Inhibitors of the FEZ-1 metallo-beta-lactamase

Metallo-beta-lactamases (MBLs) catalyze the hydrolysis of beta-lactams including penicillins, cephalosporins and carbapenems. Starting from benzohydroxamic acid (1) structure-activity studies led to the identification of selective inhibitors of the FEZ-1 MBL, e.g., 2,5-substituted benzophenone hydroxamic acid 17 has a K(i) of 6.1+/-0.7microM against the FEZ-1 MBL but does not significantly inhibit the IMP-1, BcII, CphA or L1 MBLs.     

A topology optimization based model of bone adaptation

A novel topology optimization model based on homogenization methods was developed for predicting bone density distribution and anisotropy, assuming the bone structure to be a self-optimizing biological material which maximizes its own structural stiffness. The feasibility and efficiency of this method were tested on a 2D model for a proximal femur under single and multiple loading conditions. The main aim was to compute homogenized optimal designs using an optimal laminated microstructure. The computational results showed that high bone density levels are distributed along the diaphysis and form arching struts within the femoral head. The pattern of bone density distribution and the anisotropic bone behavior predicted by the model in the multiple load case were both in good agreement with the structural architecture and bone density distribution occurring in natural femora. This approach provides a novel means of understanding the remodeling processes involved in fracture repair and the treatment of bone diseases.     

Enhanced disease resistance in Artemia by application of commercial beta-glucans sources and chitin in a gnotobiotic Artemia challenge test

The anti-infectious potential of a selection of putative immunostimulants including six commercial beta-glucans (all extracted from baker's yeast Saccharomyces cerevisiae except for Laminarin) and chitin particles were verified in Artemia nauplii by challenging them under gnotobiotic conditions with the pathogen Vibrio campbellii. Under the described experimental conditions, no differential macroscopic nutritional effect (e.g. growth) was observed among the products. Significant increased survival was observed with beta-glucan (Sigma) and Zymosan and to a lesser extent with MacroGard in challenged nauplii. A poor correlation was found between survival values of the challenged Artemia and the product compositions (such as chitin, mannose and beta-glucan content) indicating that the quality of beta-glucans (e.g. the ratio of beta-1,3 and beta-1,6 glucan, the molecular weight, the dimensional structure, type and frequency of branches), eventually in combination with other unidentified compounds, is more important than the amount of product offered. This small-scale testing under gnotobiotic conditions using freshly hatched Artemia nauplii allows for a rapid and simultaneous screening of anti-infectious and/or putative immunostimulatory polymers, and should be combined with studies on cellular and humoral immune responses in order to gain more quantitative insight into their functional properties.     

Characterizing the spatio-temporal behavior of cell populations through image auto- and cross-correlation microscopy

We propose two methods for characterizing the spatio-temporal behavior of cell populations in culture. The first method, image auto-correlation microscopy (IACM), allows us to characterize the variation in the number of objects as a function of time, thus enabling the quantification of the clustering properties of cell populations to be performed. The second method, image cross-correlation microscopy (ICCM), allows us to characterize the migration properties of cell populations. The latter method does not require estimation or measurement of the trajectories of individual cells, which is very demanding when populations of >100 cells are examined. The capabilities of the two methods are demonstrated with simulated cell populations, and their usefulness is illustrated with experiments involving invasive and noninvasive tumor cell populations.     

On molecular recognition of an uranyl chelate by monoclonal antibodies

The energy landscape of the uranyl (UO2) chelate dissociated from a monoclonal antibody U08S was investigated using dynamic force spectroscopy (DFS). The uranyl ion (UO2(2+)) is chelated with the ligand dicarboxy-phenanthroline (DCP). The monoclonal antibody U08S was raised against UO2-DCP and does not cross-react with DCP alone. The results of plotting the most probable force against the logarithm of the loading rate show two distinguished values of slopes of multiple fitting lines, as observed in our previous study on that system with monoclonal antibody U04S (Odorico et al., 2007a. Biophys. J. 93: 645-654.). It indicates an unbinding process undergoing at least two activation states. We have generated the histogram of unbinding events with respect to the composite stiffness of the complex between the protein and the uranyl compound. Combining the model of Bell and Evans with that of Williams, we have estimated the number of parallel bonds involved in the unbinding process and determined the value of stiffness for individual bonds. We propose that the uranyl compound binds to the two antibodies U04S and U0c at structurally equivalent locations and forms the interaction with similar coordination modes. In addition, the unbinding process goes through two steps; the first weakens the bonding of the central metal with AspL50 of the antibody and the second breaks other non-bonded interactions of the compound with the antibody.     

The genome of <Emphasis Type="Italic">Apis mellifera</Emphasis>: dialog between linkage mapping and sequence assembly

Two independent genome projects for the honey bee, a microsatellite linkage map and a genome sequence assembly, interactively produced an almost complete organization of the euchromatic genome. Assembly 4.0 now includes 626 scaffolds that were ordered and oriented into chromosomes according to the framework provided by the third-generation linkage map (AmelMap3). Each construct was used to control the quality of the other. The co-linearity of markers in the sequence and the map is almost perfect and argues in favor of the high quality of both.     

<Emphasis Type="Italic">Yarrowia lipolytica</Emphasis> vesicle-mediated protein transport pathways

Background  

Protein secretion is a universal cellular process involving vesicles which bud and fuse between organelles to bring proteins to their final destination. Vesicle budding is mediated by protein coats; vesicle targeting and fusion depend on Rab GTPase, tethering factors and SNARE complexes. The Génolevures II sequencing project made available entire genome sequences of four hemiascomycetous yeasts, Yarrowia lipolytica, Debaryomyces hansenii, Kluyveromyces lactis and Candida glabrata. Y. lipolytica is a dimorphic yeast and has good capacities to secrete proteins. The translocation of nascent protein through the endoplasmic reticulum membrane was well studied in Y. lipolytica and is largely co-translational as in the mammalian protein secretion pathway.     

Identification of ypqP as a New Bacillus subtilis Biofilm Determinant That Mediates the Protection of Staphylococcus aureus against Antimicrobial Agents in Mixed-Species Communities

In most habitats, microbial life is organized in biofilms, three-dimensional edifices sustained by extracellular polymeric substances that enable bacteria to resist harsh and changing environments. Under multispecies conditions, bacteria can benefit from the polymers produced by other species (“public goods”), thus improving their survival under toxic conditions. A recent study showed that a Bacillus subtilis hospital isolate (NDmed) was able to protect Staphylococcus aureus from biocide action in multispecies biofilms. In this work, we identified ypqP, a gene whose product is required in NDmed for thick-biofilm formation on submerged surfaces and for resistance to two biocides widely used in hospitals. NDmed and S. aureus formed mixed biofilms, and both their spatial arrangement and pathogen protection were mediated by YpqP. Functional ypqP is present in other natural B. subtilis biofilm-forming isolates. However, the gene is disrupted by the SPβ prophage in the weak submerged-biofilm-forming strains NCIB3610 and 168, which are both less resistant than NDmed to the biocides tested. Furthermore, in a 168 laboratory strain cured of the SPβ prophage, the reestablishment of a functional ypqP gene led to increased thickness and resistance to biocides of the associated biofilms. We therefore propose that YpqP is a new and important determinant of B. subtilis surface biofilm architecture, protection against exposure to toxic compounds, and social behavior in bacterial communities.