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PubMed2004

Dynamical heterogeneities close to a colloidal gel.

Dynamical heterogeneities in a colloidal fluid close to gelation are studied by means of computer simulations. A clear distinction between some fast particles and the rest, slow ones, is observed yielding a picture of the gel composed of two populations with different mobilities. Analyzing the statics and dynamics of both sets of particles, it is shown that the slow particles form a network of stuck particles, whereas the fast ones are able to move over long distances. Correlation functions show that the environment of the fast particles relaxes much faster than that of the slow ones, but at short times the bonds between fast particles are longer lived due to the flexibility of their structure. No stringlike motion is observed for the fast particles, but they occupy preferential sites in the surface of the structure formed by the slow ones.

Journal Article↗

PubMed2006

X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation.

Solution state x-ray diffraction fingerprinting is demonstrated as a method for experimentally assessing the accuracy of molecular dynamics (MD) simulations. Fourier transforms of coordinate data from MD simulations are used to produce reciprocal space "fingerprints" of atomic pair distance correlations that are characteristic of the ensemble and are the direct numerical analogues of experimental solution x-ray diffraction (SXD). SXD experiments and MD simulations were carried out to test the ability of experiment and simulation to resolve sequence-dependent modifications in helix conformation for B-form DNA. SXD experiments demonstrated that solution-state poly(AT) and poly(A)-poly(T) duplex DNA sequences exist in ensembles close to canonical B-form and B'-form structures, respectively. In contrast, MD simulations analyzed in terms of SXD fingerprints are shown to deviate from experiment, most significantly for poly(A)-poly(T) duplex DNA. Compared with experiment, MD simulation shortcomings were found to include both mismatches in simulated conformer structures and number population within the ensembles. This work demonstrates an experimental approach for quantitatively evaluating MD simulations and other coordinate models to simulate biopolymer structure in solution and suggests opportunities to use solution diffraction data as experimental benchmarks for developing supramolecular force fields optimized for a range of in situ applications.

DNA↗

PubMed1996

Ediacaran biota from Sonora, Mexico.

The Ediacaran biota is the earliest diverse community of macroscopic animals and protoctists. Body and trace fossils in the Clemente Formation of northwestern Sonora extend downward the geologic range of Ediacaran forms. Taxa present in the Clemente Formation include cf. Cyclomedusa plana, Sekwia sp., an erniettid (bearing an air mattress-like "pneu" body construction), and the trace fossils Lockeia ichnosp. and Palaeophycus tubularis. The trace fossils confirm the presence of sediment-dwelling animals in this shallow marine community. The body fossils are headless, tailless, and appendageless. Some may be body fossils of animals but others may be fossils of large protoctists. These body and trace fossils, recovered from thinly bedded sandstones and siltstones, occur 75 meters lower in the Sonoran stratigraphic section than a distinctive Clemente Formation oolite. The stratigraphic position of the fossils below this oolite permits long-distance correlation between fossiliferous Proterozoic strata of Mexico and the United States. Correlations utilizing both the Clemente Formation oolite and a trace fossil (Vermiforma antiqua) confirm the antiquity (600 million years or more) of this body fossil-rich community of macroscopic eukaryotes. The recently discovered body fossils are the oldest known remains of the Ediacaran biota.

Journal Article↗

PubMed2004

Multidestructive pathways triggered in photoreceptor cell death of the rd mouse as determined through gene expression profiling.

In the rd/rd mouse, photoreceptor degeneration is due to a mutation of the rod-specific enzyme cGMP phosphodiesterase, resulting in permanently opened cGMP-gated cation channels in the rod outer segment membrane that allow Na(+) and Ca(2+) ions to enter the cell, resulting in possibly toxic levels of Ca(2+). To identify pathways involved in cell death of the rd/rd rods, we evaluated gene expression in the rd/rd and wild type (wt) mouse retina (U74A oligonucleotide arrays (Affymetrix)) over the known time course of photoreceptor degeneration. 181 genes passed the selection criteria (low standard deviation and high correlation between replicates), falling into six clusters. For any given pair of genes, an expression profile correlation distance and a semantic distance (one for each class of gene ontology terms) were established using newly designed software. Gene expression in rd/rd started to deviate from wt by postnatal day 10. The reduction in photoreceptor-specific genes followed the known time course of photoreceptor degeneration. Likewise the increase in transcription factors and apoptosis- and neuroinflammation-specific genes followed the kinetics of the rise in intracellular cGMP in the rod photoreceptors. In addition, genes coding for calcium-binding proteins and those implicated in tissue and vessel remodeling were increased. These results suggest that photoreceptor degeneration in the rd/rd mouse is a process starting with Ca(2+) toxicity followed by secondary insults involving multidestructive pathways such as apoptosis and neuroinflammation, presumably boosting morphological changes. All of these components need to be addressed if rods are to be successfully protected.

