Boolean decision problems with competing interactions on scale-free networks: Critical thermodynamics

We study the critical behavior of Boolean variables on scale-free networks with competing interactions (Ising spin glasses). Our analytical results for the disorder-network-decay-exponent phase diagram are verified using Monte Carlo simulations. When the probability of positive (ferromagnetic) and negative (antiferromagnetic) interactions is the same, the system undergoes a finite-temperature spin-glass transition if the exponent that describes the decay of the interaction degree in the scale-free graph is strictly larger than 3. However, when the exponent is equal to or less than 3, a spin-glass phase is stable for all temperatures. The robustness of both the ferromagnetic and spin-glass phases suggests that Boolean decision problems on scale-free networks are quite stable to local perturbations. Finally, we show that for a given decay exponent spin glasses on scale-free networks seem to obey universality. Furthermore, when the decay exponent of the interaction degree is larger than 4 in the spin-glass sector, the universality class is the same as for the mean-field Sherrington-Kirkpatrick Ising spin glass.Comment: 14 pages, lots of figures and 2 table

A specific sugar moiety in the Lactococcus lactis cell wall pellicle is required for infection by CHPC971, a member of the rare 1706 phage species

Lactococcus lactis is a Gram-positive bacterium widely used as starter culture for the production of different dairy products, especially a large variety of cheeses. Infection of lactococcal starter cultures by bacteriophages is one of the major causes of fermentation failure and often leads to production halt. Lactococcal bacteriophages belonging to the c2, 936 and P335 species are the most commonly isolated in dairy plants and have been extensively investigated in the past three decades. Information regarding bacteriophages belonging to less commonly isolated species is, on the other hand, less extensive, although these phages can also contribute to starter culture infection. Here we report the nucleotide sequence of the newly isolated L. lactis phage CHPC971, belonging to the rare 1706-species of lactococcal phages. We investigated the nature of the host receptor recognized by the phage and collected evidence strongly suggesting that it binds to a specific sugar moiety in the cell wall pellicle of its host. An in silico analysis of the genome of phage CHPC971 identified the hypothetical genes involved in receptor binding.Importance: Gathering information on how lactococcal bacteriophages recognize their host and proliferate in the dairy environment is of vital importance for the establishment of proper starter culture rotation plans, and to avoid fermentation failure and consequent great economic losses for dairy industries. We provide strong evidence on the type of receptor recognized by a newly isolated 1706-type lactococcal bacteriophage, increasing the knowledge on phage-host interactions relevant to dairying. This information can help to prevent phage infection events that, so far, are hard to predict and avoid

The restoration of ecological interactions: plant-pollinator networks on ancient and restored heathlands

1. Attempts to restore damaged ecosystems usually emphasize structural aspects of biodiversity, such as species richness and abundance. An alternative is to emphasize functional aspects, such as patterns of interaction between species. Pollination is a ubiquitous interaction between plants and animals. Patterns in plant-pollinator interactions can be analysed with a food web or complex-systems approach and comparing pollination webs between restored and reference sites can be used to test whether ecological restoration has taken place. 2. Using an ecological network approach, we compared plant-pollinator interactions on four pairs of restored and ancient heathlands 11 and 14 years following initiation of restoration management. We used the network data to test whether visitation by pollinators had been restored and we calculated pollinator importance indices for each insect species on the eight sites. Finally, we compared the robustness of the restored and ancient networks to species loss. 3. Plant and pollinator communities were established successfully on the restored sites. There was little evidence of movement of pollinators from ancient sites onto adjacent restored sites, although paired sites correlated in pollinator species richness in both years. There was little insect species overlap within each heathland between 2001 and 2004. 4. A few widespread insect species dominated the communities and were the main pollinators. The most important pollinators were typically honeybees (Apis mellifera), species of bumblebee (Bombus spp.) and one hoverfly species (Episyrphus balteatus). The interaction networks were significantly less complex on restored heathlands, in terms of connectance values, although in 2004 the low values might reflect the negative relationship between connectance and species richness. Finally, there was a trend of restored networks being more susceptible to perturbation than ancient networks, although this needs to be interpreted with caution. 5. Synthesis and applications. Ecological networks provide a powerful tool for assessing the outcome of restoration programmes. Our results indicate that heathland restoration does not have to occur immediately adjacent to ancient heathland for functional pollinator communities to be established. Moreover, in terms of restoring pollinator interactions, heathland managers need only be concerned with the most common insect species. Our focus on pollination demonstrates how a key ecological service can serve as a yardstick for judging restoration success

