Food Characterization of the Spotted Pimelodid Fish Pimelodus Maculatus From a Polluted Urban River in Argentina

On the present study, the nourishment and the digestive system of a population of the spotted pimelodid Pimelodus maculatus Lacepède 1803 from a polluted urban river in Argentina were analyzed (Reconquista River, Buenos Aires province). The specimens are characterized by having benthic habits and an omnivore diet. In their intestinal content, a diversity of components was identified. Such components were grouped into ten alimentary items, with dietary variations according to body size while the longitude of the intestine remained proportional to standard length. Microbiological analysis in the gills, stomach and intestine showed the occurrence of Staphylococcus aureus, Escherichia coli and Salmonella sp. Fungi and yeast were also detected. Bacterial accounts were very high both in the analyzed organs as well in water samples. The ecological and sanitary significance of the identified bacteria is discussed

Induced Anticlinic Ordering and Nanophase Segregation of Bow-Shaped Molecules in a Smectic Solvent

Recent experiments indicate that doping low concentrations of bent-core molecules into calamitic smectic solvents can induce anticlinic and biaxial smectic phases. We have carried out Monte Carlo (MC) simulations of mixtures of rodlike molecules (hard spherocylinders with length/breadth ratio $L_{\rm rod}/D = 5$) and bow- or banana-shaped molecules (hard spherocylinder dimers with length/breadth ratio $L_{ban}/D = 5$ or 2.5 and opening angle $\psi$) to probe the molecular-scale organization and phase behavior of rod/banana mixtures. We find that a low concentration (3%) of $L_{ban}/D = 5$ dimers induces anticlinic (SmC$_A$) ordering in an untilted smectic (SmA) phase for $100^\circ \le \psi < 150^\circ$. For smaller $\psi$, half of each bow-shaped molecule is nanophase segregated between smectic layers, and the smectic layers are untilted. For $L_{ban}/D = 2.5$, no tilted phases are induced. However, with decreasing $\psi$ we observe a sharp transition from {\sl intralamellar} nanophase segregation (bow-shaped molecules segregated within smectic layers) to {\sl interlamellar} nanophase segregation (bow-shaped molecules concentrated between smectic layers) near $\psi = 130^\circ$. These results demonstrate that purely entropic effects can lead to surprisingly complex behavior in rod/banana mixtures.Comment: 5 pages Revtex, 7 postscript figure

Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota

The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.Comment: 20 pages, 5 figures accepted for publication in Plos Comp Bio. Supplementary video and information availabl

Current effects on neck growth in the sintering of copper spheres to copper plates by the pulsed electric current method

The effect of a pulsed dc on the sintering of copper spheres to copper plates was investigated. It was shown that the current had a marked effect on neck growth between the spheres and the plates. The enhancement of sintering under the effect of the current was attributed to electromigration. Microstructural observations on fracture surfaces of necks formed under high currents showed considerable void formation. It was also observed that the current resulted in increased evaporation and the formation of bunched evaporation steps. Formation of these steps and their location relative to the neck were consistent with current density distributions. The results of this investigation provide direct evidence for the role of the current in the sintering in the pulse electric current sintering method. (c) 2007 American Institute of Physics

Characterization of Bacteria in Biopsies of Colon and Stools by High Throughput Sequencing of the V2 Region of Bacterial 16S rRNA Gene in Human

BACKGROUND: The characterization of the human intestinal microflora and their interactions with the host have been identified as key components in the study of intestinal disorders such as inflammatory bowel diseases. High-throughput sequencing has enabled culture-independent studies to deeply analyze bacteria in the gut. It is possible with this technology to systematically analyze links between microbes and the genetic constitution of the host, such as DNA polymorphisms and methylation, and gene expression. METHODS AND FINDINGS: In this study the V2 region of the bacterial 16S ribosomal RNA (rRNA) gene using 454 pyrosequencing from seven anatomic regions of human colon and two types of stool specimens were analyzed. The study examined the number of reads needed to ascertain differences between samples, the effect of DNA extraction procedures and PCR reproducibility, and differences between biopsies and stools in order to design a large scale systematic analysis of gut microbes. It was shown (1) that sequence coverage lower than 1,000 reads influenced quantitative and qualitative differences between samples measured by UniFrac distances. Distances between samples became stable after 1,000 reads. (2) Difference of extracted bacteria was observed between the two DNA extraction methods. In particular, Firmicutes Bacilli were not extracted well by one method. (3) Quantitative and qualitative difference in bacteria from ileum to rectum colon were not observed, but there was a significant positive trend between distances within colon and quantitative differences. Between sample type, biopsies or stools, quantitative and qualitative differences were observed. CONCLUSIONS: Results of human colonic bacteria analyzed using high-throughput sequencing were highly dependent on the experimental design, especially the number of sequence reads, DNA extraction method, and sample type

Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition

Phylogenetic profiling has been widely used for comparing bacterial communities, but has so far been impossible to apply to viruses because of the lack of a single marker gene analogous to 16S rRNA. Here we developed a reference tree approach for matching viral sequences and applied it to the largest viral datasets available. The resulting technique, Shotgun UniFrac, was used to compare host-associated and non-host-associated phage communities (130 total metagenomes), and revealed a profound split similar to that found with bacterial communities. This new informatics approach complements analysis of bacterial communities and promises to provide new insights into viral community dynamics, such as top-down versus bottom-up control of bacterial communities by viruses in a range of systems

Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of data