Animals↗

PubMed2004

Discrimination of aqueous and aeolian paleoenvironments by atomic force microscopy-- a database for the characterization of martian sediments.

In the search for aqueous habitats on Mars direct proof of (ancient) flowing water is still lacking, although remote sensing has provided indications of young fluvial systems. To demonstrate that such proof can be given, we examined surface marks on recent terrestrial sand grains by atomic force microscopy (AFM) and applied a quantitative three-dimensional analysis that can numerically distinguish between aeolian and aquatic transport mechanisms in sedimentary deposits on Earth. The surfaces of natural quartz grains as well as olivine, feldspar pyroxene, and monazite sands of known origin were imaged, each image yielding a three-dimensional map of the mineral surface. A fully automated analysis of distribution patterns of the structural elements that constitute the grain surfaces shows that wind-transported quartz grains have short linear elements irregularly distributed on the surface. Linear elements on water-transported grains, however, are longer with orientations that reflect the mineral symmetry. Because the surface patterns found on aqueous grains are due to preferential etching, they can be used as diagnostic fingerprints for the existence of past or present aqueous transport systems. We used a cluster analysis of the cross-correlation distance of distribution patterns in the structures of aeolian and aquatic sand grains to build a phenogram that provides a map for the relationship of the various sediments found on earth. The analysis shows that the method is highly significant and that water and wind transport can clearly be differentiated. In particular, feldspar and olivine sands contributed even more to the discrimination than quartz grains, which indicated that the method is promising for its application on future missions to Mars. Assuming that martian aqueous sand grains exhibit similar erosional patterns to mineral grains on Earth, simple AFM experiments on a Mars lander would be capable of proving the activity of flowing water in modern runoff systems and of analyzing the paleoenvironments of Mars.

Exobiology↗

PubMed1999

Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity.

MOTIVATION: Gene regulation often depends on functional modules which feature a detectable internal organization. Overall sequence similarity of these modules is often insufficient for detection by general search methods like FASTA or even Gapped BLAST. However, it is of interest to evaluate whether modules, often known from experimental analysis of single sequences, are present in other regulatory sequences. RESULTS: We developed a new method (FastM) which combines a search algorithm for individual transcription factor binding sites (MatInspector) with a distance correlation function. FastM allows fast definition of a model of correlated binding sites derived from as little as a single promoter or enhancer. ModelInspector results are suitable for evaluation of the significance of the model. We used FastM to define a model for the experimentally verified NFkappaB/IRF1 regulatory module from the major histocompatibility complex (MHC) class I HLA-B gene promoter. Analysis of a test set of sequences as well as database searches with this model showed excellent correlation of the model with the biological function of the module. These results could not be obtained by searches using FASTA or Gapped BLAST, which are based on sequence similarity. We were also able to demonstrate association of a hypothetical GRE-GRE module with viral sequences based on analysis of several GenBank sections with this module. AVAILABILITY: The WWW version of FastM is accessible at: http://www.gsf.de/cgi-bin/fastm. pl and http://genomatix.gsf.de/cgi-bin/fastm2/fastm.pl

Algorithms↗

PubMed1993

Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids.

We present a method to determine the location and extent of protein binding regions in nucleic acids by computer-assisted analysis of sequence data. The program ConsIndex establishes a library of consensus descriptions based on sequence sets containing known regulatory elements. These defined consensus descriptions are used by the program ConsInspector to predict binding sites in new sequences. We show the programs to correctly determine the significant regions involved in transcriptional control of seven sequence elements. The internal profile of relative variability of individual nucleotide positions within these regions paralleled experimental profiles of biological significance. Consensus descriptions are determined by employing an anchored alignment scheme, the results of which are then evaluated by a novel method which is superior to cluster algorithms. The alignment procedure is able to include several closely related sequences without biasing the consensus description. Moreover, the algorithm detects additional elements on the basis of a moderate distance correlation and is capable of discriminating between real binding sites and false positive matches. The software is well suited to cope with the frequent phenomenon of optional elements present in a subset of functionally similar sequences, while taking maximal advantage of the existing sequence data base. Since it requires only a minimum of seven sequences for a single element, it is applicable to a wide range of binding sites.

