Rapid isolation of novel FK506 binding proteins from multiple organisms using gDNA and cDNA T7 phage display

Reverse chemical proteomics using T7 phage display is a powerful technique for identifying cellular receptors of biologically active small molecules. However, to date this method has generally been limited to cDNA libraries constructed from mRNA isolated from eukaryotes. In this paper, we describe the construction of the first prokaryotic T7 phage display libraries from randomly digested Pseudomonas stutzeri and Vibrio fischeri gDNA, as well as a plant cDNA library from Arabidopsis thaliana. We also describe the use of T7 phage display to identify novel proteins from environmental DNA samples using biotinylated FK506 as a model affinity probe.     

Enhanced computational prediction of polyethylene wear in hip joints by incorporating cross-shear and contact pressure in additional to load and sliding distance: Effect of head diameter

A new definition of the experimental wear factor was established and reported as a function of cross-shear motion and contact pressure using a multi-directional pin-on-plate wear testing machine for conventional polyethylene in the present study. An independent computational wear model was developed by incorporating the cross-shear motion and contact pressure-dependent wear factor into the Archard's law, in additional to load and sliding distance. The computational prediction of wear volume was directly compared with a simulator testing of a polyethylene hip joint with a 28 mm diameter. The effect of increasing the femoral head size was subsequently considered and was shown to increase wear, as a result of increased sliding distance and reduced contact pressure.     

Characterization of Wise Protein and Its Molecular Mechanism to Interact with both Wnt and BMP Signals

