Genome sequences of two novel phages infecting marine roseobacters

Two bacteriophages, DSS3Φ2 and EE36Φ1, which infect marine roseobacters Silicibacter pomeroyi DSS-3 and Sulfitobacter sp. EE-36, respectively, were isolated from Baltimore Inner Harbor water. These two roseophages resemble bacteriophage N4, a large, short-tailed phage infecting Escherichia coli K12, in terms of their morphology and genomic structure. The full genome sequences of DSS3Φ2 and EE36Φ1 reveal that their genome sizes are 74.6 and 73.3 kb, respectively, and they both contain a highly conserved N4-like DNA replication and transcription system. Both roseophages contain a large virion-encapsidated RNA polymerase gene (> 10 kb), which was first discovered in N4. DSS3Φ2 and EE36Φ1 also possess several genes (i.e. ribonucleotide reductase and thioredoxin) that are most similar to the genes in roseobacters. Overall, the two roseophages are highly closely related, and share 80–94% nucleotide sequence identity over 85% of their ORFs. This is the first report of N4-like phages infecting marine bacteria and the second report of N4-like phage since the discovery of phage N4 40 years ago. The finding of these two N4-like roseophages will allow us to further explore the specific phage–host interaction and evolution for this unique group of bacteriophages

Ornithological report 2001-2006 for the Camargue

The present ornithological report for the Camargue covers six years (2001-2006). This time-period has been marked by an accelerated global warming (the summer 2003 was particularly extreme). Owing to a constant high observation pressure, 18 new species have been recorded and many rare species have been resighted in that region (Camargue, Crau, Alpilles). Among the species or group of species which are regularly censused, the number of breeding Greater Flamingos Phoenicopterus roseus and that of wintering ducks and coots did not show any significant change. The colonial herons have continued either to increase or to fluctuate at a high level. For example, the Great White Egret Casmerodius albus has definitely settled in the delta and the Squacco Heron Ardeola ralloides has reached a new peak of 505 pairs in 2006. More efficient prospection efforts gave more precise breeding numbers for two species of solitary herons, the Great Bittern Botaurus stellaris and the Little Bittern Ixobrychus minutus. New breeding species such as the Great Cormorant Phalacrocorax carbo, White Stork Ciconia ciconia, Eurasian Spoonbill Platalea leucorodia and Greylag Anser anser increased their numbers as well as the Glossy Ibis Plegadis falcinellus of which 14 pairs has bred in 2006 and the Purple Swamphen Porphyrio porphyrio which was found for the first time breeding in 2006. The breeding species showing the most serious concern are actually the breeding gulls and terns whose figures have dramatically decreased. Without human management, this situation will even become worse in a near future. Further remarkable observations were the first case of wintering Lesser Spotted Eagle Aquila pomarina in 2001/2002, a mixed pair of Black-winged Pratincole Glareola nordmanni x Collared Pratincole G. pratincola in 2001, the settling of the Rook Corvus frugilegus in ArlesCe calendrier ornithologique couvre les six années de 2001 à 2006, une période marquée par un phénomène de réchauffement général accéléré du climat en général et par la canicule de l'été 2003 en particulier. Compte tenu de la pression d'observation élevée, 18 nouvelles espèces ont été signalées et de nombreuses espèces rares ont été revues dans la région (Camargue, Crau, Alpilles). Parmi les espèces ou groupes d'espèces qui font l'objet de recensements réguliers, les effectifs nicheurs de Flamant rose Phoenicopterus roseus de même que ceux des Anatidés et des Foulques hivernants n'appellent pas de commentaires particuliers pour ce laps de temps. Les Ardéidés coloniaux continuent soit de progresser pour certains, soit de fluctuer dans des limites qui restent élevées pour d'autres. Par exemple, la Grande Aigrette Casmerodius albus s'est installée durablement dans le delta, le Crabier chevelu Ardeola ralloides a atteint un nouveau maximum avec 505 couples en 2006. Des effectifs plus précis sont fournis pour deux espèces comme le Butoir étoilé Botaurus stellaris et le Blongios nain Ixohrychus minutus grâce à des prospections plus efficaces. Des espèces nicheuses d'installation récente comme le Grand Cormoran Phalacrocorax carho, la Cigogne blanche Ciconia ciconia, la Spatule blanche Platalea leucorodia et l'Oie cendrée Anser anser continuent de progresser de même que l'Ibis falcinelle Plegadis falcinellus dont 14 couples se sont reproduits en 2006 et la Talève sultane Porphyrio porphyrio dont la reproduction a enfin été confirmée en 2006. Parmi les espèces posant un problème grave, il faut relever les laro-limicoles nicheurs dont les effectifs se sont effondrés. Sans intervention urgente de gestion, leur situation risque d'empirer. Parmi les faits remarquables, signalons le premier cas d'hivernage de l'Aigle pomarin Aquila pomarina en 2001/2002, un couple mixte de Glaréole à ailes noires Glareola nordmanni x Glaréole à collier G. pratincola en 2001, l'installation du Corbeau freux Corvus frugilegus à Arles

