Tracing pathway activities with kinase inhibitors and reverse phase protein arrays

Controlling aberrant protein kinase activity is a promising strategy for a variety of diseases, particularly cancer. Hence, the development of kinase inhibitors is currently a focal point for pharmaceutical research. In this study we utilize a chip-based reverse phase protein array (RPA) platform for profiling of kinase inhibitors in cell-based assays. In combination with the planar wave-guide technology the assay system has an absolute LOD down to the low zeptomole range. A431 cell lysates were analyzed for the activation state of key effectors in the epidermal growth factor (EGF) and insulin signaling pathways to validate this model for compound screening. A microtiter-plate format for growing, treating, and lysing cells was shown to be suitable for this approach, establishing the value of the technology as a screening tool for characterization of large numbers of kinase inhibitors against a wide variety of cellular signaling pathways. Moreover, the reverse array format allows rapid development of site-specific phosphorylation assays, since in contrast to ELISA type systems only a single antigen-specific antibody is required.     

Immunoglobulin 1 (IgG1) Fc-glycosylation profiling of anti-citrullinated peptide antibodies from human serum

In several autoimmune disorders, including rheumatoid arthritis (RA), autoantibodies are thought to be the driving force of pathogenicity. Glycosylation of the Fc-part of human Igs is known to modulate biological activity. Hitherto, glycosylation of human IgG-Fc has been analyzed predominantly at the level of total serum IgG, revealing reduced galactosylation in RA. Given the pathogenic relevance of autoantibodies in RA, we wished, in the present study, to address the question whether distinct Fc-glycosylation features are observable at the level of antigen-specific IgG subpopulations. For this purpose, we have developed a method for the microscale purification and Fc-glycosylation analysis of anti-citrullinated peptide antibodies (ACPA). ACPA represent a group of autoantibodies that occur with unique specificity in RA patients. Their presence is associated with increased inflammatory disease activity and rapid joint destruction. Results indicate that ACPA of the IgG1 subclass vary considerably from total serum IgG1 with respect to Fc-galactosylation, with galactosylation being higher on ACPA than on serum IgG1 for some patients, while other patients show higher galactosylation on serum IgG1 than on ACPA. Using this method, studies can be performed on the biological and clinical relevance of ACPA glycosylation within RA patient cohorts.     

Electron cryo-microscopy of biological specimens on conductive titanium-silicon metal glass films

Thin films of the metal glass Ti88Si12 were produced by evaporation and characterized by AFM and conductivity measurements. Thin Ti88Si12 support films for electron microscopy were prepared by coating standard EM grids with evaporated films floated off mica, and characterized by electron imaging and electron diffraction. At room temperature, the specific resistance of a thin TiSi film was 10(6) times lower than that of an amorphous carbon film. At 77K, the specific resistance of TiSi films decreased, whereas that of carbon became immeasurably high. The effective scattering cross-section of TiSi and amorphous carbon for 120 kV electrons is roughly equal, but TiSi films for routine use can be approximately 10 times thinner due to their high mechanical strength, so that they would contribute less background noise to the image. Electron diffraction of purple membrane on a TiSi substrate confirmed that the support film was amorphous, and indicated that the high-resolution order of the biological sample was preserved. Electron micrographs of TiSi films tilted by 45 degrees relative to the electron beam recorded at approximately 4 K indicated that the incidence of beam-induced movements was reduced by 50% compared to amorphous carbon film under the same conditions. The success rate of recording high-resolution images of purple membranes on TiSi films was close to 100%. We conclude that TiSi support films are ideal for high-resolution electron cryo-microscopy (cryo-EM) of biological specimens, as they reduce beam-induced movement significantly, due to their high electrical conductivity at low temperature and their favorable mechanical properties.     

Post-embryonic development of the antennal sensilla in Melipona quadrifasciata anthidioides (Hymenoptera: Meliponini)

The sensilla are sensory organs formed by cuticular and cellular structures specialized in reception of chemical and physical stimuli from the environment and transmission to the insect's central nervous system. In function of the great concentration of sensilla, the antennae are the main organs for interaction between bees and with the environment. This work studied the presence of antennal sensilla in the different phases of pupal development of the stingless bee Melipona quadrifasciata anthidioides by means of scanning electron microscopy and light microscopy. The results showed that antennal sensilla begin their development in the transition of the prepupae to the white-eyed pupae and finish it in the pigmented-body pupae phase. The antennal sensilla were exposed to the environment in the black-eyed pupae when the old cuticle is completely digested, suggesting that only in the final pupal phases can these bees perceive the environmental stimuli.     