Cross-talk of BMP and Wnt signaling pathways has been implicated in many aspects of biological events during embryogenesis and in adulthood. A secreted protein Wise and its orthologs (Sostdc1, USAG-1, and Ectodin) have been shown to modulate Wnt signaling and also inhibit BMP signals. Modulation of Wnt signaling activity by Wise is brought about by an interaction with the Wnt co-receptor LRP6, whereas BMP inhibition is by binding to BMP ligands. Here we have investigated the mode of action of Wise on Wnt and BMP signals. It was found that Wise binds LRP6 through one of three loops formed by the cystine knot. The Wise deletion construct lacking the LRP6-interacting loop domain nevertheless binds BMP4 and inhibits BMP signals. Moreover, BMP4 does not interfere with Wise-LRP6 binding, suggesting separate domains for the physical interaction. Functional assays also show that the ability of Wise to block Wnt1 activity through LRP6 is not impeded by BMP4. In contrast, the ability of Wise to inhibit BMP4 is prevented by additional LRP6, implying a preference of Wise in binding LRP6 over BMP4. In addition to the interaction of Wise with BMP4 and LRP6, the molecular characteristics of Wise, such as glycosylation and association with heparan sulfate proteoglycans on the cell surface, are suggested. This study helps to understand the multiple functions of Wise at the molecular level and suggests a possible role for Wise in balancing Wnt and BMP signals.Wise is a secreted protein that was isolated from a functional screen of a chick cDNA library of embryonic tissues. It was identified as being able to alter the antero-posterior character of neuralized Xenopus animal caps by promoting activity of the Wnt pathway (1). Independently, the homologous protein was isolated from a functional screen to detect genes that are preferentially expressed in the rat endometrium, which had been maximally sensitized to implantation, and named USAG-1 (uterine sensitization-associated gene-1) (2). The protein was identified a third time from the GenBank^TM sequence data base of mouse as a putative secreted protein, shown to be a BMP antagonist, and named Ectodin (3). The gene has also been called Sostdc1 (Sclerostin domain-containing 1) or Sostl (Sclerostin-like) due to the homology with Sclerostin-encoding gene Sost (4, 5). USAG-1/Wise/Ectodin/Sostdc1 is expressed in various tissues, such as the surface ectoderm of the posterior axis (1, 6), branchial arches (3, 6), the dermal papilla in hair follicles (7), vibrissae (3), mammalian tooth cusps (3, 8), rat endometrium (2), developing testis (9–11), interdigital tissues (12), and embryonic and adult kidneys (13, 14).Wise appears to have a dual role in modulating the Wnt pathway. Injection of Wnt8 RNA into a ventral vegetal blastomere of Xenopus embryos at the four-cell stage induces a full secondary axis to form, and this is blocked by the addition of Wise RNA as well as other Wnt inhibitors (1). Activation of the Wnt/β-catenin pathway in hair follicles triggers regeneration of hair growth, and expression of Wise appears to have a defined role to inhibit this (15). In this context, Wise expression is repressed by the nuclear receptor co-repressor, Hairless, which results in activation of the Wnt pathway; thus, a model of periodic regeneration of hair follicles has been proposed (15, 16). In addition, Wise and its homologue USAG-1 have been shown to block Wnt1, Wnt3a, and Wnt10b activities in reporter assays (14, 15, 17). Wise was found to bind to the Wnt co-receptor, LRP6, sharing the binding domain with Wnt ligands. Importantly, Wise was found to compete with Wnt8 for binding to LRP6, therefore suggesting a mechanism for inhibition of the Wnt pathway whereby Wise blocks the binding of ligand and receptor (1). Wise may also be retained in the endoplasmic reticulum and inhibit the trafficking of LRP6 to the cell surface (18). Wise also binds LRP4 (19), a member of the LRP family functioning inhibitory to Wnt signals (20). It is noteworthy that Wise was isolated from a screen designed to detect the activation of the Wnt/β-catenin pathway, not inhibition. The exact mechanism of how Wise exerts such a context-dependent modulation on the Wnt pathway is yet to be clarified.Osteoblast differentiation of MC3T3-E1 cells, as measured by alkaline phosphatase activity, can be induced by a wide range of BMP molecules. In this assay, Ectodin, the mouse ortholog of Wise, was shown to inhibit differentiation induced by BMP2, -4, -6, or -7 in a dose-dependent manner (3). Similarly, Ectodin (also known as USAG-1) was also found to inhibit the bone differentiation induced by BMP2, -4, or -7 in C2C12 cells (14). Ectodin also inhibits BMP2- or BMP7-induced Msx2 expression in dissected mouse tooth buds in organ culture (3). In tooth buds, Ectodin expression is detected in the dental ectoderm and mesenchymal cells excluding from the enamel knot (3). Ectodin/USAG-1-deficient mice created by targeted-disruption show altered tooth morphology and extra teeth, indicating that Ectodin and BMP tightly control tooth development and patterning in mammals (8, 21–23). Furthermore, in mouse adult kidneys, the ability of BMP7 to repair established renal injury is blocked by USAG-1 (13). All of these findings indicate that USAG-1/Wise/Ectodin has a clear antagonistic effect on BMP signaling, where it binds BMP2, -4, -6, and -7 (3, 14) and presumably prevents BMP binding to its receptors.Analysis of the sequence of Wise reveals that it has the C₁X_nC₂XGXC₃X_nC₄X_nC₅XC₆ motif of a six-membered cystine knot, where C₁ forms a disulfide bond with C₄, C₂ with C₅, and C₃ with C₆ (for a review of the cystine knot, see Refs. 24–27). This arrangement results in a globular protein with three loops, “finger 1,” “heel,” and “finger 2,” held together with an eight-membered ring of C₂XGXC₃C₆XC₅C₂ (Fig. 1). BMP antagonists represent a subfamily in the cystine knot superfamily, and this is further subdivided into three subfamilies based on the size of the cystine knot. These are the CAN family (eight-membered ring), Twisted Gastrulation (nine-membered ring), and Chordin and Noggin (10-membered ring) (27). There is generally little sequence homology between family members in the heel, finger 1, and finger 2 regions, yet Wise does show a moderate homology with Sclerostin (28). Sclerostin is involved in regulating bone mass (4, 5) and also appears to antagonize both Wnt (29–32) and BMP (28, 33, 34) signals. This paper aims to analyze the dual role of Wise on Wnt and BMP pathways by probing the structural features of the protein and reconciling them to physiological properties. It also aims to reveal the molecular nature of the protein in view of possible glycosylation, secretion, and association with extracellular matrix.Open in a separate windowFIGURE 1.Structure of chick Wise protein. A, stereo ribbon representation of the chick Wise three-dimensional structural model (residues 68–186). Purple, β-strands; green, loop regions. Yellow, disulfide bonds in the cystine knot plus a further disulfide (cysteines 89 and 147) linking two fingers of the structure. N- and C-terminal ends are indicated. B, schematic drawing of the full-length chick Wise structure. Arrowhead, the predicted signal sequence cleavage site for secretion; black dot, asparagine at position 47 (N47), the glycosylated site revealed in this study. Six cysteine residues forming the “cystine knot” are shown in circles, and disulfide bonds for the knot formation are shown by dotted lines. Three loops (Finger 1, Heel, and Finger 2) are indicated. The scheme also shows the deleted parts of Wise constructs ΔN, Δheel, and ΔC.     

