Deciphering the connectivity structure of biological networks using MixNet

<p>Abstract</p> <p>Background</p> <p>As biological networks often show complex topological features, mathematical methods are required to extract meaningful information. Clustering methods are useful in this setting, as they allow the summary of the network's topology into a small number of relevant classes. Different strategies are possible for clustering, and in this article we focus on a model-based strategy that aims at clustering nodes based on their connectivity profiles.</p> <p>Results</p> <p>We present MixNet, the first publicly available computer software that analyzes biological networks using mixture models. We apply this method to various networks such as the <it>E. coli </it>transcriptional regulatory network, the macaque cortex network, a foodweb network and the <it>Buchnera aphidicola </it>metabolic network. This method is also compared with other approaches such as module identification or hierarchical clustering.</p> <p>Conclusion</p> <p>We show how MixNet can be used to extract meaningful biological information, and to give a summary of the networks topology that highlights important biological features. This approach is powerful as MixNet is adaptive to the network under study, and finds structural information without any a priori on the structure that is investigated. This makes MixNet a very powerful tool to summarize and decipher the connectivity structure of biological networks.</p

Phenotypic variation of larks along an aridity gradient:Are desert birds more flexible?

We investigated interindividual variation and intra-individual phenotypic flexibility in basal metabolic rate (BMR), total evaporative water loss (TEWL), body temperature (T-b), the minimum dry heat transfer coefficient (h), and organ and muscle size of five species of larks geographically distributed along an aridity gradient. We exposed all species to constant environments of 15degreesC or 35degreesC, and examined to what extent interspecific differences in physiology can be attributed to acclimation. We tested the hypothesis that birds from deserts display larger intra-individual phenotypic flexibility and smaller intern individual variation than species from mesic areas.Larks from arid areas had lower BMR, TEWL, and h, but did not have internal organ, sizes different from birds from mesic habitats. BMR of 15degreesC-acclimated birds was 18.0%, 29.1%, 12.2%, 25.3%, and 4.7% higher than of 35degreesC-acclimated Hoopoe Larks, Dunn's Larks, Spike-heeled Larks, Skylarks, and Woodlarks, respectively. TEWL of 15degreesC-acclimated Hoopoe Larks exceeded values for 35degreesC-acclimated individuals by 23% but did not differ between 15degreesC- and 35degreesC-acclimated individuals in the other species. The dry heat transfer coefficient was increased in 15degreesC-acclimated individuals of Skylarks and Dunn's Larks, but not in the. other species. Body temperature was on average 0.4degreesC +/- 0.15degreesC (mean +/- 1 SEM) lower in 15degreesC-acclimated individuals of all species. Increased food intake in 15degreesC-acclimated birds stimulated enlargement of intestine (26.9-38.6%), kidneys (9.8-24.4%), liver (16.5-27.2%), and. stomach (22.0-31.6%). The pectoral muscle increased in 15degreesC-acclimated Spike-heeled Larks and Skylarks, remained unchanged in Hoopoe Larks, and decreased in 15degreesC-acclimated Woodlarks and Dunn's Larks. We conclude that the degree of intra-individual flexibility varied between physiological traits and among species, but that acclimation does not account for interspecific differences in BMR, TEWL, and h in larks. We found no general support for the hypothesis that species from desert environments display larger intra-individual phenotypic flexibility than those from mesic areas.The coefficient of variation of larks acclimated to their natural environment was smaller in species from and areas than in species from mesic areas for mass-corrected BMR and surface-specific h, but not for mass-corrected TEWL. The high repeatabilities of BMR, TEWL, and h in several species indicated a within-individual consistency on which natural selection could operate.</p

Body sizes of consumers and their resources

Trophic information—who eats whom—and species' body sizes are two of the most basic descriptions necessary to understand community structure as well as ecological and evolutionary dynamics. Consumer–resource body size ratios between predators and their prey, and parasitoids and their hosts, have recently gained increasing attention due to their important implications for species' interaction strengths and dynamical population stability. This data set documents body sizes of consumers and their resources. We gathered body size data for the food webs of Skipwith Pond, a parasitoid community of grass-feeding chalcid wasps in British grasslands; the pelagic community of the Benguela system, a source web based on broom in the United Kingdom; Broadstone Stream, UK; the Grand Cariçaie marsh at Lake Neuchtel, Switzerland; Tuesday Lake, USA; alpine lakes in the Sierra Nevada of California; Mill Stream, UK; and the eastern Weddell Sea Shelf, Antarctica. Further consumer–resource body size data are included for planktonic predators, predatory nematodes, parasitoids, marine fish predators, freshwater invertebrates, Australian terrestrial consumers, and aphid parasitoids. Containing 16 807 records, this is the largest data set ever compiled for body sizes of consumers and their resources. In addition to body sizes, the data set includes information on consumer and resource taxonomy, the geographic location of the study, the habitat studied, the type of the feeding interaction (e.g., predacious, parasitic) and the metabolic categories of the species (e.g., invertebrate, ectotherm vertebrate). The present data set was gathered with the intent to stimulate research on effects of consumer–resource body size patterns on food-web structure, interaction-strength distributions, population dynamics, and community stability. The use of a common data set may facilitate cross-study comparisons and understanding of the relationships between different scientific approaches and models

Interdiffusion in L12-Ni3Al Alloyed with Re

Ternary interdiffusion in L1 2-Ni 3Al with ternary alloying addition of Re was investigated at 1473 K using solid-to-solid diffusion couples. Interdiffusion flux of Ni, Al, and Re were directly calculated from experimental concentration profiles and integrated for the determination of average ternary interdiffusion coefficients. The magnitude of main interdiffusion coefficients D̄̃ NiNiAl and D̄̃ AlAlNi was determined to be much larger than that of the main interdiffusion coefficient D̄̃ ReReAl(orNi) A moderate tendency for Re to substitute for Al sites was reflected by its influence on interdiffusion of Al, quantified by large and positive D̄̃ AlReNi coefficients. Similar trends were observed from ternary interdiffusion coefficients determined by Boltzmann-Matano analysis. Profiles of concentrations and interdiffusion fluxes were also examined to estimate binary interdiffusion coefficients in Ni 3Al, and tracer diffusion coefficients of Re (5.4 × 10 -16 ± 2.3 × 10 -16 m 2/s) in Ni 3Al. © 2009 ASM International