Genome sequence of Rhizobium sullae HCNT1 isolated from Hedysarum coronarium nodules and featuring peculiar denitrification phenotypes

The genome sequence of Rhizobium sullae strain HCNT1, isolated from root nodules of the legume Hedysarum coronarium growing in wild stands in Tuscany, Italy, is described here. Unlike other R. sullae strains, this isolate features a truncated denitrification pathway lacking NO/N2O reductase activity and displaying high sensitivity to nitrite under anaerobic conditions

Evolution of human IgH3 ' EC duplicated structures: both enhancers HS1,2 are polymorphic with variation of transcription factor's consensus sites

The enhancer complex regulatory region at the 3' of the immunoglobulin heavy cluster (IgH3'EC) is duplicated in apes along with four constant genes and the region is highly conserved throughout humans. Both human IgH3'ECs consist of three loci high sensitive (HS) to DNAse I with enhancer activity. It is thus possible that the presence of structural divergences between the two IgH3'ECs and of relative polymorphisms correspond to functional regulatory changes. To analyse the polymorphisms of these almost identical regions, it resulted mandatory to identify the presence of divergent sequences, in order to select distinctive primers for specific PCR genomic amplifications. To this aim, we first compared the two entire IgH3'ECs in silicio, utilising the updated GenBank (GB) contigs, then we analysed the two IgH3'ECs by cloning and sequencing amplicons from independent genomes. In silicio analysis showed that several inversions, deletions and short insertions had occurred after the duplication. We analysed in detail, by sequencing specific regions, the polymorphisms occurring in enhancer HS1,2-A (which lies in IgH3'EC-1, 3' to the C alpha-1 gene) and in enhancer HS1,2-B (which lies in IgH3'EC-2, 3' to C alpha-2). Polymorphisms are due to the repetition (occurring one to four times) of a 38-bp sequence present at the 3' of the core of enhancers HS1,2. The structure of both human HS1,2 enhancers has revealed not yet described polymorphic features due to the presence of variable spacer elements separating the 38-bp repetitions and to variable external elements bordering the repetition cluster. We found that one of the external elements gave rise to a divergent allele 3 in the two clusters. The frequency of the different alleles of the two loci varies in the Italian population and allele 3 of both loci are very rare. The analysis of the Callicebus moloch, Gorilla gorilla and Pan troglodytes HS1,2 enhancers showed the transformation from the ancestral structure with the 31- to the 17-by external element in hominids. The relevance of the polymorphisms in the HS1,2 enhancers is due to the variable number of binding sites for the transcription factors: NF-kappa B, CMYB, BSAP1/2, AP1/4, E47, MyoD and mu E5 and thus to the possible influence of these variations on switch, production of Ig and on maturation of B cells. (c) 2004 Elsevier B.V. All rights reserved

Determination of electromagnetic medium from the Fresnel surface

We study Maxwell's equations on a 4-manifold where the electromagnetic medium is described by an antisymmetric $2\choose 2$-tensor $\kappa$. In this setting, the Tamm-Rubilar tensor density determines a polynomial surface of fourth order in each cotangent space. This surface is called the Fresnel surface and acts as a generalisation of the light-cone determined by a Lorentz metric; the Fresnel surface parameterises electromagnetic wave-speed as a function of direction. Favaro and Bergamin have recently proven that if $\kappa$ has only a principal part and if the Fresnel surface of $\kappa$ coincides with the light cone for a Lorentz metric $g$, then $\kappa$ is proportional to the Hodge star operator of $g$. That is, under additional assumptions, the Fresnel surface of $\kappa$ determines the conformal class of $\kappa$. The purpose of this paper is twofold. First, we provide a new proof of this result using Gr\"obner bases. Second, we describe a number of cases where the Fresnel surface does not determine the conformal class of the original $2\choose 2$-tensor $\kappa$. For example, if $\kappa$ is invertible we show that $\kappa$ and $\kappa^{-1}$ have the same Fresnel surfaces.Comment: 23 pages, 1 figur

Testing an Open Source installation and server provisioning tool for the INFN CNAF Tierl Storage system