Algorithms↗

PubMed2001

Randomly driven granular fluids: collisional statistics and short scale structure.

We present a molecular-dynamics and kinetic theory study of granular material, modeled by inelastic hard disks, fluidized by a random driving force. The focus is on collisional averages and short-distance correlations in the nonequilibrium steady state, in order to analyze in a quantitative manner the breakdown of molecular chaos, i.e., factorization of the two-particle distribution function, f((2))(x(1),x(2)) approximately chif((1))(x(1))f((1))(x(2)) in a product of single-particle ones, where x(i)=[r(i),v(i)] with i=1,2 and chi represents the position correlation. We have found that molecular chaos is only violated in a small region of the two-particle phase space [x(1),x(2)], where there is a predominance of grazing collisions. The size of this singular region grows with increasing inelasticity. The existence of particle- and noise-induced recollisions magnifies the departure from mean-field behavior. The implications of this breakdown in several physical quantities are explored.

Journal Article↗

PubMed2001

Transverse instability of incoherent solitons in Kerr media.

We calculate the growth rate of the small-amplitude perturbations superimposed on a one-dimensional soliton that is fully coherent in the self-trapping dimension, yet uniform and partially incoherent in the other transverse dimension. Such solitons become transversely stable only if the correlation distance is below a specific threshold value. We show that this threshold for transverse instability fully coincides with the threshold value for modulational instability.

Journal Article↗

PubMed2004

Conformation of local denaturation in double-stranded DNA.

Double-stranded DNA (dsDNA) undergoes a denaturing transition above which the strands unbind completely. At temperatures (including the physiological temperature) below the transition the base pairs tend to unbind locally, giving way to loops, i.e., locally denatured states. In the flexible-chain model, the imaginary time Schrödinger equation describes the interstrand distance distribution of dsDNA with the time variable replaced by the sequence number. We transform the equation to the Fokker-Planck equation (FPE), which provides a convenient and powerful analytical method and, via the equivalent Langevin equation, a simulation scheme. The temperature-dependent potential that emerges in the FPE manifests how the DNA conformation changes dramatically near the transition temperature. We present several simulation plots along with analytical results illustrating the order parameter (concentration of bound base pairs), base pair distance correlation function, and loop size distribution at different temperatures.

Base Pairing↗

PubMed2006

Incoherent white-light solitons in nonlinear periodic lattices.

We predict the existence of lattice solitons made of incoherent white light: lattice solitons made of light originating from an ordinary incandescent light bulb. We find that the intensity structure and spatial power spectra associated with different temporal frequency constituents of incoherent white-light lattice solitons (IWLLSs) arrange themselves in a characteristic fashion, with the intensity structure more localized at higher frequencies, and the spatial power spectrum more localized at lower frequencies; the spatial correlation distance is larger at lower frequency constituents of IWLLSs. This characteristic shape of incoherent white-light lattice solitons reflects the fact that diffraction is stronger for lower temporal frequency constituents, while higher frequencies experience stronger effective nonlinearity and deeper lattice structure.

Journal Article↗

PubMed2000

Eliminating the transverse instabilities of kerr solitons

We show analytically, numerically, and experimentally that a transversely stable one-dimensional [(1+1)D] bright Kerr soliton can exist in a 3D bulk medium. The transverse instability of the soliton is completely eliminated if it is made sufficiently incoherent along the transverse dimension. We derive a criterion for the threshold of transverse instability that links the nonlinearity to the largest transverse correlation distance for which the 1D soliton is stable.

Journal Article↗

PubMed1986

The use of angular acoustic scattering measurements to estimate structural parameters of human and animal tissues.

