Evolving Clustered Random Networks

We propose a Markov chain simulation method to generate simple connected random graphs with a specified degree sequence and level of clustering. The networks generated by our algorithm are random in all other respects and can thus serve as generic models for studying the impacts of degree distributions and clustering on dynamical processes as well as null models for detecting other structural properties in empirical networks

Spatio-Temporal Transmission Patterns of Black-Band Disease in a Coral Community

Transmission mechanisms of black-band disease (BBD) in coral reefs are poorly understood, although this disease is considered to be one of the most widespread and destructive coral infectious diseases. The major objective of this study was to assess transmission mechanisms of BBD in the field based on the spatio-temporal patterns of the disease

Neighbor Overlap Is Enriched in the Yeast Interaction Network: Analysis and Implications

The yeast protein-protein interaction network has been shown to have distinct topological features such as a scale free degree distribution and a high level of clustering. Here we analyze an additional feature which is called Neighbor Overlap. This feature reflects the number of shared neighbors between a pair of proteins. We show that Neighbor Overlap is enriched in the yeast protein-protein interaction network compared with control networks carefully designed to match the characteristics of the yeast network in terms of degree distribution and clustering coefficient. Our analysis also reveals that pairs of proteins with high Neighbor Overlap have higher sequence similarity, more similar GO annotations and stronger genetic interactions than pairs with low ones. Finally, we demonstrate that pairs of proteins with redundant functions tend to have high Neighbor Overlap. We suggest that a combination of three mechanisms is the basis for this feature: The abundance of protein complexes, selection for backup of function, and the need to allow functional variation

Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components

Biomolecular pathways are built from diverse types of pairwise interactions, ranging from physical protein-protein interactions and modifications to indirect regulatory relationships. One goal of systems biology is to bridge three aspects of this complexity: the growing body of high-throughput data assaying these interactions; the specific interactions in which individual genes participate; and the genome-wide patterns of interactions in a system of interest. Here, we describe methodology for simultaneously predicting specific types of biomolecular interactions using high-throughput genomic data. This results in a comprehensive compendium of whole-genome networks for yeast, derived from ∼3,500 experimental conditions and describing 30 interaction types, which range from general (e.g. physical or regulatory) to specific (e.g. phosphorylation or transcriptional regulation). We used these networks to investigate molecular pathways in carbon metabolism and cellular transport, proposing a novel connection between glycogen breakdown and glucose utilization supported by recent publications. Additionally, 14 specific predicted interactions in DNA topological change and protein biosynthesis were experimentally validated. We analyzed the systems-level network features within all interactomes, verifying the presence of small-world properties and enrichment for recurring network motifs. This compendium of physical, synthetic, regulatory, and functional interaction networks has been made publicly available through an interactive web interface for investigators to utilize in future research at http://function.princeton.edu/bioweaver/

La nueva ley de instituciones bancarias, financieras y de seguros: algunos comentarios

This research was funded by Natural Sciences and Engineering Research Council of Canada discovery grants to LL and L-AG. NJB was financially supported by a Dr. Richard H. Tomlinson Fellowship and a Dr. Milton Leong Fellowship from McGill University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Background: Successful foraging is essential for survival and reproductive success. In many bird species, foraging is a learned behaviour. To cope with environmental change and survive periods in which regular foods are scarce, the ability to solve novel foraging problems by learning new foraging techniques can be crucial. Although females have been shown to prefer more efficient foragers, the effect of males' foraging techniques on female mate choice has never been studied. We tested whether females would prefer males showing the same learned foraging technique as they had been exposed to as juveniles, or whether females would prefer males that showed a complementary foraging technique. Methodology/Principal Findings: We first trained juvenile male and female zebra finches (Taeniopygia guttata) to obtain a significant proportion of their food by one of two foraging techniques. We then tested whether females showed a preference for males with the same or the alternative technique. We found that neither a male's foraging technique nor his foraging performance affected the time females spent in his proximity in the mate-choice apparatus. We then released flocks of these finches into an aviary to investigate whether assortative pairing would be facilitated by birds taught the same technique exploiting the same habitat. Zebra finches trained as juveniles in a specific foraging technique maintained their foraging specialisation in the aviary as adults. However, pair formation and nest location were random with regard to foraging technique. Conclusions/Significance: Our findings show that zebra finches can be successfully trained to be foraging specialists. However, the robust negative results of the conditions tested here suggest that learned foraging specializations do not affect mate choice or pair formation in our experimental context.Publisher PDFPeer reviewe