In large computing centers, such as the INFN CNAF Tier1 [1], is essential to be able to configure all the machines, depending on use, in an automated way. For several years at the Tier1 has been used Quattor[2], a server provisioning tool, which is currently used in production. Nevertheless we have recently started a comparison study involving other tools able to provide specific server installation and configuration features and also offer a proper full customizable solution as an alternative to Quattor. Our choice at the moment fell on integration between two tools: Cobbler [3] for the installation phase and Puppet [4] for the server provisioning and management operation. The tool should provide the following properties in order to replicate and gradually improve the current system features: implement a system check for storage specific constraints such as kernel modules black list at boot time to avoid undesired SAN (Storage Area Network) access during disk partitioning; a simple and effective mechanism for kernel upgrade and downgrade; the ability of setting package provider using yum, rpm or apt; easy to use Virtual Machine installation support including bonding and specific Ethernet configuration; scalability for managing thousands of nodes and parallel installations. This paper describes the results of the comparison and the tests carried out to verify the requirements and the new system suitability in the INFN-T1 environment

A competitive polymerase chain reaction-based approach for the identification and semiquantification of mitochondrial DNA in differently heat-treated bovine meat and bone meal

The risk of bovine spongiform encephalopathy propagation was drastically reduced after the European Union (EU) Health Authorities adopted restrictions involving a ban on animal-derived proteins in the diet of farm animals. Currently, the EU's officially recommended method for controlling meat and bone meal (MBM) in animal feed is the microscopic method, which involves the identification of bone fragments on the basis of their morphological characteristics. Recently, we demonstrated that a polymerase chain reaction (PCR)-based assay can be used for the detection of taxon-specific DNA in MBM and animal feeds. To ensure the safe rendering of animal by-products, the EU Council requires that this material be treated at 133degreesC at 300 kPa for 20 min. Here we investigate the relationship between DNA degradation, PCR amplification, and MBM heat treatment. With a competitive PCR-based approach, we compare the amplification efficiency of bovine mitochondrial DNA target sequences of different lengths in several heat-treated MBM samples. For our method, a synthetic competitive DNA is used as an internal control for both DNA extraction and PCR reaction. A correlation between an increase in treatment temperature and a reduction in the size of the target sequences suitable for amplification was observed, suggesting progressive DNA fragmentation due to the temperature. We show that short amplicons (147 bp) can be used to detect the presence of bovine mtDNA in MBM samples treated according to the current European regulations. The use of such a competitive approach to compare amplification efficiency levels of targets of different lengths might represent a useful tool for the determination of both the amount of MBM in animal feeds and its proper heat treatment

Measurement of the t¯t production cross section in pp collisions at √s = 7 TeV using the kinematic properties of events with leptons and jets

A measurement of the tt production cross section in proton-proton collisions at a centre-of-mass energy of 7 TeV has been performed at the LHC with the CMS detector. The analysis uses a data sample corresponding to an integrated luminosity of 36 pb−1 and is based on the reconstruction of the final state with one isolated, high transverse-momentum electron or muon and three or more hadronic jets. The kinematic properties of the events are used to separate the tt signal from W+jets and QCD multijet background events. The measured cross section is 173+39−32 (stat+syst) pb, consistent with standard model expectations

Measurement of the Drell-Yan cross section in pp collisions at \sqrt {s} = 7 TeV

The Drell-Yan differential cross section is measured in pp collisions at sqrt(s) = 7 TeV, from a data sample collected with the CMS detector at the LHC, corresponding to an integrated luminosity of 36 inverse picobarns. The cross section measurement, normalized to the measured cross section in the Z region, is reported for both the dimuon and dielectron channels in the dilepton invariant mass range 15-600 GeV. The normalized cross section values are quoted both in the full phase space and within the detector acceptance. The effect of final state radiation is also identified. The results are found to agree with theoretical predictions

Search for supersymmetry in pp collisions at 7 TeV in events with jets and missing transverse energy

A search for supersymmetry with R-parity conservation in proton-proton collisions at a centre-of-mass energy of 7 TeV is presented. The data correspond to an integrated luminosity of 35 inverse picobarns collected by the CMS experiment at the LHC. The search is performed in events with jets and significant missing transverse energy, characteristic of the decays of heavy, pair-produced squarks and gluinos. The primary background, from standard model multijet production, is reduced by several orders of magnitude to a negligible level by the application of a set of robust kinematic requirements. With this selection, the data are consistent with the standard model backgrounds, namely t t-bar, W + jet and Z + jet production, which are estimated from data control samples. Limits are set on the parameters of the constrained minimal supersymmetric extension of the standard model. These limits extend those set previously by experiments at the Tevatron and LEP colliders