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PubMed1999

Formation and processing of organics in the early solar system.

Until pristine samples can be returned from cometary nuclei, primitive meteorites represent our best source of information about organic chemistry in the early solar system. However, this material has been affected by secondary processing on asteroidal parent bodies which probably did not affect the material now present in cometary nuclei. Production of meteoritic organic matter apparently involved the following sequence of events: Molecule formation by a variety of reaction pathways in dense interstellar clouds; Condensation of those molecules onto refractory interstellar grains; Irradiation of organic-rich interstellar-grain mantles producing a range of molecular fragments and free radicals; Inclusion of those interstellar grains into the protosolar nebula with probable heating of at least some grain mantles during passage through the shock wave bounding the solar accretion disc; Agglomeration of residual interstellar grains and locally produced nebular condensates into asteroid-sized planetesimals; Heating of planetesimals by decay of extinct radionuclides; Melting of ice to produce liquid water within asteroidal bodies; Reaction of interstellar molecules, fragments and radicals with each other and with the aqueous environment, possibly catalysed by mineral grains; Loss of water and other volatiles to space yielding a partially hydrated lithology containing a complex suite of organic molecules; Heating of some of this organic matter to generate a kerogen-like complex; Mixing of heated and unheated material to yield the meteoritic material now observed. Properties of meteoritic organic matter believed to be consistent with this scenario include: Systematic decrease of abundance with increasing C number in homologous series of characterisable molecules; Complete structural diversity within homologous series; Predominance of branched-chain isomers; Considerable isotopic variability among characterisable molecules and within kerogen-like material; Substantial deuterium enrichment in all organic fractions; Some fractions significantly enriched in nitrogen-15; Modest excesses of L-enantiomers in some racemisation-resistant molecules but no general enantiomeric preference. Despite much speculation about the possible role of Fischer-Tropsch catalytic hydrogenation of CO in production of organic molecules in the solar nebula, no convincing evidence for such material has been found in meteorites. A similarity between some meteoritic organics and those produced by Miller-Urey discharge synthesis may reflect involvement of common intermediates rather than the operation of electric discharges in the early solar system. Meteoritic organic matter constitutes a useful, but not exact, guide to what we shall find with in situ analytical and sample-return missions to cometary nuclei.

Amino Acids↗
PubMedDate not supplied

Efficient numerical methods for nonlinear-facilitated transport and exchange in a blood-tissue exchange unit.

The analysis of experimental data obtained by the multiple-indicator method requires complex mathematical models for which capillary blood-tissue exchange (BTEX) units are the building blocks. This study presents a new, nonlinear, two-region, axially distributed, single capillary, BTEX model. A facilitated transporter model is used to describe mass transfer between plasma and intracellular spaces. To provide fast and accurate solutions, numerical techniques suited to nonlinear convection-dominated problems are implemented. These techniques are the random choice method, an explicit Euler-Lagrange scheme, and the MacCormack method with and without flux correction. The accuracy of the numerical techniques is demonstrated, and their efficiencies are compared. The random choice, Euler-Lagrange and plain MacCormack method are the best numerical techniques for BTEX modeling. However, the random choice and Euler-Lagrange methods are preferred over the MacCormack method because they allow for the derivation of a heuristic criterion that makes the numerical methods stable without degrading their efficiency. Numerical solutions are also used to illustrate some nonlinear behaviors of the model and to show how the new BTEX model can be used to estimate parameters from experimental data.

Algorithms↗
PubMedDate not supplied

Age-related thymic atrophy in the guinea pig.

We have characterized age-related thymic atrophy in the guinea pig, including identification of antibodies that allow immunohistochemical assessment of thymopoiesis. Age-related thymic atrophy in guinea pigs more closely resembles what occurs in humans histologically and in thymus weight, cellularity, and percent functional area than do other rodent models. The guinea pig model is thus particularly well-suited to study the role of the thymic perivascular space in age-related thymic atrophy. We next tested the hypothesis that dietary supplementation with Vitamin C could prevent or delay age-related thymic atrophy. Thymus histology, weight, cellularity, and percent functional area did not differ at 12 months between groups that received 3, 30, or 150 mg Vitamin C daily from 4 months of age. Thus long-term supplementation with up to 130 mg/kg/day Vitamin C is insufficient to influence the time course and extent of age-related thymic atrophy in guinea pigs.

Aging↗
PubMed2003

In vivo molecular-genetic imaging: multi-modality nuclear and optical combinations.

