Crystal structure of TNF-alpha mutant R31D with greater affinity for receptor R1 compared with R2

Crystal structures have been determined of recombinant human tumor necrosis factor-alpha (TNF-alpha) and its R31D mutant that preferentially binds to TNF receptor R1 with more than seven times the relative affinity of binding to receptor R2. Crystals of the wild-type TNF were of space group P4(1)2(1)2 and had unit cell dimensions of a = b = 94.7 and c = 117.4 A. Refinement of the structure gave an R-factor of 22.3% at 2.5 A resolution. The crystals of TNF R31D mutant diffracted to 2.3 A resolution, and were of identical space group to the wild type with unit cell dimensions of a = b = 95.4 and c = 116.2 A, and the structure was refined to an R-factor of 21.8%. The trimer structures of the wild-type and mutant TNF were similar with a root mean square (r.m.s.) deviation of 0.56 A for Calpha atoms; however, the subunits within each trimer were more variable with an average r.m.s. deviation of 1.00 A on Calpha atoms for pairwise comparison of subunits. Model complexes of TNF with receptors R1 and R2 have been used to predict TNF-receptor interactions. Arg31 in all three subunits of wild-type TNF is predicted to form an ionic interaction with the equivalent glutamic acid in both receptors R1 and R2. Asp31 of the TNF R31D mutant is predicted to interact differently with the two receptors. The side chain of Asp31 in two subunits of the TNF mutant is predicted to form hydrogen bond interactions with Ser59 or Cys70 of R1, while it has no predicted interactions with R2. The loss of three strong ionic interactions of Arg31 and the electrostatic repulsion of Asp31 with Glu in the receptors is consistent with the reduced binding of the R31D mutant to both receptors relative to wild-type TNF. The replacement of these ionic interactions by two weaker hydrogen bond interactions between Asp31 of the R31D mutant and R1, compared with no interactions with R2, is in agreement with the observed preferential binding of the R31D mutant to R1 over R2. Analysis of the structure and function of receptor-discriminating mutants of TNF will help understand the biological role of TNF and facilitate its use as an antitumor agent.      

Composition-Size Effects in Nickel–Zinc Ferrite Nanoparticles Prepared by Aqueous Coprecipitation

Nickel–zinc ferrite nanoparticles across the solid solution range, Ni_{1− x} Zn _x Fe₂O₄, from nickel ferrite to zinc ferrite were prepared by aqueous precipitation of mixed nitrate solutions at the same pH of 12.3. There is a linear relationship between the nanoparticle diameter and composition, decreasing with increasing zinc concentration across the solid solution. The nanoparticles are highly resistant to coarsening and some of them are faceted, suggesting that they are close to thermodynamic equilibrium. Measurements of the surface charge density of the nanoparticles, based on simultaneous conductimetric and potentiometeric titration, are presented as a function of composition for the zinc-rich compositions. A trend exists between the surface charge density and the zinc concentration, suggesting that they may be stabilized by charge.     

Experimental evaluation of fishway modifications on the passage behaviour of adult Chinook salmon and steelhead at Lower Granite Dam,Snake River,USA

Previous studies of Pacific salmonid passage over Snake River dams indicated slowed passage at transition pools, the transition area between the fishway entrance and the fish ladder. In 2001 and 2002, we conducted an experiment to determine if modified weirs affected adult salmon and steelhead passage times and route selection through the Lower Granite Dam transition pool. Fish attraction flows through the lower ladder weirs were experimentally increased using removable panels. During the experiment we monitored radio‐tagged adult Chinook salmon and steelhead to determine passage routes and times through the transition pool. The weir treatment increased the number of spring–summer Chinook salmon passing straight through the transition pool compared to those exiting the transition pool to the collection channel or tailrace. Mean passage times through the transition pool differed among routes and were significantly lower during treatment periods for the exit‐to‐collection channel route in spring‐summer Chinook salmon, but not for other routes. Passage times among routes differed in steelhead, but there was no evidence of treatment effects on route use or passage time. Fall Chinook exhibited similar trends in route use and passage time to spring–summer Chinook, but differences were not significant, perhaps because of relatively small sample size. Total dam passage times did not differ by treatment or route for any run. Fish depth during passage of the transition pool suggested that most fish passed through submerged orifices and supported the hypothesis that increased water velocity through these orifices caused the increase in straight‐through passage in spring–summer Chinook. Collectively, the results suggested the weir modifications provided improvement to passage through the transition pool for spring–summer Chinook and no evidence of negative effects on other runs. The results from this study were used to develop new design criteria and modifications of the Lower Granite Dam fishway. Copyright © 2006 John Wiley & Sons, Ltd.     

