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At least 739 records · Page 41Linked to original sources
PubMed1999

A high frequency of sequence alterations is due to formalin fixation of archival specimens.

Genomic analysis of archival tissues fixed in formalin is of fundamental importance in biomedical research, and numerous studies have used such material. Although the possibility of polymerase chain reaction (PCR)-introduced artifacts is known, the use of direct sequencing has been thought to overcome such problems. Here we report the results from a controlled study, performed in parallel on frozen and formalin-fixed material, where a high frequency of nonreproducible sequence alterations was detected with the use of formalin-fixed tissues. Defined numbers of well-characterized tumor cells were amplified and analyzed by direct DNA sequencing. No nonreproducible sequence alterations were found in frozen tissues. In formalin-fixed material up to one mutation artifact per 500 bases was recorded. The chance of such artificial mutations in formalin-fixed material was inversely correlated with the number of cells used in the PCR-the fewer cells, the more artifacts. A total of 28 artificial mutations were recorded, of which 27 were C-T or G-A transitions. Through confirmational sequencing of independent amplification products artifacts can be distinguished from true mutations. However, because this problem was not acknowledged earlier, the presence of artifacts may have profoundly influenced previously reported mutations in formalin-fixed material, including those inserted into mutation databases.

Base Sequence↗
PubMed2002

Molecular imaging of amyloid beta peptides in mouse brain sections using mass spectrometry.

A method is presented for direct spatial analysis of amyloid beta peptides in biological tissue sections. The technique takes advantage of the very high sensitivity of matrix-assisted laser desorption/ionization mass spectrometry and is implemented on a commercial instrument with modifications to only a few components and the software. With this setup, hundreds of molecular images can be generated simultaneously and within just a few minutes. The current features are an instrumental resolution of 50 microm and a sensitivity down to the attomol range. This new technology is applied to the study of amyloid beta peptide distribution in brain sections from mice, showing features reminiscent of Alzheimer's disease.

Alzheimer Disease↗
PubMed2003

Measurement of chemoresistance markers in patients with stage III non-small cell lung cancer: a novel approach for patient selection.

BACKGROUND: The long-term survival of patients with stage III non-small cell lung cancer treated with a combination of chemotherapy and radiation is 10% to 20%. Survival could potentially be increased and toxicity limited if one could identify patients most likely to respond to a particular treatment regimen. This project prospectively evaluated a panel of potential immunohistochemical markers of chemoresistance in a population of patients with pathology-confirmed stage III non-small cell lung cancer in order to determine the prognostic value of each marker in relation to response to chemotherapy or survival. METHODS: Immunohistochemical staining was performed on histologically positive mediastinal nodal specimens obtained from 59 patients (mean age, 62 years; range, 41 to 79 years) without evidence of distant metastatic disease treated with navelbine-based chemotherapy and external beam radiation therapy between 1996 and 2001. Included were markers for apoptosis (p53, bcl-2), drug efflux/degradation (MDR, GST-pi), growth factors (EGFr, Her2-neu), and mismatch repair (hMLH1, hMSH2). After chemotherapy, patients underwent radiologic evaluation for response measured by standard criteria. RESULTS: After a median 41 months of follow-up (range, 17 to 55 months), 43 patients had recurrent disease and 38 of these patients were dead of cancer (median cancer-free survival of 10 months and overall survival of 18 months). Patients who demonstrated a complete or partial response (n = 38) had a significantly improved survival (p = 0.002) compared with those with stable or progressive cancer (n = 21). Multivariable Cox step-wise regression analysis of marker expression associated overexpression of p53 and low expression of hMSH2 with poor treatment response and cancer death. CONCLUSIONS: These preliminary data suggest that marker expression may allow the separation of patients into low- and high-risk groups with respect to survival after combined navelbine-based chemotherapy and XRT. This could represent a novel method of selecting patients for a particular treatment regimen if these data are reproduced in a larger prospective trial.