Multi-modality, noninvasive in vivo imaging is increasingly being used in molecular-genetic studies and will soon become the standard approach for reporter gene imaging studies in small animals. The coupling of nuclear and optical reporter genes, as described here, represents only the beginning of a far wider application of this technology in the future. Optical imaging and optical reporter systems are cost-effective and time-efficient; they require less resources and space than PET or MRI, and are particularly well suited for imaging small animals, such as mice. Optical reporter systems are also very useful for the quantification and selection of transduced cells using FACS, and for performing in vitro assays to validate the function and sensitivity of constitutive and specific-inducible reporter systems. However, optical imaging techniques are limited by depth of light penetration and do not yet provide optimal quantitative or tomographic information. These issues are not limiting for PET- or MRI-based reporter systems, and PET- and MRI-based animal studies are more easily generalized to human applications. Many of the shortcomings of each modality alone can be overcome by the use of dual- or triple-modality reporter constructs that incorporate the opportunity for PET, fluorescence and bioluminescence imaging.

Animals↗
PubMed1999

Low-salt crystallization of T7 RNA polymerase: a first step towards the transcription bubble complex.

DNA-dependent RNA polymerase is the key enzyme responsible for the biosynthesis of RNA, a process known as transcription. This process, which decodes the genetic information from DNA, is one of the most significant events in a biological system. The crystallization of both native and a chimeric T7/T3 RNAP using high salt conditions has been reported previously but these conditions proved unsuitable for DNA-RNAP complex formation since at high salt concentrations the DNA binding affinity to RNAP is reduced. A search for low-salt crystallization conditions has yielded new low-salt crystals of native T7-RNAP, a chimeric T7-RNAP (T7/T3 RNAP) which contains the T3 promoter recognition sequence, and a T7-RNAP containing an N-terminal histidine tag. The crystals, which are better suited for DNA-RNAP complex formation, belong to space group P3121 with a = 136, c = 156 A, contain a single molecule per asymmetric unit and diffract to 2.7 A resolution. Packing analysis shows that the new low-salt crystals have packing contacts similar to those observed in the high-salt T7-RNAP crystals reported previously. The diffraction anisotropicity observed in crystals of T7 RNAP is explained in term of crystal packing.

Base Sequence↗
PubMed1982

[Cerebral tomodensitometry in neuropediatrics].

CAT scan is now the primary diagnostic procedure for intracranial lesions in children. It is particularly well-suited for investigating intracranial hypertension, tumors and other space-occupying lesions, hydrocephalus, and malformations. Because it is non-invasive, this technique tends to be unduly performed as a screening procedure, with a resulting oversaturation of neuroradiological facilities. CAT scan should not be used as a routine examination, but only in well-selected cases. Careful clinical assessment and a good knowledge of pediatric neurology are still essential. New techniques are now becoming available and neuroradiologists will be able to select the best investigation for each particular case.

Brain Diseases↗
PubMedDate not supplied

Child care in the United States today.

This article describes the consumers and providers of child care in the United States. It uses data from nationally representative surveys and research studies conducted from the late 1960s through 1995 to examine the child care arrangements parents select for their young children, comparing today's arrangements with those made by parents decades ago. It then discusses the availability of child care, examining both the number of child care spaces available and whether quality programs are available to suit the needs and resources of parents. The article concludes with speculation about how proposed new policies and continuing trends may lead to future changes in child care.

Child↗
PubMed2003

Evolutionary algorithms for the selection of single nucleotide polymorphisms.

BACKGROUND: Large databases of single nucleotide polymorphisms (SNPs) are available for use in genomics studies. Typically, investigators must choose a subset of SNPs from these databases to employ in their studies. The choice of subset is influenced by many factors, including estimated or known reliability of the SNP, biochemical factors, intellectual property, cost, and effectiveness of the subset for mapping genes or identifying disease loci. We present an evolutionary algorithm for multiobjective SNP selection. RESULTS: We implemented a modified version of the Strength-Pareto Evolutionary Algorithm (SPEA2) in Java. Our implementation, Multiobjective Analyzer for Genetic Marker Acquisition (MAGMA), approximates the set of optimal trade-off solutions for large problems in minutes. This set is very useful for the design of large studies, including those oriented towards disease identification, genetic mapping, population studies, and haplotype-block elucidation. CONCLUSION: Evolutionary algorithms are particularly suited for optimization problems that involve multiple objectives and a complex search space on which exact methods such as exhaustive enumeration cannot be applied. They provide flexibility with respect to the problem formulation if a problem description evolves or changes. Results are produced as a trade-off front, allowing the user to make informed decisions when prioritizing factors. MAGMA is open source and available at http://snp-magma.sourceforge.net. Evolutionary algorithms are well suited for many other applications in genomics.

Algorithms↗
PubMed1998

Evidence of phase transitions in heart period dynamics.