Quantitative genetic analysis of life-history traits of Caenorhabditis elegans in stressful environments

In Figure 1 of [Harvey et al (Evolutionary Biology 2008, 8:15)] the plotted data were inverted. The correct Figure is shown below. The text and statistical analyses in [Harvey et al (Evolutionary Biology 2008, 8:15)] are correct.     

Calibration of a fuzzy cellular automata model of urban dynamics in Saudi Arabia

An urban cellular automata model has been designed, developed and tested for the city of Riyadh in Saudi Arabia as a research project. The model uses fuzzy set theory to capture the uncertainty associated with the transition rules and employs two automated methods of calibration: a genetic algorithm and simulated annealing. This paper describes the results of the calibration process for three time periods: 1987–1997, 1997–2005 and 1987–2005, which are characterised by different patterns of urban development. Nine different scenarios have been devised to capture the effect of different primary drivers to development including transport, urban agglomeration and topography and their interactions. The results showed that the genetic algorithm produces a better calibrated model than parallel simulated annealing. The model that contains all primary drivers and all interactions produced the best performing calibrated model overall.     

Capitalizing on nature: how to implement an ecosystem approach

The Natural Capital Initiative (www.naturalcapitalinitiative.org.uk) held its first conference ‘Valuing our life support systems’ at Savoy Place, London, from 29 April to 1 May 2009. The aim of the conference was to discuss different perspectives on, and solutions to, the conservation and sustainable use of ecosystem services. It particularly focused on the link between the environment and the economy, and how to implement an ecosystem approach to environmental management. This event brought together scientists across the natural and social sciences, alongside representatives from government, non-governmental organizations, business and industry.     

Developmental Trajectories of Girls' BMI Across Childhood and Adolescence

This study describes qualitatively distinct trajectories of BMI change among girls participating in a longitudinal study of non‐Hispanic, white girls (n = 182) and their parents, assessed at daughters' ages 5, 7, 9, 11, 13, and 15 years. Height, weight, body fat, fasting blood glucose and lipids, blood pressure, waist circumference, and pubertal status were measured, and participants self‐reported dietary, physical activity, and television (TV) viewing patterns. Growth mixture models were used to model heterogeneity in girls' BMI trajectories over 10 years. Statistical support was strongest for four distinct BMI trajectories: (i) upward percentile crossing (UPC; n = 25, 14%); (ii) delayed downward percentile crossing (DDPC; n = 37, 20%); (iii) 60th percentile tracking (60PT; n = 52, 29%); and (iv) 50th percentile tracking (50PT; n = 68, 37%). Girls in the UPC group had more metabolic risk factors at age 15 years, even after adjusting for concurrent weight status. Girls in the UPC group had mothers with the highest BMIs at study entry and were breast‐fed for a shorter duration. This novel approach for examining differences in growth trajectories revealed four distinct BMI trajectories that predicted adolescent metabolic health outcomes in girls. The present study provides support for BMI monitoring in girls and for the potential utility of combining data on BMI tracking with data on familial characteristics for the early identification of girls at elevated risk for obesity and metabolic syndrome.     

Temporal dynamics and genetic diversity of chemotactic‐competent microbial populations in the rhizosphere

The contribution of chemotaxis to the competitive colonization of the rhizosphere for the vast majority of the soil community is unknown. We have developed and applied a molecular diagnostic tool, based on a gene encoding the central regulator of bacterial chemotaxis (cheA), to characterize and temporally track specific populations of native microbes with chemotaxis potential that are present in soil exposed to two rhizospheres: wheat and cowpea. The data show that the chemotactic‐competent communities present in the rhizospheres of the two plants are distinct and less diverse than the bulk soil, indicating the development of unique microbial communities. Consistent with the supposition that selection and recruitment of specific soil microbes takes place in the rhizosphere, the dynamics of specific cheA phylotypes provides support for the hypothesis that chemotaxis provides a competitive advantage to some soil microbes. This is the first study to examine and profile the genetic diversity of chemotaxis genes in natural populations. As such, it illustrates our limited understanding of microbial chemotaxis for the majority of soil microbes. It also highlights the value of a culture‐independent approach for examining chemotaxis populations in order to build empirical lines of evidence for its role in structuring of microbial assemblages.