Aged↗
PubMed1986

Influence of inhibitor binding on the internal motions of lysozyme.

Time-resolved laser-induced fluorescence depolarization measurements of internal motions in lysozyme are presented. The fluorescent dye eosin binds in a one-to-one complex with the enzyme, and is used both to measure the overall tumbling time constants and to probe the motions of residues in the region of binding. The precision and accuracy of the present method for determining the overall tumbling time constants compare favorably with those from other methods used in the literature. The extent of the internal motions, as described by a model independent order parameter, S2, is temperature dependent, and changes when the inhibitor N,N',N"-triacetylchitotriose, (GlcNAc)3, is bound to the active site of the enzyme. The observed temperature dependence and changes in S2 upon binding of (GlcNAc)3 are interpreted in terms of a nonharmonic model of the effective potential that is consistent with the picture of concerted motions in the protein. The values of the parameters of the potential that reproduce the data with and without the bound inhibitor imply that (GlcNAc)3 binding causes an increase in the rigidity of the protein, which agree qualitatively with other results on the lysozyme-(GlcNAc)3 system.

Kinetics↗
PubMed1986

Adrenergic modulation of the delayed rectifier potassium channel in calf cardiac Purkinje fibers.

We have investigated the modulation of the delayed rectifier potassium channel in calf cardiac Purkinje fibers by the neurohormone norepinephrine. We find that 0.5 microM norepinephrine increases this K channel current by a factor of 2.7. A maximal increase of about four was found for concentrations of 1 microM and above. Norepinephrine produced a small (less than 5 mV) and variable shift of the K channel reversal potential toward more negative values. The kinetics of the potassium channel are well described by a two-exponential process, both in the absence and presence of norepinephrine. However, norepinephrine substantially decreases the slower time constant with no significant effect on the fast time constant. Potassium channel activation curves in the presence of norepinephrine are very similar to control curves except at large positive potentials. A simple sequential three-state model for this channel can reproduce these data both with and without norepinephrine. The logarithms of the rate constants derived from this model are quadratic functions of voltage, suggesting the involvement of electric field-induced dipoles in the gating of this channel. Most of the kinetic effects of norepinephrine appear to be on a single rate constant.

Animals↗
PubMed1995

Calculation of translational friction and intrinsic viscosity. II. Application to globular proteins.

The translational friction coefficients and intrinsic viscosities of four proteins (ribonuclease A, lysozyme, myoglobin, and chymotrypsinogen A) are calculated using atomic-level structural details. Inclusion of a 0.9-A-thick hydration shell allows calculated results for both hydrodynamic properties of each protein to reproduce experimental data. The use of detailed protein structures is made possible by relating translational friction and intrinsic viscosity to capacitance and polarizability, which can be calculated easily. The 0.9-A hydration shell corresponds to a hydration level of 0.3-0.4 g water/g protein. Hydration levels within this narrow range are also found by a number of other techniques such as nuclear magnetic resonance spectroscopy, infrared spectroscopy, calorimetry, and computer simulation. The use of detailed protein structures in predicting hydrodynamic properties thus allows hydrodynamic measurement to join the other techniques in leading to a unified picture of protein hydration. In contrast, earlier interpretations of hydrodynamic data based on modeling proteins as ellipsoids gave hydration levels that varied widely from protein to protein and thus challenged the existence of a unified picture of protein hydration.

Algorithms↗
PubMed1996

Fast voltage clamp discloses a new component of presteady-state currents from the Na(+)-glucose cotransporter.