Theoretical formulations are developed, based on mathematical models of inhomogeneous continua for the expected angular variation of bulk scattering from human and animal tissues. These results are compared with experimental data on angular scattering from liver, muscle, and blood, reported in a companion paper [J. Acoust. Soc. Am. 79, 2034-2047 (1986)], and deductions are drawn as to the appropriateness of the various models for representing the mechanical structure of the different tissues. On this basis, the experimental data and theoretical formulations are used to derive estimates, appropriate to the frequency range of observation (4-7 MHz), of correlation distance (or effective scatterer spacing) d, the local variabilities of density and compressibility, gamma rho = delta rho/rho and gamma kappa = delta kappa/kappa 0, and their ratio gamma rho/gamma kappa. For blood, liver, and skeletal muscle, the values derived at 6 MHz for d are approximately 5, 55, and 75 microns and for gamma rho/gamma kappa are 0.5, 0.15, and 0.28, respectively. These results are, in particular, at variance with the commonly made assumption, based on evidence from low-frequency measurements, that the ratio gamma rho/gamma kappa is sufficiently small that density terms can be ignored in calculations of human tissue scattering.

Acoustic Stimulation↗

PubMed1999

Predictive fluorescent amplified-fragment length polymorphism analysis of Escherichia coli: high-resolution typing method with phylogenetic significance.

The fluorescent amplified-fragment length polymorphism (FAFLP) assay potentially amplifies a unique set of genome fragments from each bacterial clone. It uses stringently hybridizing primers which carry a fluorescent label. Precise fragment sizing is achieved by the inclusion of an internal size standard in every lane. Therefore, a unique genotype identifier(s) can be found in the form of fragments of precise size or sizes, and these can be generated reproducibly. In order to evaluate the potential of FAFLP as an epidemiological typing method with a valid phylogenetic basis, we applied it to 87 strains of Escherichia coli. These comprised the EcoR collection, which has previously been classified by multilocus enzyme electrophoresis (MLEE) and which represents the genetic diversity of the species E. coli, plus 15 strains of the clinically important serogroup O157. FAFLP with an unlabelled nonselective EcoRI primer (Eco+0) and a labelled selective MseI primer (Mse+TA) gave strain-specific profiles. Fragments of identical sizes (in base pairs) were assumed to be identical, and the genetic distances between the strains were calculated. A phylogenetic tree derived from measure of distance correlated closely with the MLEE groupings of the EcoR collection and placed the verocytotoxin-producing O157 strains on an outlier branch. Our data indicate that FAFLP is suitable for epidemiological investigation of E. coli infection, providing well-defined and reproducible identifiers of genotype for each strain. Since FAFLP objectively samples the whole genome, each strain or isolate can be assigned a place within the broad context of the whole species and can also be subjected to a high-resolution comparison with closely related strains to investigate epidemiological clonality.

Bacterial Typing Techniques↗

PubMed2002

Dynamic single-section CT demonstrates reduced cerebral blood flow in acute intracerebral hemorrhage.

Optimum blood pressure (BP) management in acute intracerebral hemorrhage (ICH) remains controversial. BP reduction may limit hematoma expansion, but may also exacerbate ischemia. Reduced regional cerebral blood flow (rCBF) has been reported in ICH. Its extent and precise pattern, however, remain uncertain. Dynamic single-section CT perfusion (CTP) is rapid, easily performed and offers superior spatial resolution to PET, SPECT and MRI. It may be the most applicable method for assessing the effects of BP management on rCBF in ICH. We sought to assess whether CTP can identify rCBF abnormalities in acute ICH in 5 patients with ICH who underwent CTP within 24 h of symptom onset. rCBF was measured in serially expanded 2-mm rings around the hematoma and compared with rCBF in the uninvolved hemisphere. Mean time to CTP was 9 h (range 3-23). Mean ICH volume was 25 ml (range 9-64). Perihematoma perfusion was reduced in all patients compared with contralateral hemisphere rCBF. rCBF reduction was most pronounced immediately adjacent to the hematoma (p < 0.05 at 2 mm, p = 0.084 at 4 mm, p > 0.2 at 6 and 8 mm). Perihematoma rCBF increased as a function of the distance from hematoma perimeter. Rate of rCBF increase over distance correlated with time from onset (p = 0.006). We conclude that CTP identifies a rim of reduced rCBF in ICH. A gradient of hypoperfusion appears to extend at least 4 mm beyond the hematoma edge and may be time dependent. Whether reduced CBF is associated with perihematoma ischemia requires additional study.

Aged↗

PubMed1997

Effect of verapamil in intermittent claudication A randomized, double-blind, placebo-controlled, cross-over study after individual dose-response assessment.