Novel Variants of <em>Streptococcus thermophilus</em> Bacteriophages Are Indicative of Genetic Recombination among Phages from Different Bacterial Species

Bacteriophages are the main cause of fermentation failures in dairy plants. The majority of Streptococcus thermophilus phages can be divided into either cos- or pac-type phages and are additionally characterized by examining the V2 region of their antireceptors. We screened a large number of S. thermophilus phages from the Chr. Hansen A/S collection, using PCR specific for the cos- or pac-type phages, as well as for the V2 antireceptor region. Three phages did not produce positive results with the assays. Analysis of phage morphologies indicated that two of these phages, CHPC577 and CHPC926, had shorter tails than the traditional S. thermophilus phages. The third phage, CHPC1151, had a tail size similar to those of the cos- or pac-type phages, but it displayed a different baseplate structure. Sequencing analysis revealed the genetic similarity of CHPC577 and CHPC926 with a subgroup of Lactococcus lactis P335 phages. Phage CHPC1151 was closely related to the atypical S. thermophilus phage 5093, homologous with a nondairy streptococcal prophage. By testing adsorption of the related streptococcal and lactococcal phages to the surface of S. thermophilus and L. lactis strains, we revealed the possibility of cross-interactions. Our data indicated that the use of S. thermophilus together with L. lactis, extensively applied for dairy fermentations, triggered the recombination between phages infecting different bacterial species. A notable diversity among S. thermophilus phage populations requires that a new classification of the group be proposed. IMPORTANCE Streptococcus thermophilus is a component of thermophilic starter cultures commonly used for cheese and yogurt production. Characterizing streptococcal phages, understanding their genetic relationships, and studying their interactions with various hosts are the necessary steps for preventing and controlling phage attacks that occur during dairy fermentations

Challenges for identifying the neural mechanisms that support spatial navigation: the impact of spatial scale.

Spatial navigation is a fascinating behavior that is essential for our everyday lives. It involves nearly all sensory systems, it requires numerous parallel computations, and it engages multiple memory systems. One of the key problems in this field pertains to the question of reference frames: spatial information such as direction or distance can be coded egocentrically-relative to an observer-or allocentrically-in a reference frame independent of the observer. While many studies have associated striatal and parietal circuits with egocentric coding and entorhinal/hippocampal circuits with allocentric coding, this strict dissociation is not in line with a growing body of experimental data. In this review, we discuss some of the problems that can arise when studying the neural mechanisms that are presumed to support different spatial reference frames. We argue that the scale of space in which a navigation task takes place plays a crucial role in determining the processes that are being recruited. This has important implications, particularly for the inferences that can be made from animal studies in small scale space about the neural mechanisms supporting human spatial navigation in large (environmental) spaces. Furthermore, we argue that many of the commonly used tasks to study spatial navigation and the underlying neuronal mechanisms involve different types of reference frames, which can complicate the interpretation of neurophysiological data

A comparative genomics approach for identifying host-range determinants in <i>Streptococcus thermophilus</i> bacteriophages

The authors would like to thank: Mimi Birkelund, Ditte E. Christiansen, Goncalo Covas, and Denise Coutinho for their help in collecting data; Ana Rute Neves for valuable discussions; Witold Kot and Lars H. Hansen for sequencing of phage genomes at Aarhus University (Roskilde, Denmark). This work is part of an Industrial PhD Project funded by Innovation Fund Denmark and Chr. Hansen A/S, grant no. 4135-00104B.Comparative genomics has proven useful in exploring the biodiversity of phages and understanding phage-host interactions. This knowledge is particularly useful for phages infecting Streptococcus thermophilus, as they constitute a constant threat during dairy fermentations. Here, we explore the genetic diversity of S. thermophilus phages to identify genetic determinants with a signature for host specificity, which could be linked to the bacterial receptor genotype. A comparative genomic analysis was performed on 142 S. thermophilus phage genomes, 55 of which were sequenced in this study. Effectively, 94 phages were assigned to the group cos (DT1), 36 to the group pac (O1205), six to the group 5093, and six to the group 987. The core genome-based phylogeny of phages from the two dominating groups and their receptor binding protein (RBP) phylogeny corresponded to the phage host-range. A role of RBP in host recognition was confirmed by constructing a fluorescent derivative of the RBP of phage CHPC951, followed by studying the binding of the protein to the host strain. Furthermore, the RBP phylogeny of the cos group was found to correlate with the host genotype of the exocellular polysaccharide-encoding operon. These findings provide novel insights towards developing strategies to combat phage infections in dairies.publishersversionpublishe