The human Na(+)-glucose cotransporter (hSGLT1) has been shown to generate, in the absence of sugar, presteady-state currents in response to a change in potential, which could be fitted with single exponentials once the voltage had reached a new constant value. By the cut-open oocyte technique (voltage rising-speed approximately 1 mV/microsecond), phlorizin-sensitive transient currents could be detected with a higher time resolution during continuous intracellular perfusion. In the absence of sugar and internal Na+, and with 90 mM external Na+ concentration ([Na+]o), phlorizin-sensitive currents exhibited two relaxation time-constants: tau 1 increased from 2 to 10 ms when Vm decreased from +60 mV to -80 mV and remained at 10 ms for more negative Vm; tau 2 ranged from 0.4 to 0.8 ms in a weakly voltage-dependent manner. According to a previously proposed model, these two time constants could be accounted for by 1) Na+ crossing a fraction of the membrane electrical field to reach its binding site on the carrier and 2) conformational change of the free carrier. To test this hypothesis, the time constants were measured as [Na+]o was progressively reduced to 0 mM. At 30 and 10 mM external Na+, tau 1 reached the same plateau value of 10 ms but at more negative potentials (-120 and -160 mV, respectively). Contrary to the prediction of the model, two time constants continued to be detected in the bilateral absence of Na+ (at pH 8.0). Under these conditions, tau 1 continuously increased through the whole voltage range and did not reach the 10 ms level even when Vm had attained -200 mV while tau 2 remained in the range of 0.4-0.8 ms. These results indicate that 1) conformational change of the free carrier across the membrane must occur in more than one step and 2) Na+ binding/debinding is not responsible for either of the two observed exponential components of transient currents. By use of the simplest kinetic model accounting for the portion of the hSGLT1 transport cycle involving extracellular Na+ binding/debinding and the dual-step conformational change of the free carrier, tau 1 and tau 2 were fitted throughout the voltage range, and a few sets of parameters were found to reproduce the data satisfactorily. This study shows that 1) tau 1 and tau 2 correspond to two steps in the conformational change of the free carrier, 2) Na+ binding/debinding modulates the slow time constant (tau 1) and 3) a voltage-independent slow conformational change of the free carrier accounts for the observed plateau value of 10 ms.

Animals↗
PubMed1996

Ryanodine receptor adaptation and Ca2+(-)induced Ca2+ release-dependent Ca2+ oscillations.

A simplified mechanism that mimics "adaptation" of the ryanodine receptor (RyR) has been developed and its significance for Ca2+(-)induced Ca2+ release and Ca2+ oscillations investigated. For parameters that reproduce experimental data for the RyR from cardiac cells, adaptation of the RyR in combination with sarco/endoplasmic reticulum Ca2+ ATPase Ca2+ pumps in the internal stores can give rise to either low [Cai2+] steady states or Ca2+ oscillations coexisting with unphysiologically high [Cai2+] steady states. In this closed-cell-type model rapid, adaptation-dependent Ca2+ oscillations occur only in limited ranges of parameters. In the presence of Ca2+ influx and efflux from outside the cell (open-cell model) Ca2+ oscillations occur for a wide range of physiological parameter values and have a period that is determined by the rate of Ca2+ refilling of the stores. Although the rate of adaptation of the RyR has a role in determining the shape and the period of the Ca2+ spike, it is not essential for their existence. This is in marked contrast with what is observed for the inositol 1,4,5-trisphosphate receptor for which the biphasic activation and inhibition of its activity by Ca2+ are sufficient to produce oscillations. Results for this model are compared with those based on Ca2+(-)induced Ca2+ release alone in the bullfrog sympathetic neuron. This kinetic model should be suitable for analyzing phenomena associated with "Ca2+ sparks," including their merger into Ca2+ waves in cardiac myocytes.

Animals↗
PubMed2000

Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation.

The primary analysis of the sequences for our Hemiascomycete random sequence tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written scripts and computer visualization routines. Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then against protein sequences from other completely sequenced organisms and, finally, against protein sequences from all other organisms. Blast alignments were individually inspected to help recognize genes within our random genomic sequences despite the fact that only parts of them were available. For each yeast species, validated alignments were used to infer the proper genetic code, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cerevisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences. Annotated sequences were submitted to the EMBL database, and the general annotation tables produced served as a basis for our comparative description of the evolution, redundancy and function of the Hemiascomycete genomes described in other articles of this issue.

