Design and implementation of a database for Brucella melitensis genome annotation

The genome sequences of three Brucella biovars and of some species close to Brucella sp. have become available, leading to new relationship analysis. Moreover, the automatic genome annotation of the pathogenic bacteria Brucella melitensis has been manually corrected by a consortium of experts, leading to 899 modifications of start sites predictions among the 3198 open reading frames (ORFs) examined. This new annotation, coupled with the results of automatic annotation tools of the complete genome sequences of the B. melitensis genome (including BLASTs to 9 genomes close to Brucella), provides numerous data sets related to predicted functions, biochemical properties and phylogenic comparisons. To made these results available, alphaPAGe, a functional auto-updatable database of the corrected sequence genome of B. melitensis, has been built, using the entity-relationship (ER) approach and a multi-purpose database structure. A friendly graphical user interface has been designed, and users can carry out different kinds of information by three levels of queries: (1) the basic search use the classical keywords or sequence identifiers; (2) the original advanced search engine allows to combine (by using logical operators) numerous criteria: (a) keywords (textual comparison) related to the pCDS's function, family domains and cellular localization; (b) physico-chemical characteristics (numerical comparison) such as isoelectric point or molecular weight and structural criteria such as the nucleic length or the number of transmembrane helix (TMH); (c) similarity scores with Escherichia coli and 10 species phylogenetically close to B. melitensis; (3) complex queries can be performed by using a SQL field, which allows all queries respecting the database's structure. The database is publicly available through a Web server at the following url: http://www.fundp.ac.be/urbm/bioinfo/aPAGe.     

Diagnosis of mineral clogging hazards in subsurface drainage systems

The paper presents a global review of drain clogging hazard criteria. Some of them are simple granulometric formulae, some include an evaluation of soil structural stability, and some others are based on laboratory tests which reproduce water-flow through a soil core. A recent development is then described. Terzaghi's theory of critical hydraulic gradient explains structural break-up of soil samples by water-flow towards drain pipes. Based on this theoretical approach, a laboratory test has been designed to determine experimental values of the hydraulic gradient causing soil breaking. This test is used to compare the stability of different soil materials and to diagnose mineral clogging hazards.Due to the existence of numerous granulometric criteria there is evidence that no global criterion can be found. If a proper granulometric criterion is suited to a given climatological and pedological context, the hydraulic laboratory test is probably the most cost-effective method to diagnose mineral clogging hazard, especially when no field references are available.     

Inclusion of Tithonia diversifolia in multinutrient blocks for WestAfrican dwarf goats fed Brachiaria straw

Recent investigations suggest that the development of multinutrient feed blocks with inclusion of tree and shrub leaves could improve the nutritive value and digestibility of straw. In order to test these possibilities, three types of multinutrient blocks (MNB) namely: MNB0 (wheat bran?=?100 %; Tithonia diversifolia leaf?=?0 %), MNB50 (wheat bran?=?50 %; T. diversifolia leaf?=?50 %) and MNB100 (wheat bran?=?0 %; T. diversifolia leaf?=?100 %) were fed for 15 days in a 3?×?3 Latin square arrangement to West African dwarf goats consuming Brachiaria ruziziensis straw. The blocks presented a good cohesion and a good hardness. The inclusion of T. diversifolia improved levels of crude protein, mineral, feed unit for milk production (UFL) and feed unit for meat production (UFV), but decreased palatability. The effects on the digestibility of B. ruziziensis straw were evaluated in nine West African dwarf goats fed individually with MNB0 + straw, MNB50 + straw and MNB100 + straw. The dry matter, organic matter and crude fibre digestibility of B. ruziziensis straw increased slightly with increasing level of inclusion of T. diversifolia. The apparent digestibility of nitrogen was comparable for all diets independent of the level of inclusion of T. diversifolia. This study showed that the inclusion of T. diversifolia leaves in the MNBs can be recommended to improve the feeding of goats during periods of drought.     

Cyclic dynamics in a simple vertebrate predator-prey community

The collared lemming in the high-Arctic tundra in Greenland is preyed upon by four species of predators that show marked differences in the numbers of lemmings each consumes and in the dependence of their dynamics on lemming density. A predator prey model based on the field-estimated predator responses robustly predicts 4-year periodicity in lemming dynamics, in agreement with long-term empirical data. There is no indication in the field that food or space limits lemming population growth, nor is there need in the model to consider those factors. The cyclic dynamics are driven by a 1-year delay in the numerical response of the stoat and stabilized by strongly density-dependent predation by the arctic fox, the snowy owl, and the long-tailed skua.     

Structures of SAS-6 suggest its organization in centrioles

Centrioles are cylindrical, ninefold symmetrical structures with peripheral triplet microtubules strictly required to template cilia and flagella. The highly conserved protein SAS-6 constitutes the center of the cartwheel assembly that scaffolds centrioles early in their biogenesis. We determined the x-ray structure of the amino-terminal domain of SAS-6 from zebrafish, and we show that recombinant SAS-6 self-associates in vitro into assemblies that resemble cartwheel centers. Point mutations are consistent with the notion that centriole formation in vivo depends on the interactions that define the self-assemblies observed here. Thus, these interactions are probably essential to the structural organization of cartwheel centers.     

An antigen produced by splicing of noncontiguous peptides in the reverse order

CD8-positive T lymphocytes recognize peptides that are usually derived from the degradation of cellular proteins and are presented by class I molecules of the major histocompatibility complex. Here we describe a human minor histocompatibility antigen created by a polymorphism in the SP110 nuclear phosphoprotein gene. The antigenic peptide comprises two noncontiguous SP110 peptide segments spliced together in reverse order to that in which they occur in the predicted SP110 protein. The antigenic peptide could be produced in vitro by incubation of precursor peptides with highly purified 20S proteasomes. Cutting and splicing probably occur within the proteasome by transpeptidation.