BACKGROUND: The calcium antagonist verapamil is a vasodilator drug that has been shown to increase oxygen extraction of ischemic tissues in coronary and peripheral vascular disease. METHODS AND RESULTS: Since the balance between the positive and the negative effects of vasodilation may be delicate in ischemic diseases a dose-response study (dose range, 120 to 480 mg) was established to determine optimal, individual dosages of slow-release verapamil in 44 patients with stable intermittent claudication (Fontaine classification stage II) with respect to walking capacity. A randomized, double-blind, placebo-controlled, cross-over study (4 weeks) was performed to assess clinical and hemodynamic effects of verapamil. The optimal daily dose of verapamil on maximal walking ability was 120 (8 patients), 240 (8 patients), 360 (14 patients), and 480 mg (14 patients). Walking distances were measured at a metronome-controlled speed of 60 steps per minute on level surface. Optimal individual doses of verapamil increased mean pain-free walking distance by 29% from 44.9 to 57.8 meters (P < .01) and maximal walking distance by 49% from 100.7 to 149.8 meters (P < .001) compared with placebo. The increase in maximal walking distance correlated positively only with initial systolic ankle pressure (r = .49, P < .001) and ankle/brachial pressure index (r = .37, P < .013). Verapamil had no effect on systolic ankle pressure, ankle/brachial pressure index, peripheral leg temperature, or blood pressure, which suggests that the drug may have extrahemodynamic effects, possibly brought about through improved oxygen metabolism. CONCLUSIONS: Verapamil showed significant clinical benefits in patients with moderate intermittent claudication in this short-term study. Individual optimization of drug dosage should be considered an option both in trials and in the clinical setting in these patients.

Aged↗

PubMed2005

Health-related quality of life in patients with pulmonary arterial hypertension.

BACKGROUND: Improved outcomes with expanding treatment options for patients with pulmonary arterial hypertension present the opportunity to consider additional end-points in approaching therapy, including factors that influence health-related quality of life. However, comparatively little is known about health-related quality of life and its determinants in patients with pulmonary arterial hypertension. METHODS: Health-related quality of life was evaluated in a cross sectional study of 155 outpatients with pulmonary arterial hypertension using generic and respiratory-disease specific measurement tools. Most patients had either World Health Organization functional Class II or III symptoms. Demographic, hemodynamic and treatment variables were assessed for association with health-related quality of life scores. RESULTS: Patients with pulmonary arterial hypertension suffered severe impairments in both physical and emotional domains of health-related quality of life. Patients with idiopathic ("primary") pulmonary arterial hypertension had the best, and those with systemic sclerosis the worst health-related quality of life. Greater six-minute walk distance correlated with better health-related quality of life scores, as did functional Class II versus Class III symptoms. Hemodynamic measurements, however, did not correlate with health-related quality of life scores. No differences in health-related quality of life were found between patients who were being treated with calcium channel antagonists, bosentan or continuously infused epoprostenol at the time of quality of life assessment. CONCLUSION: Health-related quality of life is severely impaired in patients with pulmonary arterial hypertension and is associated with measures of functional status. Specific associations with impaired health-related quality of life suggest potential areas for targeted intervention.

Adolescent↗

PubMed1995

Protein translation components are colocalized in granules in oligodendrocytes.

The intracellular distribution of various components of the protein translational machinery was visualized in mouse oligodendrocytes in culture using high resolution fluorescence in situ hybridization and immunofluorescence in conjunction with dual channel confocal laser scanning microscopy. Arginyl-tRNA synthetase, elongation factor 1a, ribosomal RNA, and myelin basic protein mRNA were all co-localized in granules in the processes, veins and membrane sheets of the cell. Colocalization was evaluated by dual channel cross correlation analysis to determine the correlation index (% colocalization) and correlation distance (granule radius), and by single granule ratiometric analysis to determine the distribution of the different components in individual granules. Most granules contained synthetase, elongation factor, ribosomal RNA and myelin basic protein mRNA. These results indicate that several different components of the protein synthetic machinery, including aminoacyl-tRNA synthetases, elongation factors, ribosomes and mRNAs, are colocalized in granules in oligodendrocytes. We propose that these granules are supramolecular complexes containing all of the necessary macromolecular components for protein translation and that they represent a heretofore undescribed subcellular organization of the protein synthetic machinery. This spatial organization may increase the efficiency of protein synthesis and may also provide a vehicle for transport and localization of specific mRNAs within the cell.

Amino Acyl-tRNA Synthetases↗