Amino Acid Sequence↗
PubMed2002

Simple physical models connect theory and experiment in protein folding kinetics.

Our understanding of the principles underlying the protein-folding problem can be tested by developing and characterizing simple models that make predictions which can be compared to experimental data. Here we extend our earlier model of folding free energy landscapes, in which each residue is considered to be either folded as in the native state or completely disordered, by investigating the role of additional factors representing hydrogen bonding and backbone torsion strain, and by using a hybrid between the master equation approach and the simple transition state theory to evaluate kinetics near the free energy barrier in greater detail. Model calculations of folding phi-values are compared to experimental data for 19 proteins, and for more than half of these, experimental data are reproduced with correlation coefficients between r=0.41 and 0.88; calculations of transition state free energy barriers correlate with rates measured for 37 single domain proteins (r=0.69). The model provides insight into the contribution of alternative-folding pathways, the validity of quasi-equilibrium treatments of the folding landscape, and the magnitude of the Arrhenius prefactor for protein folding. Finally, we discuss the limitations of simple native-state-based models, and as a more general test of such models, provide predictions of folding rates and mechanisms for a comprehensive set of over 400 small protein domains of known structure.

Bacterial Proteins↗
PubMed2002

Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures.

We carry out a theoretical study of the vibrational and relaxation properties of naturally occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model, we provide a full characterization of the spectrum and eigenmodes of vibration at various temperatures by merely exploiting the knowledge of the protein native structure. It is shown that the rate at which perturbations decay at the folding transition correlates well with experimental folding rates. This validation is carried out on a list of about 30 two-state folders. Furthermore, the qualitative analysis of residues mean square displacements (shown to reproduce crystallographic data accurately) provides a reliable and statistically accurate method to identify crucial folding sites/contacts. This novel strategy is validated against clinical data for human immunodeficiency virus type 1 (HIV-1) protease. Finally, we compare the spectra and eigenmodes of vibration of natural proteins against randomly generated compact structures and regular random graphs. The comparison reveals a distinctive enhanced flexibility of natural structures accompanied by slow relaxation times at the folding temperature. The fact that these properties are connected intimately to the presence and assembly of secondary motifs hints at the special criteria adopted by evolution in the selection of viable folds.

Biological Evolution↗
PubMed2003

Bisphenol A suppresses osteoclastic and osteoblastic activities in the cultured scales of goldfish.

The direct effect of bisphenol A on osteoclasts and osteoblasts was examined using a culture system of goldfish scales. Tartrate-resistant acid phosphatase (TRAP) and alkaline phosphatase (ALP) were used as markers of osteoclasts and osteoblasts, respectively. Bisphenol A (10(5) M) significantly suppressed both TRAP and ALP activities. These data were reproduced in an in vivo experiment. From an analysis of a reverse transcription-polymerase chain reaction in the in vitro-cultured scales, it was demonstrated that the insulin-like growth factor (IGF)-1 mRNA expression decreased by a bisphenol A treatment. On the other hand, 17beta-estradiol (E(2)) stimulated both TRAP and ALP activities and did not change IGF-1 mRNA expression, suggesting that bisphenol A has a different effect from E(2) on bone metabolism. This study is the first to demonstrate that bisphenol A functions to suppress directly osteoblasts and osteoclasts among vertebrates, which strongly suggests that this scale in an in vitro assay system can be utilized for the evaluation of the effects of endocrine disrupters on bone cells.

Acid Phosphatase↗
PubMed1998

Transgenic nematodes as biomonitors of microwave-induced stress.

