SMC-based immunity against extrachromosomal DNA elements.

SMC and SMC-like complexes promote chromosome folding and genome maintenance in all domains of life. Recently, they were also recognized as factors in cellular immunity against foreign DNA. In bacteria and archaea, Wadjet and Lamassu are anti-plasmid/phage defence systems, while Smc5/6 and Rad50 complexes play a role in anti-viral immunity in humans. This raises an intriguing paradox - how can the same, or closely related, complexes on one hand secure the integrity and maintenance of chromosomal DNA, while on the other recognize and restrict extrachromosomal DNA? In this minireview, we will briefly describe the latest understanding of each of these complexes in immunity including speculations on how principles of SMC(-like) function may explain how the systems recognize linear or circular forms of invading DNA

Laue Lens Development for Hard X-rays (>60 keV)

Results of reflectivity measurements of mosaic crystal samples of Cu (111) are reported. These tests were performed in the context of a feasibility study of a hard X-ray focusing telescope for space astronomy with energy passband from 60 to 600 keV. The technique envisaged is that of using mosaic crystals in transmission configuration that diffract X-rays for Bragg diffraction (Laue lens). The Laue lens assumed has a spherical shape with focal length $f$. It is made of flat mosaic crystal tiles suitably positioned in the lens. The samples were grown and worked for this project at the Institute Laue-Langevin (ILL) in Grenoble (France), while the reflectivity tests were performed at the X-ray facility of the Physics Department of the University of Ferrara.Comment: 6 pages, 12 figures, accepted for publication in IEEE Transactions on Nuclear Scienc

Heterogeneous-k-core versus Bootstrap Percolation on Complex Networks

We introduce the heterogeneous-$k$-core, which generalizes the $k$-core, and contrast it with bootstrap percolation. Vertices have a threshold $k_i$ which may be different at each vertex. If a vertex has less than $k_i$ neighbors it is pruned from the network. The heterogeneous-$k$-core is the sub-graph remaining after no further vertices can be pruned. If the thresholds $k_i$ are $1$ with probability $f$ or $k \geq 3$ with probability $(1-f)$, the process forms one branch of an activation-pruning process which demonstrates hysteresis. The other branch is formed by ordinary bootstrap percolation. We show that there are two types of transitions in this heterogeneous-$k$-core process: the giant heterogeneous-$k$-core may appear with a continuous transition and there may be a second, discontinuous, hybrid transition. We compare critical phenomena, critical clusters and avalanches at the heterogeneous-$k$-core and bootstrap percolation transitions. We also show that network structure has a crucial effect on these processes, with the giant heterogeneous-$k$-core appearing immediately at a finite value for any $f > 0$ when the degree distribution tends to a power law $P(q) \sim q^{-\gamma}$ with $\gamma < 3$.Comment: 10 pages, 4 figure

Frequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions

A total of 1246 Pseudomonas strains were isolated from the rhizosphere of two perennial grasses (Lolium perenne and Molinia coerulea) with different nitrogen requirements. The plants were grown in their native soil under ambient and elevated atmospheric CO2 content (pCO2) at the Swiss FACE (Free Air CO2 Enrichment) facility. Root-, rhizosphere-, and non-rhizospheric soil-associated strains were characterized in terms of their ability to reduce nitrate during an in vitro assay and with respect to the genes encoding the membrane-bound (named NAR) and periplasmic (NAP) nitrate reductases so far described in the genus Pseudomonas. The diversity of corresponding genes was assessed by PCR-RFLP on narG and napA genes, which encode the catalytic subunit of nitrate reductases. The frequency of nitrate-dissimilating strains decreased with root proximity for both plants and was enhanced under elevated pCO2 in the rhizosphere of L. perenne. NAR (54% of strains) as well as NAP (49%) forms were present in nitrate-reducing strains, 15.5% of the 439 strains tested harbouring both genes. The relative proportions of narG and napA detected in Pseudomonas strains were different according to root proximity and for both pCO2 treatments: the NAR form was more abundant close to the root surface and for plants grown under elevated pCO2. Putative denitrifiers harbored mainly the membrane-bound (NAR) form of nitrate reductase. Finally, both narG and napA sequences displayed a high level of diversity. Anyway, this diversity was correlated neither with the root proximity nor with the pCO2 treatmen

Understanding edge-connectivity in the Internet through core-decomposition

Internet is a complex network composed by several networks: the Autonomous Systems, each one designed to transport information efficiently. Routing protocols aim to find paths between nodes whenever it is possible (i.e., the network is not partitioned), or to find paths verifying specific constraints (e.g., a certain QoS is required). As connectivity is a measure related to both of them (partitions and selected paths) this work provides a formal lower bound to it based on core-decomposition, under certain conditions, and low complexity algorithms to find it. We apply them to analyze maps obtained from the prominent Internet mapping projects, using the LaNet-vi open-source software for its visualization

Rhythmogenic neuronal networks, pacemakers, and k-cores

Neuronal networks are controlled by a combination of the dynamics of individual neurons and the connectivity of the network that links them together. We study a minimal model of the preBotzinger complex, a small neuronal network that controls the breathing rhythm of mammals through periodic firing bursts. We show that the properties of a such a randomly connected network of identical excitatory neurons are fundamentally different from those of uniformly connected neuronal networks as described by mean-field theory. We show that (i) the connectivity properties of the networks determines the location of emergent pacemakers that trigger the firing bursts and (ii) that the collective desensitization that terminates the firing bursts is determined again by the network connectivity, through k-core clusters of neurons.Comment: 4+ pages, 4 figures, submitted to Phys. Rev. Let