Complexity measures of non-linear dynamics are a useful tool for quantifying observed stretching, folding, scaling and mixing processes in the Takens-reconstructed state space of heart period dynamics. Although such measures are not suited to provide evidence of deterministic chaos or to estimate true fractal dimensions and Lyapunov spectra in heart period time series, they allow the classification of RR dynamics and the identification of changes in RR complexity (RRC). The aim of this study was to develop appropriate measures and examine their utility in identifying the physiological effect of changes between the sleeping and waking state. Twenty-four hour electrocardiography (EEG) recordings and diaries noting their waking/sleeping period were obtained from 78 healthy subjects, aged 20 to 55 years. The approximate information dimension (ApD1) and the approximate Kolmogorov entropy (ApEn), introduced by Pincus, Kaplan and others, were modified in order to allow the calculation of strictly local values. That is, the local or pointwise dimensions and entropies were calculated for each reference vector with respect to its symmetric neighbourhood in time. For each subject the values for the local measures were averaged for 10-min periods, resulting in 144 global values over 24 h. Similarly, low- and high-frequency spectral parameters were calculated. All measures were examined and compared for the waking and the sleeping periods. All complexity measures as well as to a lesser degree high-frequency power showed a linear dependency on mean RR interval with a large individual variation. For the RRC measures this linear correlation was separated into two different clusters corresponding to the sleeping and waking periods. In almost all cases the correlation was greater in the waking period. In particular, in many cases no correlation was observed in the sleeping period. However, the r values for LF were appreciably lower and indicated solely a weak relationship to the RR interval in the waking period. Analysis of variance combining mean RR interval with RRC or spectral parameters singly and in couples revealed that the best separation with respect to physiological state could be achieved with the complexity measures, in particular with ApEn. The results show evidence of at least two dynamical regimes (phases) of heart period dynamics and a close but different functional relationship within the phases between RR interval and RR complexity. The separation between these regimes and the relatively sudden shift from one regime to the other suggest the existence of a phase transition with respect to waking and sleeping periods in terms of synergetics.

Adult↗
PubMed1983

Spaceflight and the telltale heart.

Cardiac arrhythmias have not been a common occurrence during manned spaceflights. Cardiovascular deconditioning, on the other hand, is a universal finding both during and after exposure to microgravity. Exercise capability is reduced only in the immediate postflight period as is cardiac output. These adaptive changes do not impair crew health or their ability to perform effectively in weightless flight. We believe that these effects are mediated by a decreased effective circulating blood volume and that they are completely reversible. In any case, an effective countermeasure is available to obviate or mitigate any untoward deconditioning effects on deorbit and return to Earth's gravity.

Adaptation, Physiological↗
PubMed1985

Fluorescence monitoring of rapid changes in membrane potential in heart muscle.

The rising phase of rat cardiac action potentials was measured in physiological solutions using the voltage-sensitive dye RH 237. A newly designed optical system and an argon ion laser for excitation allowed measurements without averaging over small areas (20-90 microns diameter) with high time resolution (response time 10-90%, 0.12 ms). The mean value of the fractional change in the fluorescence signal was approximately 3%/100 mV. The signal-to-noise ratio was approximately 60 rms (spot diameter 70 microns) allowing signal differentiation after digital filtering. Multiple measurements within the same spot showed a decrease in the fractional fluorescence change of 20 to 25% after 45 min without changes in the shape of the rising phase and with no measureable phototoxic effects. The optically measured rising phases showed rise times significantly (P less than 0.01) shorter and maximum upstroke velocities equal to or most often greater than those obtained with microelectrode techniques. Comparing simultaneous optical and electrical measurements within the same spot the microelectrode signal was often slightly delayed. This refined system seems well suited to detect fast cellular electrical activities with time and space resolutions comparable or even superior to those obtained using microelectrode techniques.

Action Potentials↗
PubMed2002

De novo design of biocatalysts.

The challenging field of de novo enzyme design is beginning to produce exciting results. The application of powerful computational methods to functional protein design has recently succeeded at engineering target activities. In addition, efforts in directed evolution continue to expand the transformations that can be accomplished by existing enzymes. The engineering of completely novel catalytic activity requires traversing inactive sequence space in a fitness landscape, a feat that is better suited to computational design. Optimizing activity, which can include subtle alterations in backbone conformation and protein motion, is better suited to directed evolution, which is highly effective at scaling fitness landscapes towards maxima. Improved rational design efforts coupled with directed evolution should dramatically improve the scope of de novo enzyme design.

Antibodies, Catalytic↗
PubMed1992

Peptidergic neurons of teleost retinas.