Transgenic nematodes (Caenorhabditis elegans strain PC72), carrying a stress-inducible reporter gene (Escherichia coli beta-galactosidase) under the control of a C. elegans hsp16 heat-shock promoter, have been used to monitor toxicant responses both in water and soil. Because these transgenic nematodes respond both to heat and toxic chemicals by synthesising an easily detectable reporter product, they afford a useful preliminary screen for stress responses (whether thermal or non-thermal) induced by microwave radiation or other electromagnetic fields. We have used a transverse electromagnetic (TEM) cell fed from one end by a source and terminated at the other end by a matched load. Most studies were conducted using a frequency of 750 MHz, at a nominal power setting of 27 dBm. The TEM cell was held in an incubator at 25 degrees C inside a shielded room; corresponding controls were shielded and placed in the same 25 degrees C incubator; additional baseline controls were held at 15 degrees C (worm growth temperature). Stress responses were measured in terms of beta-galactosidase (reporter) induction above control levels. The time-course of response to continuous microwave radiation showed significant differences from 25 degrees C controls both at 2 and 16 h, but not at 4 or 8 h. Using a 5 x 5 multiwell plate array exposed for 2 h, the 25 microwaved samples showed highly significant responses compared with a similar control array. The wells most strongly affected were those in the rows closest to the source, whereas the most distant row did not rise above control levels, suggesting a shadow effect. These differential responses are difficult to reconcile with general heating effects, although localised power absorption affords a possible explanation. Experiments in which the frequency and/or power settings were varied suggested a greater response at 21 than at 27 dBm, both at 750 and 300 MHz, although extremely variable responses were observed at 24 dBm and 750 MHz. Thus, lower power levels tended, if anything, to induce larger responses (with the above-mentioned exception), which is opposite to the trend anticipated for any simple heating effect. These results are reproducible and data acquisition is both rapid and simple. The evidence accrued to date suggests that microwave radiation causes measurable stress to transgenic nematodes, presumably reflecting increased levels of protein damage within cells (the common signal thought to trigger hsp gene induction). The response levels observed are comparable to those observed with moderate concentrations (ppm) of metal ions such as Zn2+ and Cu2+. We conclude that this approach deserves further and more detailed investigation, but that it has already demonstrated clear biological effects of microwave radiation in terms of the activation of cellular stress responses (hsp gene induction).

Animals↗
PubMed2002

Steady state and dynamic modelling of nitrogen in the River Kennet: impacts of land use change since the 1930s.

Steady state and dynamic models have been developed and applied to the River Kennet system. Annual nitrogen exports from the land surface to the river have been estimated based on land use from the 1930s and the 1990s. Long term modelled trends indicate that there has been a large increase in nitrogen transport into the river system driven by increased fertiliser application associated with increased cereal production, increased population and increased livestock levels. The dynamic model INCA (Integrated Nitrogen in Catchments) has been applied to simulate the day-to-day transport of N from the terrestrial ecosystem to the riverine environment. This process-based model generates spatial and temporal data and reproduces the observed instream concentrations. Applying the model to current land use and 1930s land use indicates that there has been a major shift in the short term dynamics since the 1930s, with increased river and groundwater concentrations caused by both non-point source pollution from agriculture and point source discharges.

Agriculture↗
PubMed1995

Antenatal assessment of twin gestation.

We have identified that twin gestation presents considerable risks to the well-being of both infants that can be traced to either related maternal or intrinsic fetoplacental factors. A protocol for the assessment of twin gestation is established, beginning with a basis in ultrasound identification of twinning and correct gestational dating. Because most hazards for twins are related to abnormal growth, discrepant growth between twins, and abnormalities of placentation, the approach to assessing well-being requires good serial biometry of twins. This critical review addresses the individual and combined application of standard tests used for evaluation of intrauterine health in single pregnancies: (1) ultrasound fetal growth curves; (2) Doppler velocimetry of the umbilical artery; (3) nonstress tests; (4) amniotic fluid assessment and (5) biophysical profile testing. The best current evidence suggests that there are clear deficiencies in the basis for growth nomograms for twin gestations, and with the exception of femur length, most individual anatomic measurements start to deviate from singleton standards between 21 and 30 weeks' gestation. Regardless of formulae used, estimated fetal weight provides the best discriminator for discordant growth. Dynamic assessment of fetal well-being is best provided by a combination of Doppler velocimetry and nonstress testing. Semiquantitative amniotic fluid assessment, other than establishing pathological conditions (eg, twin transfusion syndrome), is problematic and difficult to reproduce. Inadequate data exist to establish the value of the biophysical profile in twins. Given the limitations of present knowledge, serial assessment of twins beginning in the midtrimester with ultrasound observation, and adding combinations of Doppler velocimetry and nonstress testing in the third trimester, seems to represent the most reasonable current clinical approach to twin well-being.

