) coupled with reverse transcription. mRNA samples could be simply analyzed for the quantification directly with reverse transcript obtained from a single reaction. This helps to avoid considerable errors generated by a series of the tedious manual steps. Also, unlike real-time PCR, reverse transcripts can be directly quantified by CE-SSCP in this method without further data estimation. Reproducibility and accuracy of CE-SSCP for mRNA quantification was examined using enhanced green fluorescent protein (eGFP) mRNA transcribed in vitro. Specific reverse transcription primer was determined for the accurate quantification of eGFP mRNA from total RNA obtained from the recombinant Escherichia coli. Using elongation factor Tu mRNA as an internal standard, it was shown that sample-to-sample variation could be minimized. Expression kinetics at both mRNA level and protein level was studied and the potential of CE-SSCP in expression analysis was demonstrated by comparison with the eGFP activity assay.

Electrophoresis, Capillary↗

PubMed1992

Clinical utility of ambulatory blood pressure monitoring in target organ complications and equipment choices.

Although population studies have demonstrated a relationship between casual office blood pressures and target organ events, the variability of these blood pressure measurements for individual patients has generated an interest in the role of ambulatory blood pressure monitoring for defining the presence of hypertension and assessing the response to therapy. Noninvasive devices provide fewer data than intra-arterial ambulatory blood pressure monitoring devices, but are safer. No current noninvasive device performs well during ambulation. Rigorous evaluation of these rapid proliferating electronic devices is important, as would be the case with any new antihypertensive agent. Although ambulatory blood pressure measurements correlate better with target organ damage for groups of patients than do casual office measurements, the predictability and limited data on reproducibility for individual patients does not support widespread application for routine testing for hypertensive patients. Ambulatory blood pressure monitoring should be viewed as a standard research tool for the evaluation of new cardiovascular drugs.

Ambulatory Care↗

PubMed2002

The influence of material and design features on the mechanical properties of transpedicular spinal fixation implants.

This study describes the finding and performance of mechanical strength and corrosion testing procedures for comparative examination of multiple internal transpedicular spine fixators. Seven different implant models from five different manufacturers were compared regarding their bending strength and fatigue resistance. Because of the unacceptably high levels of time and material that they require, ISO and ASTM testing standards are not applicable to comparative testing. In addition, there is a lack of knowledge about clinically defined and proven strength-limit values. Therefore, actual standard testing procedures have been modified and extended to corrosion testing. Overall, the effort necessary to obtain reproducible comparative data has been reduced significantly. Although a reduced number of implants of each type were available for destructive testing, the results revealed fundamental differences in the tested implants between different materials and design features. During fatigue testing some of the implants showed poor corrosion properties. Because spinal fixation implants tend to be used as long-duration implants, corrosion testing as well as comparative strength testing with clinically successful implant models should be performed as preclinical evaluations.

Biocompatible Materials↗

PubMed2002

Distance and exposure dependent effective dielectric function.

In an effort to develop a dielectric screening function for molecular dynamics simulations of biomolecules in implicit solvent, effective dielectric constants (D(eff)) for a large number of atom pairs in a typical globular protein are calculated by continuum electrostatics. Plots of D(eff) versus the intercharge distance are in general sigmoidal with the characteristics of the curve depending on the distance of the two charges from the dielectric boundary and, secondarily, on the extent to which the area surrounding each charge is occupied by solvent (the "exposure"). The D(eff) values were fitted to an empirical, analytical function of these parameters that reproduces the data reasonably well, although considerable scatter exists in the range of D(eff) from 30 to 80. In the system used for parameterization, the mean square deviation of electrostatic interaction energies with this function is 0.48 kcal/mol, compared to 1.45 for an analytical Generalized Born model and 1.52 for the linear distance-dependent dielectric model. When tested in other proteins of varying size and compactness, the present function is superior to both of the above models, except for a fully unfolded polypeptide chain, where the Generalized Born model is superior.

Journal Article↗

PubMed2004

Multicut-HDMR with an application to an ionospheric model.

A new High Dimensional Model Representation (HDMR) tool, Multicut-HDMR, is introduced and applied to an ionospheric electron density model. HDMR is a general set of quantitative model assessment and analysis tools for improving the efficiency of deducing high-dimensional input-output system behavior. HDMR describes an output [f(x)] in terms of its input variables (x = [x(1), x(2), em leader, x(n)]) via a series of finite, hierarchical, correlated function expansions. Various forms of HDMR are constructed for different purposes such as modeling laboratory or field data, or reproducing a complicated mathematical model. The Cut-HDMR technique, which expresses f(x) with respect to a specified reference point x in the input space, is appropriate when the input space is sampled in an orderly fashion. However, if the desired domain of the input space is too large, the HDMR function expansion may not converge, and Cut-HDMR will be unable to accurately approximate f(x). The new Multicut-HDMR technique addresses this problem through the use of multiple reference points in the input space.

