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Determining bilayer hydrocarbon thickness from neutron diffraction measurements using strip-function models.

Neutron diffraction methods provide information about the distribution of matter in biological and model membrane systems. The information is derived from plots (profiles) of scattering length density along an axis normal to the membrane plane. Without the use of specific deuteration, the generally low resolution of the profiles limits their interpretation in terms of specific chemical constituents (e.g., lipid headgroup, lipid hydrocarbon, protein, and water). A fundamental and useful structural assignment to make is the boundary between the headgroup and hydrocarbon regions of bilayers. We demonstrate here that strip-function model representations of neutron scattering length density profiles of bilayers are sufficient to determine accurately the position of the headgroup-hydrocarbon boundary. The resulting hydrocarbon thickness of the bilayer is useful for determining the area per lipid molecule and consequently the molecular packing arrangements of the membrane constituents. We analyze data obtained from dioleoylphosphatidylcholine (DOPC) bilayers at 66% RH using standard Fourier profile analyses and from DOPC deuterated specifically at the C-2 carbon of the acyl chains using difference Fourier analysis. We demonstrate that strip-function models accurately define the positions of the C-2 carbons and thus the hydrocarbon thickness (dhc) of the bilayer. We then show, using quasi-molecular models, that the strip-model analysis probably provides an accurate measure of dhc because of the exceptionally high scattering length density difference between the carbonyl and methylene groups.

Deuterium↗

Immunohistochemical localization of the somatostatin sst(4) receptor in rat brain.

The biological actions of the neuromodulator somatostatin are mediated through a family of G-protein-coupled receptors, of which five members, sst(1-5), have been identified. Although the messenger RNA distribution of the sst(4) receptor has been reported, no information about the distribution of the receptor protein in the central nervous system is available. We have therefore raised a polyclonal peptide antibody against a rat carboxy-terminal sst(4) peptide. The selectivity of the affinity-purified antibody was demonstrated by western blotting of membrane proteins isolated from Chinese hamster ovary-K1 cells expressing the recombinant sst(4) receptor and from the rat hippocampus. This resulted in both cases in the identification of a single band of approximately 42,000 mol. wt. Furthermore, the sst(4) receptor antibody selectively labelled Chinese hamster ovary-K1 cells expressing the recombinant sst(4) receptor in immunocytochemistry. No cross-reactivity was observed with other recombinant somatostatin receptors. Immunohistochemistry on adult rat brain sections showed the sst(4) receptor to have a widespread distribution. This included labelling of cell bodies as well as processes in the cerebral cortex, hippocampus and several nuclei in the brainstem. All signals were absent following antibody preabsorption with the synthetic sst(4) peptide. This study provides the first detailed analysis of the distribution of sst(4) receptor protein in the rat brain.

Age Factors↗

GC-MS analysis of amino acids rapidly provides rich information for isotopomer balancing.

Gas chromatography-mass spectrometry (GC-MS) is a rapid method that provides rich information on isotopomer distributions for metabolic flux analysis. First, we established a fast and reliable experimental protocol for GC-MS analysis of amino acids from total biomass hydrolyzates, and common experimental pitfalls are discussed. Second, a suitable interface for the use of mass isotopomer data is presented. For this purpose, a general, matrix-based correction procedure that accounts for naturally occurring isotopes is introduced. Simulated and experimentally determined mass distributions of unlabeled amino acids showed a deviation of less than 3% for 89% of the analyzed fragments. Third, to investigate general properties of GC-MS-based isotopomer balancing, altered flux ratios through glycolysis and pentose phosphate pathway and/or exchange fluxes were simulated. Different fluxes were found to exert specific and significant influence on the mass isotopomer distributions, thus indicating that GC-MS data contain valuable information for metabolic flux analysis. Fourth, comparison of different methods revealed that GC-MS analysis provides the largest number of independent constraints on amino acid isotopomer abundance, followed by correlation spectroscopy and fractional enrichment analysis by nuclear magnetic resonance.

Amino Acids↗

Biological optimization of heterogeneous dose distributions in systemic radiotherapy.