Diseases in Twins↗
PubMed2003

Modelling of diffusion-limited retardation of contaminants in hydraulically and lithologically nonuniform media.

A new reactive transport modelling approach and examples of its application are presented, dealing with the impact of sorption/desorption kinetics on the spreading of solutes, e.g. organic contaminants, in groundwater. Slow sorption/desorption is known from the literature to be strongly responsible for the retardation of organic contaminants. The modelling concept applied in this paper quantifies sorption/desorption kinetics by an intra-particle diffusion approach. According to this idea, solute uptake by or release from the aquifer material is modelled at small scale by a "slow" diffusion process where the diffusion coefficient is reduced as compared to the aqueous diffusion coefficient due to (i) the size and shape of intra-particle pores and (ii) retarded transport of solutes within intra-particle pores governed by a nonlinear sorption isotherm. This process-based concept has the advantage of requiring only measurable model parameters, thus avoiding fitting parameters like first-order rate coefficients. In addition, the approach presented here allows for modelling of slow sorption/desorption in lithologically nonuniform media. Therefore, it accounts for well-known experimental findings indicating that sorptive properties depend on (i) the grain size distribution of the aquifer material and (ii) the lithological composition (e.g. percentage of quartz, sandstone, limestone, etc.) of each grain size fraction. The small-scale physico-chemical model describing sorption/desorption is coupled to a large-scale model of groundwater flow and solute transport. Consequently, hydraulic heterogeneities may also be considered by the overall model. This coupling is regarded as an essential prerequisite for simulating field-scale scenarios which will be addressed by a forthcoming publication. This paper focuses on mathematical model formulation, implementation of the numerical code and lab-scale model applications highlighting the sorption and desorption behavior of an organic contaminant (Phenanthrene) with regard to three lithocomponents exhibiting different sorptive properties. In particular, it is shown that breakthrough curves (BTCs) for lithologically nonuniform media cannot be obtained via simple arithmetic averaging of breakthrough curves for lithologically uniform media. In addition, as no analytical solutions are available for model validation purposes, simulation results are compared to measurements from lab-scale column experiments. The model results indicate that the new code can be regarded as a valuable tool for predicting long-term contaminant uptake or release, which may last for several hundreds of years for some lithocomponents. In particular, breakthrough curves simulated by pure forward modelling reproduce experimental data much better than a calibrated standard first-order kinetics reactive transport model, thus indicating that the new approach is of high quality and may be advantageously used for supporting the design of remediation strategies at contaminated sites where some lithocomponents and/or grain size classes may provide a long-term pollutant source.

Adsorption↗
PubMed2000

Evaluation of an experimental system for the in vitro assessment of ultrasonic contrast agents.

The ultrasonic properties of microbubble contrast agents need to be fully understood if reproducible images and quantitative results are to be produced. Additional aspects of the physical and chemical environment into which the contrast agents are introduced also need to be taken into account, and their effect on contrast agent performance evaluated. A setup that provides an accurate and reproducible data-acquisition system is presented and evaluated in this paper. The linear range of this system is assessed, as well as its accuracy and precision. A new approach to the investigation of contrast agents, based on normalised backscatter, is discussed. Also, a common technique of degassing, widely used in other areas, is described and evaluated to determine its appropriateness to contrast agent studies.

Contrast Media↗