Biomedical subjects

Peter Salamon

Publications and source records attributed to Peter Salamon.

10 recordsLinked to original sources

PubMed2006

A review and numerical assessment of the random walk particle tracking method.

We review the basic mathematical concepts of random walk particle tracking (RWPT) and its advantages and limitations. Three different numerical approaches to overcome the local mass conservation problem of the random walk methodology are examined: (i) the interpolation method, (ii) the reflection principle, and (iii) the generalized stochastic differential equations (GSDE). Analytical solutions of the spatial moments for a two-layer system are compared to model predictions using the different techniques and results demonstrate that the interpolation method reproduces correctly average velocity, but fails to reproduce macrodispersion at higher hydraulic conductivity contrasts between the two layers. On the contrary, the reflection principle and the GSDE approach underestimate average velocity, but reproduce macrodispersion better for high contrasts. The different behavior is based on an artificial shift of mass for increasing heterogeneities for the GSDE approach and the reflection principle, whereas the interpolation method suffers from the smoothing of the dispersion tensor. The behavior of these approaches was furthermore analyzed in two-dimensional heterogeneous hydraulic conductivity fields, which are characterized by different random function models. Solute transport was simulated correctly by all three approaches for the reference fields having Gaussian structures or non-Gaussian structures with an isotropic spatial correlation, even for a variance of the natural log of hydraulic conductivity of sigma(lnK)(2)=4. However, for the non-Gaussian model with a strong anisotropic spatial correlation and a variance of sigma(lnK)(2)=2 and higher, the interpolation method was the only technique modelling solute transport correctly. Furthermore, we discuss the general applicability of random walk particle tracking in comparison to the standard transport models and conclude that in advection-dominated problems using a high spatial discretization or requiring the performance of many model runs, RWPT represents a good alternative for modelling contaminant transport.

Models, Chemical↗

PubMed2006

The marine viromes of four oceanic regions.

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct "marine-ness" quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.

Bacteriophages↗

PubMed2005

A diffusion approach to labeling rows and columns in an irregular array.

A robust algorithm is presented for labeling rows and columns in an irregular array. The algorithm is based on hierarchical pattern matching to a local lattice, which is used as a template. Starting from the best local match, the pattern is expanded hierarchically to encompass the entire array. An application to labeling digitized images of an array of tissue sections mounted on a microscope slide is discussed.

Algorithms↗

PubMed2005

PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information.

BACKGROUND: Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS http://phage.sdsu.edu/phaccs, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity. RESULTS: PHACCS builds models of possible community structure using a modified Lander-Waterman algorithm to predict the underlying contig spectrum. PHACCS finds the most appropriate structure model by optimizing the model parameters until the predicted contig spectrum is as close as possible to the experimental one. This model is the basis for making estimates of uncultured viral community richness, evenness, diversity index and abundance of the most abundant genotype. CONCLUSION: PHACCS analysis of four different environmental phage communities suggests that the power law is an important rank-abundance form to describe uncultured viral community structure. The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts.

Algorithms↗

PubMed2004

Fitness threshold accepting over extremal optimization ranks.

We treat the problem of selecting the next degree of freedom for update in an extremal optimization algorithm designed to find the ground state of a system with a complex energy landscape. We show that there exists a best distribution for selecting the next degree of freedom in order to optimize any linear function of the state probabilities, e.g., the expected number of visits to the ground state. We dub the class of algorithms using this best distribution in conjunction with extremal optimization fitness threshold accepting. In addition, we construct an extended random walk and use it to show that fitness threshold accepting is optimal also for several other measures of algorithm performance, such as maximizing the expected probability of seeing the ground state and minimizing the expected value of the lowest energy seen.

Journal Article↗

PubMed2004

Diversity and population structure of a near-shore marine-sediment viral community.

Viruses, most of which are phage, are extremely abundant in marine sediments, yet almost nothing is known about their identity or diversity. We present the metagenomic analysis of an uncultured near-shore marine-sediment viral community. Three-quarters of the sequences in the sample were not related to anything previously reported. Among the sequences that could be identified, the majority belonged to double-stranded DNA phage. Temperate phage were more common than lytic phage, suggesting that lysogeny may be an important lifestyle for sediment viruses. Comparisons between the sediment sample and previously sequenced seawater viral communities showed that certain phage phylogenetic groups were abundant in all marine viral communities, while other phage groups were under-represented or absent. This 'marineness' suggests that marine phage are derived from a common set of ancestors. Several independent mathematical models, based on the distribution of overlapping shotgun sequence fragments from the library, were used to show that the diversity of the viral community was extremely high, with at least 10(4) viral genotypes per kilogram of sediment and a Shannon index greater than 9 nats. Based on these observations we propose that marine-sediment viral communities are one of the largest unexplored reservoirs of sequence space on the planet.

Biodiversity↗

PubMed2003

Metagenomic analyses of an uncultured viral community from human feces.

Here we present the first metagenomic analyses of an uncultured viral community from human feces, using partial shotgun sequencing. Most of the sequences were unrelated to anything previously reported. The recognizable viruses were mostly siphophages, and the community contained an estimated 1,200 viral genotypes.

Bacteriophages↗

PubMed2002

Structure of best possible strategies for finding ground states.

Finding the ground state of a system with a complex energy landscape is important for many physical problems including protein folding, spin glasses, chemical clusters, and neural networks. Such problems are usually solved by heuristic search methods whose efficacy is judged by empirical performance on selected examples. We present a proof that for a wide range of objective functions threshold accepting is the best possible strategy within a large class of algorithms that simulate random walks on the landscape. In particular, it can perform better than simulated annealing, Tsallis and Glauber statistics.

Journal Article↗

PubMed2002

Genomic analysis of uncultured marine viral communities.

Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common significant hits among the known sequences were to viruses. The viral hits included sequences from all of the major families of dsDNA tailed phages, as well as some algal viruses. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2-3% of the total population in both communities, which was estimated to contain between 374 and 7,114 viral types. Overall, diversity of the viral communities was extremely high. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.

Bacteriophages↗

PubMedDate not supplied

A thermodynamic model describing the nature of the crista junction: a structural motif in the mitochondrion.

The use of electron tomography has allowed the three-dimensional membrane topography of the mitochondrion to be better understood. The most striking feature of this topology is the crista junction, a structure that may serve to divide functionally the inner membrane and intermembrane spaces. In situ these junctions seem to have a preferred size and shape independent of the source of the mitochondrion with few exceptions. When mitochondria are isolated and have a condensed matrix the crista junctions enlarge and become nondiscrete. Upon permeation of the inner membrane and subsequent swelling of the matrix space, the uniform circular nature of the crista junction reappears. We examine the distribution of shapes and sizes of crista junctions and suggest a thermodynamic model that explains the distribution based on current theories of bilayer membrane shapes. The theory of spontaneous curvature shows the circular junction to be a thermodynamically stable structure whose size and shape is influenced by the relative volume of the matrix. We conclude that the crista junction exists predominantly as a circular junction, with other shapes as exceptions made possible by specific characteristics of the lipid bilayer.

Animals↗