Calibration and Characterization of the IceCube Photomultiplier Tube

Over 5,000 PMTs are being deployed at the South Pole to compose the IceCube neutrino observatory. Many are placed deep in the ice to detect Cherenkov light emitted by the products of high-energy neutrino interactions, and others are frozen into tanks on the surface to detect particles from atmospheric cosmic ray showers. IceCube is using the 10-inch diameter R7081-02 made by Hamamatsu Photonics. This paper describes the laboratory characterization and calibration of these PMTs before deployment. PMTs were illuminated with pulses ranging from single photons to saturation level. Parameterizations are given for the single photoelectron charge spectrum and the saturation behavior. Time resolution, late pulses and afterpulses are characterized. Because the PMTs are relatively large, the cathode sensitivity uniformity was measured. The absolute photon detection efficiency was calibrated using Rayleigh-scattered photons from a nitrogen laser. Measured characteristics are discussed in the context of their relevance to IceCube event reconstruction and simulation efforts.Comment: 40 pages, 12 figure

All-particle cosmic ray energy spectrum measured with 26 IceTop stations

We report on a measurement of the cosmic ray energy spectrum with the IceTop air shower array, the surface component of the IceCube Neutrino Observatory at the South Pole. The data used in this analysis were taken between June and October, 2007, with 26 surface stations operational at that time, corresponding to about one third of the final array. The fiducial area used in this analysis was 0.122 km^2. The analysis investigated the energy spectrum from 1 to 100 PeV measured for three different zenith angle ranges between 0{\deg} and 46{\deg}. Because of the isotropy of cosmic rays in this energy range the spectra from all zenith angle intervals have to agree. The cosmic-ray energy spectrum was determined under different assumptions on the primary mass composition. Good agreement of spectra in the three zenith angle ranges was found for the assumption of pure proton and a simple two-component model. For zenith angles {\theta} < 30{\deg}, where the mass dependence is smallest, the knee in the cosmic ray energy spectrum was observed between 3.5 and 4.32 PeV, depending on composition assumption. Spectral indices above the knee range from -3.08 to -3.11 depending on primary mass composition assumption. Moreover, an indication of a flattening of the spectrum above 22 PeV were observed.Comment: 38 pages, 17 figure

An improved method for measuring muon energy using the truncated mean of dE/dx

The measurement of muon energy is critical for many analyses in large Cherenkov detectors, particularly those that involve separating extraterrestrial neutrinos from the atmospheric neutrino background. Muon energy has traditionally been determined by measuring the specific energy loss (dE/dx) along the muon's path and relating the dE/dx to the muon energy. Because high-energy muons (E_mu > 1 TeV) lose energy randomly, the spread in dE/dx values is quite large, leading to a typical energy resolution of 0.29 in log10(E_mu) for a muon observed over a 1 km path length in the IceCube detector. In this paper, we present an improved method that uses a truncated mean and other techniques to determine the muon energy. The muon track is divided into separate segments with individual dE/dx values. The elimination of segments with the highest dE/dx results in an overall dE/dx that is more closely correlated to the muon energy. This method results in an energy resolution of 0.22 in log10(E_mu), which gives a 26% improvement. This technique is applicable to any large water or ice detector and potentially to large scintillator or liquid argon detectors.Comment: 12 pages, 16 figure

Search for Relativistic Magnetic Monopoles with IceCube

We present the first results in the search for relativistic magnetic monopoles with the IceCube detector, a subsurface neutrino telescope located in the South Polar ice cap containing a volume of 1 km$^{3}$. This analysis searches data taken on the partially completed detector during 2007 when roughly 0.2 km$^{3}$ of ice was instrumented. The lack of candidate events leads to an upper limit on the flux of relativistic magnetic monopoles of \Phi_{\mathrm{90%C.L.}}\sim 3\e{-18}\fluxunits for $\beta\geq0.8$. This is a factor of 4 improvement over the previous best experimental flux limits up to a Lorentz boost $\gamma$ below $10^{7}$. This result is then interpreted for a wide range of mass and kinetic energy values.Comment: 11 pages, 11 figures. v2 is minor text edits, no changes to resul

Lateral Distribution of Muons in IceCube Cosmic Ray Events

In cosmic ray air showers, the muon lateral separation from the center of the shower is a measure of the transverse momentum that the muon parent acquired in the cosmic ray interaction. IceCube has observed cosmic ray interactions that produce muons laterally separated by up to 400 m from the shower core, a factor of 6 larger distance than previous measurements. These muons originate in high pT (> 2 GeV/c) interactions from the incident cosmic ray, or high-energy secondary interactions. The separation distribution shows a transition to a power law at large values, indicating the presence of a hard pT component that can be described by perturbative quantum chromodynamics. However, the rates and the zenith angle distributions of these events are not well reproduced with the cosmic ray models tested here, even those that include charm interactions. This discrepancy may be explained by a larger fraction of kaons and charmed particles than is currently incorporated in the simulations

A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation

What physical mechanism leads to organization of a highly condensed and confined circular chromosome? Computational modeling shows that confinement-induced organization is able to overcome the chromosome's propensity to mix by the formation of topological domains. The experimentally observed high precision of separate subcellular positioning of loci (located on different chromosomal domains) in Escherichia coli naturally emerges as a result of entropic demixing of such chromosomal loops. We propose one possible mechanism for organizing these domains: regulatory control defined by the underlying E. coli gene regulatory network requires the colocalization of transcription factor genes and target genes. Investigating this assumption, we find the DNA chain to self-organize into several topologically distinguishable domains where the interplay between the entropic repulsion of chromosomal loops and their compression due to the confining geometry induces an effective nucleoid filament-type of structure. Thus, we propose that the physical structure of the chromosome is a direct result of regulatory interactions. To reproduce the observed precise ordering of the chromosome, we estimate that the domain sizes are distributed between 10 and 700 kb, in agreement with the size of topological domains identified in the context of DNA supercoiling