Histogram approaches for lossy compression of digital holograms of three-dimensional objects.

We present a novel nonuniform quantization compression technique-histogram quantization-for digital holograms of 3-D real-world objects. We exploit a priori knowledge of the distribution of the values in our data. We compare this technique to another histogram based approach: a modified version of Max's algorithm that has been adapted in a straight-forward manner to complex-valued 2-D signals. We conclude the compression procedure by applying lossless techniques to our quantized data. We demonstrate improvements over previous results obtained by applying uniform and nonuniform quantization techniques to the hologram data.     

Men as caregivers: reciprocal relationships or obligation?

The adult cuticular wing of Drosophila is covered by an array of distally pointing hairs that reveals the planar polarity of the wing. We report here that mutations in dachsous disrupt this regular pattern, and do so by affecting frizzled signaling. dachsous encodes a large membrane protein that contains many cadherin domains and dachsous mutations cause deformed body parts. We found that mutations in dachsous also result in a tissue polarity phenotype that at the cellular level is similar to frizzled, dishevelled and prickle, as many cells form a single hair of abnormal polarity. Although their cellular phenotype is similar to frizzled, dishevelled and prickle, dachsous mutant wings display a unique and distinctive abnormal hair polarity pattern including regions of reversed polarity. The development of this pattern requires the function of frizzled pathway genes suggesting that in a dachsous mutant the frizzled pathway is functioning - but in an abnormal way. Genetic experiments indicated that dachsous was not required for the intracellular transduction of the frizzled signal. However, we found that dachsous clones disrupted the polarity of neighboring wild-type cells suggesting the possibility that dachsous affected the intercellular signaling function of frizzled. Consistent with this hypothesis we found that frizzled clones in a dachsous mutant background displayed enhanced domineering non-autonomy, and that the anatomical direction of this domineering non-autonomy was altered in regions of dachsous wings that have abnormal hair polarity. The direction of this domineering nonautonomy was coincident with the direction of the abnormal hair polarity. We conclude that dachsous causes a tissue polarity phenotype because it alters the direction of frizzled signaling.     

Pathogenic mechanisms in the rheumatoid nodule: comparison of proinflammatory cytokine production and cell adhesion molecule expression in rheumatoid nodules and synovial membranes from the same patient

OBJECTIVE: To investigate the production of proinflammatory cytokines and expression of cell adhesion molecules in the rheumatoid nodule. METHODS: Cytokine content (tumor necrosis factor alpha [TNFalpha], interleukin-1beta [IL-1beta], and IL-1 receptor antagonist [IL-1Ra]), at the messenger RNA (mRNA) and protein levels, and cell adhesion molecule expression were studied in 16 rheumatoid nodules and 6 synovial membranes. RESULTS: Macrophages in the rheumatoid nodules contained TNFalpha, IL-1beta, and IL-1Ra mRNA and protein, particularly in perivascular cells of the stroma and in the palisading layer. All cell adhesion molecules studied were expressed in both the rheumatoid nodules and synovial membranes, with increased expression of E-selectin in the rheumatoid nodule compared with the synovial membrane, and with the absence of vascular cell adhesion molecule 1 expression on cells of the palisading layer in the rheumatoid nodule. CONCLUSION: The presence of similar proinflammatory cytokines and cell adhesion molecules in the rheumatoid nodule and synovial membrane suggests that similar pathogenic processes result in the chronic inflammation and tissue destruction in these lesions.