Journal Article↗

PubMed2004

Accurate mass measurement and tandem mass spectrometry of intact globin chains identify the low proportion variant hemoglobin Lepore-Boston-Washington from the blood of a heterozygote.

Within a mixture of proteins, minor polymorphic components are difficult to identify using a conventional proteomic approach. Their identification generally requires multi-dimensional separation steps, before or after proteolytic cleavage, followed by sequence analysis of the proteolytic products. In this study, we investigated the potential of tandem mass spectrometry for protein characterization by identifying the delta-beta hybrid human hemoglobin variant Lepore-Boston-Washington using electrospray ionization tandem mass spectrometry. Hemoglobin Lepore-Boston-Washington occurs mainly in heterozygotes, where it comprises approximately 10% of the total non-alpha-chains, the dominant non-alpha-chain being the normal beta (approximately 90%). Furthermore, Hemoglobin Lepore-Boston-Washington has an average molecular mass (15,865.23 Da) that is only 2 Da lower than that of the normal beta-chain (15,867.24 Da). Consequently, it cannot be resolved from the normal beta-chain by mass spectrometry. Here we show how Hemoglobin Lepore-Boston-Washington was identified directly from the diluted blood of a heterozygote by analyzing the product ions from the Lepore-Boston-Washington and normal beta-chain ions without prior separation of the individual chains. This study shows the potential of the tandem mass spectrometry for identifying a minor component in an unseparated mixture of proteins.

Amino Acid Sequence↗

PubMed1993

Competitive EIA for anti-HIV-2 detection in The Gambia: use as a screening assay and to identify possible dual infections.

The performance of a competitive EIA for the detection of HIV-2-specific antibody utilising a viral lysate antigen was assessed over a 3 year period in The Gambia, West Africa, and compared with a commercially available assay, ELAVIA-2, using three panels of sera. An immunodominant region of the transmembrane glycoprotein of an HIV-2 isolate (ANT 53) was also cloned and expressed in E. coli as a beta-galactosidase fusion protein and the resulting recombinant protein substituted in place of the existing viral lysate antigen. Competitive EIAs were found to be both a specific and sensitive means of reliably determining the HIV-2 status of an individual with a high predictive value, particularly when a strategy of concordant positive results in the two EIAs was used. When either anti-HIV-2 competitive EIAs were used in conjunction with a competitive EIA for anti-HIV-1 detection it was possible in the vast majority of cases to identify the virus-type infecting an individual and speciate HIV-1 and HIV-2 infections. A few sera which showed similar regression profiles when diluted over a serial tenfold dilution steps were identified as possible dual infections.

Acquired Immunodeficiency Syndrome↗

PubMed1989

Canine bone blood flow estimated with microspheres.

Blood flow rate in the periosteal and endosteal cortices of the diaphysis of long bones was determined in eight anesthetized adult dogs using the radioactively labeled microsphere method. The flow rate in endosteal and periosteal cortices is not significantly different unless the endosteal cortex contains cancellous bone from the medullary cavity. The highest flow rate is in the ulna, with 6.50 ml/min/100 g for the endosteal cortex and 5.15 ml/min/100 g for the periosteal cortex. The lowest flow rate is in the femur, with 2.89 ml/min/100 g for the endosteal cortex and 2.29 ml/min/100 g for the periosteal cortex. The results of this study indicate that variation of blood flow does exist between bones of dogs. However, the flow rates of individual bone on the left and right sides in the same dog are not significantly different. This indicates that the data are reproducible and reliable, and differences are not an inaccuracy of the radioactively labeled microsphere method. The results also demonstrate that there are no significant differences in bone blood flow as measured with small numbers (fewer than 400 microspheres per sample) and large numbers (more than 400 microspheres per sample) of microspheres. The adequate number of microspheres in each bone sample is 150-250. Therefore, a dose of 0.5 x 10(6) spheres/kg body weight can be sufficient.

Animals↗

PubMed1981

Continuous flow bead-bed dissolution apparatus for suppositories.

A bead-bed dissolution apparatus for suppositories was evaluated by measuring the release of benzocaine from various vehicles. During dissolution, suppositories soften, deform, disintegrate, and eventually pass through a phase change from a solid to an oil. The control of the interfacial area during dissolution is a key factor in obtaining experimentally reproducible release data. The proposed suppository dissolution apparatus was designed to provide greater constancy of the exposed suppository area for dissolution. The apparatus consisted of a glass bead-bed containing the suppository. A continuous flow of liquid was passed through the bead-bed at a constant rate. Direct contact of the suppository was maintained with the dissolution medium, confining the suppository within the beads.

Benzocaine↗

PubMed1982

Phase equilibria of nafcillin sodium-water.

