AbdB-like Hox proteins stabilize DNA binding by the Meis1 homeodomain proteins

Recent studies show that Hox homeodomain proteins from paralog groups 1 to 10 gain DNA binding specificity and affinity through cooperative binding with the divergent homeodomain protein Pbx1. However, the AbdB-like Hox proteins from paralogs 11, 12, and 13 do not interact with Pbx1a, raising the possibility of different protein partners. The Meis1 homeobox gene has 44% identity to Pbx within the homeodomain and was identified as a common site of viral integration in myeloid leukemias arising in BXH-2 mice. These integrations result in constitutive activation of Meis1. Furthermore, the Hoxa-9 gene is frequently activated by viral integration in the same BXH-2 leukemias, suggesting a biological synergy between these two distinct classes of homeodomain proteins in causing malignant transformation. We now show that the Hoxa-9 protein physically interacts with Meis1 proteins by forming heterodimeric binding complexes on a DNA target containing a Meis1 site (TGACAG) and an AbdB-like Hox site (TTTTACGAC). Hox proteins from the other AbdB-like paralogs, Hoxa-10, Hoxa-11, Hoxd-12, and Hoxb-13, also form DNA binding complexes with Meis1b, while Hox proteins from other paralogs do not appear to interact with Meis1 proteins. DNA binding complexes formed by Meis1 with Hox proteins dissociate much more slowly than DNA complexes with Meis1 alone, suggesting that Hox proteins stabilize the interactions of Meis1 proteins with their DNA targets.     

Construction and characterization of a set of E. coli strains deficient in all known loci affecting the proteolytic stability of secreted recombinant proteins

Even though secretion offers numerous advantages for the production of proteins in Escherichia coli, the expression of many heterologous proteins is severely limited by degradation in the periplasmic space. We found that mutations in rpoH, the RNA polymerase sigma factor responsible for heat shock protein synthesis, affect the stability of heterologous secreted proteins. A particularly dramatic increase in expression was further observed in rpoH degP double mutants. To minimize proteolytic degradation, we constructed a family of 25 isogenic strains deficient in all known cell envelope proteases (DegP, Protease III, Tsp(Prc), and OmpT), as well as the rpoH15 mutant allele, and characterized their growth in both shake flasks and fermentors. The availability of this set of strains permits the selection of a suitable host based on the optimal combination between the optimum reduction in protease activity and acceptable growth properties.     

Cross-specialty linkage and extrapolation of resource-based relative value scales

We used the fluorescent labelled dopamine D1-receptor antagonist Bodipy-SCH 23390 for the cellular localization of D1-ligand binding sites in the retinae of different vertebrates (teleosts, Xenopus, turtle, rat and rabbit). Competition experiments with unfixed cryosections of fish retina were performed to characterize the binding conditions of Bodipy-labelled SCH 23390. Tissue bound [3H]SCH 23390 was displaceable with increased amounts of bodipy-SCH 23390. The pharmacological specificity of the D1 fluorescent antagonist was determined by competition experiments with an excess of unlabelled SCH 23390. This treatment significantly reduced the level of fluorescence of the retina confirming the specificity of the binding. We observed a homogeneously distributed fluorescence signal in both plexiform layers in unfixed cryosections of fish, frog, turtle, rat and rabbit. Similar staining intensities of both plexiform layers were found in frog, turtle, rat and rabbit retina. In teleosts, the label of the outer plexiform layer was markedly more intense. Non-specific label was associated with photoreceptor outer and inner segments. The specific labelling of both plexiform layers indicates a mismatch of dopamine releasing and D1-binding sites, and suggests a possible extrasynaptic localization of the D1-receptor. The physiological significance of the observed distribution of D1-ligand binding sites is discussed with respect to the role of dopamine in controlling adaptational processes in the retina.     

The Effect of Nonuniform Chemistry on Interfacial Fracture Toughness

The adhesion of metallic-ceramic interfaces is generally ascribed to the mixture of several mechanisms, including chemical bonding, texture, strain transfer, and plasticity. This study examines the impact of alterations in chemical bonding along an interface on the nanometer scale on the interfacial fracture energy. Using a well-characterized system of W/SiO₂, small areas of the interface were masked with polymer tubes to prohibit the area from adhering well to the W film. This showed that the interfacial fracture energy was proportional to the area of higher adhesion. This finding was then used to study the growth of a Ti interlayer used for adhesion promotion in a Pt/SiO₂ system. Because the adhesion energy slowly grew from values near the Pt/SiO₂ to values typical of Ti/SiO₂, the growth mechanism for DC magnetron sputtering of thin film Ti on SiO₂ was inferred to be island growth instead of layer-by-layer growth. This article is based on a presentation given in the symposium entitled “Deformation and Fracture from Nano to Macro: A Symposium Honoring W.W. Gerberich’s 70th Birthday,” which occurred during the TMS Annual Meeting, March 12–16, 2006 in San Antonio, Texas and was sponsored by the Mechanical Behavior of Materials and Nanomechanical Behavior Committees of TMS.     