In retinas of teleost fish, neuropeptides typically have subtle, modulatory actions. The peptide effects typically have long latencies and durations, and, in some instances, they are known to be mediated by second messengers. Peptidergic neurons in teleost retinas have certain morphological features in common that are consistent with their function. Most peptidergic neurons are stratified amacrine cells with long, varicose processes; the processes of peptidergic centrifugal axons are also narrowly stratified and ramify extensively in the retina. The peptidergic amacrine cells are relatively infrequent, and, likewise, the centrifugal axons originate from a small number of perikarya in the brain. Cells that are so sparsely distributed and whose processes overlap so extensively are better-suited for modulation than for conveying detailed representations of visual space.

Animals↗
PubMedDate not supplied

Multimodality in vivo molecular-genetic imaging.

Multimodality imaging is increasingly being used in molecular-genetic studies in small animals. The coupling of nuclear and optical reporter genes represents the beginning of a far wider application of this technology. Optical imaging and optical reporter systems are cost-effective and time-efficient, they require less resources and space than PET or MRI, and they are particularly well suited for small animal imaging and for in vitro assays to validate different reporter systems. However, optical imaging techniques are limited by depth of light penetration and scatter and do not yet provide optimal quantitative or tomographic information. These issues are not limiting for PET- or MRI-based reporter systems, and PET- and MRI-based animal studies are more easily generalized to human applications. Many of the shortcomings of each modality alone can be overcome by the use of dual- or triple-modality reporter constructs that incorporate the opportunity for PET, fluorescence and bioluminescence imaging. We optimistically expect that some form of tomographic, small animal optical imaging capability will be developed soon, and that this will provide the opportunity for the colocalization of optical signals to anatomical structures provided by tomographic CT and MR imaging.

Animals↗
PubMed1982

Human leukocyte elastase, cathepsin G, and lactoferrin: family of neutrophil granule glycoproteins that bind to an alveolar macrophage receptor.

Interactions between polymorphonuclear neutrophils and mononuclear phagocytes are potentially of great importance in a variety of inflammatory processes. As part of a continuing effort to elucidate the physiologic importance of human alveolar macrophage receptor-mediated binding of neutrophil (leukocyte) elastase, I have studied the binding of leukocyte elastase and two other neutrophil granule glycoproteins, cathepsin G and lactoferrin, to human alveolar macrophages. Saturable binding of all three ligands at 0 degrees C was observed, with equilibrium dissociation constants of 4.0 x 10(-7), 2.0 x 10(-7), and 1.7 x 10(-6) M, respectively. All bound to a similar number (54-73 x 10(6)) of sites per cell. Binding of all three ligands was inhibited by the polysaccharide fucoidin, and extensive cross-inhibition of their binding to macrophages was observed. The results indicate that alveolar macrophages possess a relatively low-affinity, high-volume receptor for a family of neutrophil granule glycoproteins, which would be ideally suited for clearing released neutrophil granule contents from the extracellular space in inflamed tissues.

Binding, Competitive↗
PubMed2002

NAD(P)H, a primary target of 1O2 in mitochondria of intact cells.

Direct reaction of NAD(P)H with oxidants like singlet oxygen ((1)O(2)) has not yet been demonstrated in biological systems. We therefore chose different rhodamine derivatives (tetramethylrhodamine methyl ester, TMRM; 2',4',5',7'-tetrabromorhodamine 123 bromide; and rhodamine 123; Rho 123) to selectively generate singlet oxygen within the NAD(P)H-rich mitochondrial matrix of cultured hepatocytes. In a cell-free system, photoactivation of all of these dyes led to the formation of (1)O(2), which readily oxidized NAD(P)H to NAD(P)(+). In hepatocytes loaded with the various dyes only TMRM and Rho 123 proved suited to generating (1)O(2) within the mitochondrial matrix space. Photoactivation of the intracellular dyes (TMRM for 5-10 s, Rho 123 for 60 s) led to a significant (29.6 +/- 8.2 and 30.2 +/- 5.2%) and rapid decrease in mitochondrial NAD(P)H fluorescence followed by a slow increase. Prolonged photoactivation (> or =15 s) of TMRM-loaded cells resulted in even stronger NAD(P)H oxidation, the rapid onset of mitochondrial permeability transition, and apoptotic cell death. These results demonstrate that NAD(P)H is the primary target for (1)O(2) in hepatocyte mitochondria. Thus NAD(P)H may operate directly as an intracellular antioxidant, as long as it is regenerated. At cell-injurious concentrations of the oxidant, however, NAD(P)H depletion may be the event that triggers cell death.

Animals↗
PubMed2005

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

MOTIVATION: Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were 'close enough'. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for alpha-helices and beta-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise. RESULTS: This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental beta-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to uncover large consistent sets of interactions. AVAILABILITY: Our algorithm has been implemented in the platform-independent Python code. The software can be freely obtained for academic use by request from the authors.

Algorithms↗