The standard computational method developed for internal radiation dosimetry is the MIRD (medical internal radiation dose) formalism, based on the assumption that tumor control is given by uniform dose and activity distributions. In modern systemic radiotherapy, however, the need for full 3D dose calculations that take into account the heterogeneous distribution of activity in the patient is now understood. When information on nonuniform distribution of activity becomes available from functional imaging, a more patient specific 3D dosimetry can be performed. Application of radiobiological models can be useful to correlate the calculated heterogeneous dose distributions to the current knowledge on tumor control probability of a homogeneous dose distribution. Our contribution to this field is the introduction of a parameter, the F factor, already used by our group in studying external beam radiotherapy treatments. This parameter allows one to write a simplified expression for tumor control probability (TCP) based on the standard linear quadratic (LQ) model and Poisson statistics. The LQ model was extended to include different treatment regimes involving source decay, incorporating the repair "micro" of sublethal radiation damage, the relative biological effectiveness and the effective "waste" of dose delivered when repopulation occurs. The sensitivity of the F factor against radiobiological parameters (alpha, beta, micro) and the influence of the dose volume distribution was evaluated. Some test examples for 131I and 90Y labeled pharmaceuticals are described to further explain the properties of the F factor and its potential applications. To demonstrate dosimetric feasibility and advantages of the proposed F factor formalism in systemic radiotherapy, we have performed a retrospective planning study on selected patient case. F factor formalism helps to assess the total activity to be administered to the patient taking into account the heterogeneity in activity uptake and dose distribution, giving the same TCP of a homogeneous prescribed dose distribution. Animal studies and collection of standardized clinical data are needed to ascertain the effects of nonuniform dose distributions and to better assess the radiobiological input parameters of the model based on LQ model.

Humans↗

Distribution of spontaneous mutants and inferences about the replication mode of the RNA bacteriophage phi6.

When a parent virus replicates inside its host, it must first use its own genome as the template for replication. However, once progeny genomes are produced, the progeny can in turn act as templates. Depending on whether the progeny genomes become templates, the distribution of mutants produced by an infection varies greatly. While information on the distribution is important for many population genetic models, it is also useful for inferring the replication mode of a virus. We have analyzed the distribution of mutants emerging from single bursts in the RNA bacteriophage phi6 and find that the distribution closely matches a Poisson distribution. The match suggests that replication in this bacteriophage is effectively by a stamping machine model in which the parental genome is the main template used for replication. However, because the distribution deviates slightly from a Poisson distribution, the stamping machine is not perfect and some progeny genomes must replicate. By fitting our data to a replication model in which the progeny genomes become replicative at a given rate or probability per round of replication, we estimated the rate to be very low and on the on the order of 10(-4). We discuss whether different replication modes may confer an adaptive advantage to viruses.

Bacteriophage phi 6↗

Age trends in adiposity and central body fat distribution among adult white men resident in Peterborough, East Anglia, England.

The pattern of fat distribution is related to a large number of variables of clinical importance. Many anthropometric indices have been derived which are surrogate measures of central fat distribution. However, systematic information on age variations in regional adiposity and central fat distribution is incomplete. The present study investigates the age variations in regional adiposity and five indices of central fat distribution among 262 adult White men resident in Peterborough, East Anglia, England. The five indices were studied: subscapular/triceps (STSR), abdomen/triceps (ATSR) and centripetal fat (CPFR) skinfold ratios, waist/hip ratio (WHR) and conicity index (CI). In general, the age patterns show progressive trend towards increasing central body fat distribution. The associations of age with all five central fat distribution indices were significant. These significant associations remained even after controlling for the body mass index (BMI). Therefore, this study provided evidence that there is a significant positive trend of increased central adiposity and fat distribution with increasing age in native English men. This trend is independent of BMI, which is a measure of overall adiposity. Such trends of enhanced fat accumulation in the central region of the body with age could have serious health implications especially with regard to chronic diseases like coronary heart disease (CHD), hypertension (HT) and non-insulin dependent diabetes mellitus (NIDDM). Future studies should also investigate whether the same phenomenon exists in other ethnic groups resident in Britain like South Asians who have very high prevalence of CHD and NIDDM.

Adipose Tissue↗

[Spatial analysis on the distribution of hemorrhagic fever with renal syndrome by geographic information system in Haidian district, Beijing].

OBJECTIVE: To analyze the spatial distribution of hemorrhagic fever with renal syndrome (HFRS) in Haidian district, Beijing and to explore the geographical characteristics of HFRS in highly endemic areas. METHODS: Administration boundary layer was established under the background of 1:100,000 map in the ArcInfo 8.1 software. The HFRS cases from 1997 to 2002 were positioned on the map. Highly endemic areas were identified by spatial cluster analysis using SaTScan 3.0 software. Distribution of HFRS cases was shown in different colors and contours by spatial analysis of geographic information system (GIS). RESULTS: Spatial Cluster Analysis of confirmed cases of HFRS identified in 1997 - 2002 in Haidian district showed that HFRS patients were not randomly distributed. The highly endemic areas were founded in Sujiatuo township, Yongfeng township, Shangzhuang township, Wenquan town and Bei'anhe township (relative risk = 4.43, P = 0.001). A thematic map of HFRS in haidian district was set up. CONCLUSION: HFRS infections were not randomly distributed, since the distribution was related to geographic-environmental factors.