Symmetry breaking and training from incomplete data with Radial Basis Boltzmann Machines

A Radial Basis Boltzmann Machine (RBBM) is a specialized Boltzmann Machine architecture that combines feed-forward mapping with probability estimation in the input space, and for which very efficient learning rules exist. The hidden representation of the network displays symmetry breaking as a function of the noise in the dynamics. Thus, generalization can be studied as a function of the noise in the neuron dynamics instead of as a function of the number of hidden units. We show that the RBBM can be seen as an elegant alternative of k-nearest neighbor, leading to comparable performance without the need to store all data. We show that the RBBM has good classification performance compared to the MLP. The main advantage of the RBBM is that simultaneously with the input-output mapping, a model of the input space is obtained which can be used for learning with missing values. We derive learning rules for the case of incomplete data, and show that they perform better on incomplete data than the traditional learning rules on a 'repaired' data set.     

Pharmacokinetics of liposomal amphotericin B (Ambisome) in critically ill patients

The liposomal formulation of amphotericin B (AmBisome) greatly reduces the acute and chronic side effects of the parent drug. The present study describes the pharmacokinetic characteristics of AmBisome applied to 10 patients at a dose of 2.8 to 3.0 mg/kg of body weight and compares them to the pharmacokinetics observed in 6 patients treated with amphotericin B deoxycholate at the standard dose of 1.0 mg/kg. Interpatient variabilities of amphotericin B peak concentrations (Cmax) and areas under concentration-time curves (AUC) were 8- to 10-fold greater for patients treated with AmBisome than for patients treated with amphotericin B deoxycholate. At the threefold greater dose of AmBisome, median Cmaxs were 8.4-fold higher (14.4 versus 1.7 microg/ml) and median AUCs exceeded those observed with amphotericin B deoxycholate by 9-fold. This was in part explained by a 5.7-fold lower volume of distribution (0.42 liters/kg) in AmBisome-treated patients. The elimination of amphotericin B from serum was biphasic for both formulations. However, the apparent half-life of elimination was twofold shorter for AmBisome (P = 0.03). Neither hemodialysis nor hemofiltration had a significant impact on AmBisome pharmacokinetics as analyzed in one patient. In conclusion, the liposomal formulation of amphotericin B significantly (P = 0.001) reduces the volume of drug distribution, thereby allowing for greater drug concentrations in serum. The low toxicity of AmBisome therefore cannot readily be explained by its serum pharmacokinetics.     

Quenching of chlorophyll a fluorescence in the aggregates of LHCII: steady state fluorescence and picosecond relaxation kinetics

The protein composition, steady state and time-resolved fluorescence emission spectra were studied in solubilized and aggregated LHCII complexes, that were prepared according to two different isolation protocols: (1) by fractionation of cation-depleted thylakoid membranes using the non-ionic detergent Triton X-100 according to the procedure of Burke et al. [(1978) Arch. Biochem. Biophys. 187, 252-263] or (2) by solubilization with N-beta-dodecyl maltoside (beta-DM) of photosystem II (PSII) membrane fragments in the presence of cations [Irrgang et al. (1988) Eur. J. Biochem. 178, 207-217]. Based on the analysis of the decay-associated emission spectra measured at 10 and 80 K five long-wavelength chlorophyll species were identified in aggregated LHCII complexes. These five forms are characterized by emission maxima at 681.5, 683, 687, 695, or 702 nm. All of these forms were found in both types of LHCII preparations but the relative amounts and temperature dependency of these species were markedly different in the aggregated LHCII complexes isolated by the two procedures. It was found that these differences cannot be simply explained by effects due to using a less mild detergent as beta-DM or by an ionic influence of Ca2+. Biochemical analysis of the protein composition showed that beta-DM type LHCII consists of all the chlorophyll (Chl)binding proteins belonging to the antenna system of PSII except the CP29 type II gene product (CP29). In contrast, the Triton X-100-solubilized LHCII is highly depleted in CP26 (CP 29 type I gene product) and is contaminated by a variety of unidentified polypeptides. It is proposed that the aggregates of LHCII prepared using Triton X-100 acquire specific spectral and kinetic features due to interaction between the bulk of LHCII subunits and minor protein(s).