The phase diagram for the binary system nafcillin sodium-water, was determined using differential scanning calorimetry (DSC) and polarized light microscopy. In the temperature range of -20-30 degrees, three crystalline forms and an amphiphilic liquid crystalline phase were detected. The stable crystalline form of nafcillin sodium (form alpha) and water exhibit a eutectic mixture containing 28% drug (w/w) at -1 degrees. In more dilute solutions a lower temperature eutectic (-5 degrees) occurs. The composition and form of nafcillin sodium in this eutectic are not known. The form -5 degrees eutectic was found to be metastable above 28% concentration and converted to form alpha. Two other crystalline forms were observed at 9 degrees (form beta) and 22 degrees (form gamma) at concentrations above 40%. The crystalline forms could not be further characterized due to their transient nature and existence in highly concentrated mixtures. A lamellar mesophase is present near ambient temperature in mixtures containing more than 55% nafcillin sodium. The phase equilibria were highly susceptible to supercooling. Temperature cycling methods were devised which gave reproducible DSC data and allowed construction of the phase diagram.

Calorimetry, Differential Scanning↗

PubMed1984

Myofacial pain dysfunction syndrome: a clinical study of asymptomatic subjects.

The diagnosis of myofacial pain dysfunction (MPD), commonly called temporomandibular joint syndrome, has traditionally been made on the presence of a group of clinical symptoms that produce pain and limitation of movement. The cause of this common illness has been the subject of controversy for over half a century. There has been a lack of agreement on diagnosis, a cause, and treatment. Advanced bioelectronic technology now makes an accurate diagnosis possible, based not merely on clinical symptoms, but on reproducible scientific data. A cause of MPD is discernable and reliable treatment possible, as well as long lasting resolution objectively monitorable with the Mandibular Kinesiograph (MKG 5-R) and Bioelectric Processor (EMIR). A study of mandibular movement and masticular muscle function of 26 "normal" subjects (i.e., clinically asymptomatic) revealed that the overwhelming majority did indeed have dysfunction of the muscles which move and posture the mandible. The significance of this study is twofold. First it demonstrates a valid testing procedure for measuring mandibular movement and muscle function. Second it establishes the fact that most individuals have a physical predisposition to MPD. Changes in the adaptive capacity of the neuromusculature by physical or emotional trauma could then precipitate MPD.

Adult↗

PubMed2003

A computer model of rigidity and related motor dysfunction in Parkinson's disease.

This work explores the involvement of spinal circuits in the generation of parkinsonian rigidity and related motor dysfunction. A computer model of spinal proprioceptive input processing, derived from previous work on spasticity modeling, was adapted to the simulation of parkinsonian rigidity. Model parameters were varied to generate simulations reproducing experimental data obtained using the pendulum test of the leg in 10 parkinsonian patients and 3 healthy subjects. Convenient reproductions of experimental traces in rigidity were obtained by the combination of a low reflex gain and a decrease in reflex threshold. These findings are consistent with studies reporting an increase of spinal interneuron excitability and proprioception deficits in Parkinson's disease (PD). Moreover, as the threshold parameter was much lowered, our model generated typical features of parkinsonian resting tremor, endorsing the hypothesis of a participation of a spinal oscillator in this disorder. Finally, tuning the reflex gain during simulations of rigidity resulted in the generation of active movement, opening some hypotheses on pathophysiology of motor dysfunction in PD, and notably, of akinesia. More generally, this work accredits the hypothesis of the involvement of an aperiodic, altered supra-spinal motor drive in PD, resulting in spinal dysfunction, through specific descending motor pathways. This may lead to a search for new (spinal) pharmacological targets in PD. It emphasizes further the value of computer modeling in understanding motor control in health and disease.

Computer Simulation↗

PubMed2001

Molecular dynamics simulations of a highly charged peptide from an SH3 domain: possible sequence-function relationship.

A seven-residue peptide that is highly conserved in SH3 domains despite being far from the active site has been shown by NMR to be stable in solution. This peptide, biologically important because it is a likely folding nucleus for SH3 domains, provides a challenging subject for molecular dynamics because it is highly charged. We present stable, 10-ns simulations of both the native-like diverging turn structure and a helical model. Free energies of these two conformations, estimated through MM-PBSA analysis using several force fields, suggest a comparable free energy (DeltaDeltaG < or =6 kcal/mol) for native and helix conformations. NOE intensities calculated from the native trajectory reproduce experimental data quite well, suggesting that the conformations sampled by the trajectory reasonably represent those observed in the NMR experiment. The molecular dynamics results, as well as sequence analysis of a diverse 690-member family of SH3 domain proteins, suggest that the presence of two elements is essential for formation of the diverging turn structure: a pair of residues with low helical propensity in the turn region and, as previously recognized, two hydrophobic residues to close the end of the diverging turn. Thus, these two sequence features may form the structural basis for the function of this peptide as a folding nucleus in this family of proteins.

Computer Simulation↗