China↗

How infectious diseases got left out--and what this omission might have meant for bioethics.

In this article, we first document the virtually complete absence of infectious disease examples and concerns at the time bioethics emerged as a field. We then argue that this oversight was not benign by considering two central issues in the field, informed consent and distributive justice, and showing how they might have been framed differently had infectiousness been at the forefront of concern. The solution to this omission might be to apply standard approaches in liberal bioethics, such as autonomy and the harm principle, to infectious examples. We argue that this is insufficient, however. Taking infectious disease into account requires understanding the patient as victim and as vector. Infectiousness reminds us that as autonomous agents we are both embodied and vulnerable in our relationships with others. We conclude by applying this reunderstanding of agency to the examples of informed consent and distributive justice in health care.

Bioethical Issues↗

Analysis of the alpha-satellite DNA from African green monkey cells by restriction nucleases.

By the use of restriction endonucleases the organization of the alpha-satellite DNA from African green monkey cells (Cercopithecus aethiops) has been analyzed. With endo R-HindIII, endo R-AluI and with endo R-EcoRI at conditions of low salt and high pH (endo R-EcoRI) all of the satellite was digested while only a part of the satellite was cleaved with endo R-Bsu and endo R-EcoRI under standard conditions. With each of the four nucleases a series of fragments was formed which were multiplies in size of a basic repeat unit linked in tandem arrays in the intact satellite. The quantitative evaluation of the digestion with each nuclease as well as with combinations of two nucleases yielded information about the distribution of the cleavage sites. While the arrangement of the endo R-HindIII cleavage sites conforms to a random distribution across the entire satellite, the results from the endo R-Bsu and endo R-EcoRI cleavage patterns are consistent with a picture where the cleavage sites are clustered in fractions of the satellite. Since endo R-AluI recognizes the central four nucleotide pairs of the endo R-HindIII cleavage site, the redigestion of the endo R-HindIII dimer with endo R-AluI gave information about the distribution of mutations in the satellite. The results of these experiments together with the comparison of the sequence divergence determined from digestion with endo R-HindIII and endo R-EcoRI lend support to the hypothesis that mutations have affected all bases in the satellite evenly. The gamma-satellite, another fraction of the African green monkey DNA, could be separated by Ag+/CsSO4 density gradient centrifugation into two components. With the three restriction nucleases used both components gave a background of fragments of heterogenous length on gel electrophoresis with some faint bands of no apparent regularity in one case.

Animals↗

Descriptive information of topographic parameters computed at the optic nerve head with the Heidelberg retina tomograph.

PURPOSE: To analyze the frequency distribution and descriptive information of topometric data obtained with the Heidelberg Retina Tomograph (HRT) in a normal population. METHODS: Topographic measurements of the optic disc were acquired and evaluated using the HRT in 225 subjects between 12 and 90 years of age. After randomly selecting one eye per subject, the frequency distributions, mean values, minima, maxima, and first, fifth, fiftieth, ninety-fifth, and ninety-ninth percentiles were evaluated for topographic parameters computed by the HRT. The influence of age, intraocular pressure (IOP), disc size, and disc shape on optic disc topometric data was analyzed. A principal component analysis of the topometric parameters was performed. The frequency distributions, mean values, minima, maxima, and first, fifth, fiftieth, ninety-fifth, and ninety-ninth percentiles of the interocular difference in topographic parameters were evaluated. RESULTS: All topographic parameters showed a unimodal but not necessarily normal distribution. None of the parameters showed a relevant correlation with age, IOP (in the normal range), and overall shape of the anterior optic nerve, but a few parameters showed a clinically significant correlation with disc size. A principal component analysis identified four relevant factors (optic nerve cup, retinal nerve fiber layer, optic disc size, and optic nerve cup shape) in the entire data set of optic nerve topometric data. The absolute value of all interocular differences in topographic parameters showed an asymmetric but unimodal distribution. CONCLUSION: The mathematical description of the optic nerve cup shape provides information on optic nerve head topography independently from cupping, nerve fiber layer thickness, and disc size. Potentially, quantification of further aspects in optic nerve head topography might improve the discriminatory power of computerized quantitative optic nerve head analysis.

Adolescent↗

Representing stereochemical information in macromolecular electron-density distributions by multi-dimensional histograms.

Previous studies have demonstrated the value of ideal electron-density histograms as targets for the corresponding histograms of experimental electron-density maps. The electron-density histogram makes use of density values as independent objects, and no relationship between them is taken into account. Extension to include the relationships between neighboring density values leads naturally to a multi-dimensional histogram defined as the joint frequency of the density values and their higher order derivatives. We show here that the multi-dimensional histogram including additional dimensions composed of the gradient magnitude and Laplacian of the density is minimally dependent on molecular folding and packing, and captures substantially more stereochemical information than the conventional electron-density histogram. The gradient histogram appears to be much more sensitive to phase errors than the conventional electron-density histogram. Potential uses of the multi-dimensional histogram include improved targets for density modification and more reliable figures of merit for evaluating correct phases.

Journal Article↗

Determination of vesicle size distributions by freeze-fracture electron microscopy.

The most common electron microscopic technique for obtaining information on size distributions of uncollapsed membrane vesicles is based on the method of van Venetie (1980). This technique involves the sizing of only those vesicles that were freeze fractured at their equatorial planes. As a result, only a small number of images can be used to generate size distributions. Further, the technique is susceptible to systematic error. An alternate approach is to consider the complete distribution of image sizes and use this distribution to determine the average size and distribution of the vesicles. It is shown that the mean vesicle size is 4/pi times the mean image size. As well, a parameter, m, which can be determined from the image distribution, can be used to characterize the vesicle distribution. The advantage of this new approach is that images of all vesicles are used, leading to a statistically better determination of vesicle sizes.

Freeze Fracturing↗

Grid requirements for the integration of biomedical information resources for health applications.

OBJECTIVES: The goal of this paper is to identify how Grid technology can be applied for the development and deployment of integration systems, bringing together distributed and heterogeneous biomedical information sources for medical applications. METHODS: The integration of new genetic and medical knowledge in clinical workflows requires the development of new paradigms for information management in which the ability to access and relate disparate data sources is essential. We adopt a requirements perspective based on the user needs we have identified in the development of the INFOGENMED system to assess current Grid technology against those requirements. RESULTS: The gap between Grid features and distributed biomedical information integration needs is characterized. Results from prospective studies are also reported. CONCLUSIONS: Grid infrastructures offer advanced features for the deployment of collaborative computational environments across virtual organizations. New Grid developments are in line with the problem of multiple site information integration. From the INFOGENMED point of view, Grid infrastructures need to evolve to implement structured data access services and semantic content description and discovery.

Computational Biology↗

Codes for sound-source location in nontonotopic auditory cortex.

We evaluated two hypothetical codes for sound-source location in the auditory cortex. The topographical code assumed that single neurons are selective for particular locations and that sound-source locations are coded by the cortical location of small populations of maximally activated neurons. The distributed code assumed that the responses of individual neurons can carry information about locations throughout 360 degrees of azimuth and that accurate sound localization derives from information that is distributed across large populations of such panoramic neurons. We recorded from single units in the anterior ectosylvian sulcus area (area AES) and in area A2 of alpha-chloralose-anesthetized cats. Results obtained in the two areas were essentially equivalent. Noise bursts were presented from loudspeakers spaced in 20 degrees intervals of azimuth throughout 360 degrees of the horizontal plane. Spike counts of the majority of units were modulated >50% by changes in sound-source azimuth. Nevertheless, sound-source locations that produced greater than half-maximal spike counts often spanned >180 degrees of azimuth. The spatial selectivity of units tended to broaden and, often, to shift in azimuth as sound pressure levels (SPLs) were increased to a moderate level. We sometimes saw systematic changes in spatial tuning along segments of electrode tracks as long as 1.5 mm but such progressions were not evident at higher sound levels. Moderate-level sounds presented anywhere in the contralateral hemifield produced greater than half-maximal activation of nearly all units. These results are not consistent with the hypothesis of a topographic code. We used an artificial-neural-network algorithm to recognize spike patterns and, thereby, infer the locations of sound sources. Network input consisted of spike density functions formed by averages of responses to eight stimulus repetitions. Information carried in the responses of single units permitted reasonable estimates of sound-source locations throughout 360 degrees of azimuth. The most accurate units exhibited median errors in localization of <25 degrees, meaning that the network output fell within 25 degrees of the correct location on half of the trials. Spike patterns tended to vary with stimulus SPL, but level-invariant features of patterns permitted estimates of locations of sound sources that varied through 20-dB ranges. Sound localization based on spike patterns that preserved details of spike timing consistently was more accurate than localization based on spike counts alone. These results support the hypothesis that sound-source locations are represented by a distributed code and that individual neurons are, in effect, panoramic localizers.

Action Potentials↗

Integrating the roles of information and competitive ability on the spatial distribution of social foragers.

Understanding and predicting the spatial distribution of social foragers among patchily distributed resources is a problem that has been addressed with numerous approaches over the 30 yr since the ideal free distribution (IFD) was first introduced. The two main approaches involve perceptual constraints and unequal competitors. Here we present a model of social foragers choosing among resource patches. Each forager makes a probabilistic choice on the basis of the information acquired through past foraging experiences. Food acquisition is determined by the forager's competitive ability. This model predicts that perceptual constraints have a greater influence on the spatial distribution of foragers than unequal competitive abilities but that competitive ability plays an important role in determining an individual's information state and behavior. Better competitors have access to more information; consequently, we find that competitive abilities and perceptual constraints are integrated through the social environment occupied by individual foragers. Relative competitive abilities influence the forager's information state, and the ability to use information determines the resulting spatial distribution.

Animals↗

Backscattered electron imaging of lectin binding sites in tissues following freeze-fracture cytochemistry.

Recently, cytochemical techniques have been applied for localizing membrane components; however, transmission electron microscopy only provides two-dimensional information about their distribution. Scanning electron microscopy, on the other hand, offers the possibility of examining the three-dimensional architecture of biological samples. The fracture-label cytochemical technique was combined with the backscattered electron imaging (BEI) mode of the scanning electron microscope to visualize the in vivo distribution of lectin binding sites on freeze-fractured biological membranes in tissues and cells. Pancreatic and testicular tissues, fixed with glutaraldehyde, were freeze-fractured and labeled with Helix pomatia lectin-gold or Ricinus communis I-gold complexes. The labeled specimens were then critical-point dried and replicated with platinum-carbon for routine transmission electron microscopy or with carbon alone for BEI. Lectin-gold labeling of fractured plasma and intracellular membranes observed with BEI showed a labeling pattern similar to that seen by the replica method. However, BEI-fracture-label provided additional information about the distribution of the labeling with respect to three-dimensional organization of tissues and cells. Large sample areas could be examined, making this technique particularly useful as a survey method for specimens that are either differentially labeled or composed of heterogenous cell populations.

Animals↗

The waiting time distribution as a graphical approach to epidemiologic measures of drug utilization.

The emergence of large, computerized pharmacoepidemiologic databases has enabled us to study drug utilization with the individual user as the statistical unit. A recurrent problem in such analyses, however, is the overwhelming volume and complexity of data. We here describe a graphical approach that effectively conveys some essential utilization parameters for a drug. The waiting time distribution for a group of drug users is a charting of their first prescription presentations within a specified time window. For a drug used for chronic treatment, most current users will be captured at the beginning of the window. After a few months, the graph will be dominated by new, incident users. As examples, we present waiting time distributions for insulin, ulcer drugs, systemic corticosteroids, antidepressants, and disulfiram. Appropriately analyzed and interpreted, the waiting time distributions can provide information about the period prevalence, point prevalence, incidence, duration of use, seasonality, and rate of prescription renewal or relapse for specific drugs. Each of these parameters has a visual correlate. The waiting time distributions may be an informative supplement to conventional drug utilization statistics, and possibly also a useful screening tool for unusual prescribing patterns.

Adrenal Cortex Hormones↗

Studies of multiple sclerosis in communities concerned about environmental exposures.

Multiple sclerosis (MS) is an autoimmune disease that differentially affects women, people 30-60 years old, and Caucasians. Evidence indicates that it is a complex disease determined by both environmental factors and genetic susceptibility. People across the United States have expressed concern about perceived clusters of MS in their communities and the role of environmental exposures in the development of the disease. The Agency for Toxic Substances and Disease Registry (ATSDR) has funded several studies to address this issue, including a cluster investigation, several prevalence studies, and a case-control study. The cluster investigation illustrated that there are few data regarding the number of individuals with MS in the United States. Prevalence studies were conducted in Ohio, Missouri, and Texas to address this deficiency. The results support a regional difference in MS prevalence, although the reason for this difference is unclear. The results also underscore the need for additional epidemiological information about the distribution of MS in other areas of the United States and information on the underlying etiology of the disease. A case-control study is currently being conducted to examine potential risk factors for MS, including the role of environmental exposures and genetic susceptibility. Future research on MS should focus on large-scale studies and include collaboration among researchers with varied fields of expertise, such as epidemiology, neurology, and genetics.

Adult↗