New insights into the morphology of Trypanosoma cruzi reservosome

Reservosomes are late endosomes present only in members of the Schizotrypanum subgenus of the Trypanosoma genus and are defined as the site of storage of endocytosed macromolecules and lysosomal enzymes. They have been extensively described in Trypanosoma cruzi epimastigote: are bounded by a membrane unit, present an electron-dense protein matrix with electron-lucent lipid inclusions, being devoid of inner membranes. Here we performed a detailed ultrastructural analysis of these organelles using a variety of electron microscopy techniques, including ultrathin sectioning, uranyl acetate stained preparations, and freeze fracture, either in intact epimastigotes or in isolated reservosomes. New informations were obtained. First, both isolated and in situ reservosomes presented small profiles of inner membranes that are morphologically similar to the membrane surrounding the organelle. In uranyl acetate stained preparations, internal membrane profiles turned out to be longer than they appeared in ultrathin section images and traversed the organelle diameter. Internal vesicles were also found. Second, endocytosed cargo are not associated with internal vesicles and reach reservosomes on board of vesicles that fuse with the boundary membrane, delivering cargo directly into reservosome lumen. Third, electron-lucent bodies with saturated lipid core surrounded by a membrane monolayer and with unusual rectangular shape were also observed. Fourth, it was possible to demonstrate the presence of intramembranous particles on the E face of both internal vesicles and the surrounding membrane. Collectively, these results indicate that reservosomes have a complex internal structure, which may correlate with their multiple functions.     

A logical approach to efficient Max-SAT solving

Weighted Max-SAT is the optimization version of SAT and many important problems can be naturally encoded as such. Solving weighted Max-SAT is an important problem from both a theoretical and a practical point of view. In recent years, there has been considerable interest in finding efficient solving techniques. Most of this work focuses on the computation of good quality lower bounds to be used within a branch and bound DPLL-like algorithm. Most often, these lower bounds are described in a procedural way. Because of that, it is difficult to realize the logic that is behind.In this paper we introduce an original framework for Max-SAT that stresses the parallelism with classical SAT. Then, we extend the two basic SAT solving techniques: search and inference. We show that many algorithmic tricks used in state-of-the-art Max-SAT solvers are easily expressible in logical terms in a unified manner, using our framework.We also introduce an original search algorithm that performs a restricted amount of weighted resolution at each visited node. We empirically compare our algorithm with a variety of solving alternatives on several benchmarks. Our experiments, which constitute to the best of our knowledge the most comprehensive Max-SAT evaluation ever reported, demonstrate the practical usability of our approach.     

Sequential Monte Carlo in reachability heuristics for probabilistic planning

Some of the current best conformant probabilistic planners focus on finding a fixed length plan with maximal probability. While these approaches can find optimal solutions, they often do not scale for large problems or plan lengths. As has been shown in classical planning, heuristic search outperforms bounded length search (especially when an appropriate plan length is not given a priori). The problem with applying heuristic search in probabilistic planning is that effective heuristics are as yet lacking.In this work, we apply heuristic search to conformant probabilistic planning by adapting planning graph heuristics developed for non-deterministic planning. We evaluate a straight-forward application of these planning graph techniques, which amounts to exactly computing a distribution over many relaxed planning graphs (one planning graph for each joint outcome of uncertain actions at each time step). Computing this distribution is costly, so we apply Sequential Monte Carlo (SMC) to approximate it. One important issue that we explore in this work is how to automatically determine the number of samples required for effective heuristic computation. We empirically demonstrate on several domains how our efficient, but sometimes suboptimal, approach enables our planner to solve much larger problems than an existing optimal bounded length probabilistic planner and still find reasonable quality solutions.     

Viscoelastic and rheological behavior of concentrated colloidal suspensions

Molecular approaches are discussed to the density (), viscoeleastic (), and rheological () behavior of the viscosity(,,) of concentrated colloidal suspensions with 0.3 < < 0.6, where, is the volume fraction, the applied frequency, and ; the shear rate. These theories are based on the calculation of the pair distribution functionP ₂(r,,), wherer is the relative position of a pair of colloidal particles. The linear viscoelastic behavior(,,=0) follows from an equation forP ₂(r,,) derived from the Smoluchowski equation for small, generalized to large by introducing the spatial ordering and (cage) diffusion typical for concentrated suspensions. The rheological behavior(,,=0) follows from an equation forP ₂(r,) of a dense hard-sphere fluid derived from the Liouville equation. This leads to a hard-sphere viscosity^hs(,) which yields the colloidal one(,) by the scaling relation(,) ₀=^hs(,) _B, where ₀ is the solvent viscosity. _B is the dilute hard-sphere (Boltzmann ) viscosity and the's are appropriately scaled,(,) and(,) agree well with experiment. A unified theore for(,,) is clearly needed and pursued.Paper presented at the Twelfth Symposium on Thermophysical Properties, June 19–24, 1994. Boulder, Colorado, U.S.A.     

Effects of double-muscling on carcass quality, beef tenderness and myofibrillar protein degradation in Belgian Blue White bulls

Carcass properties and meat quality characteristics of 32 Belgian Blue White double-muscled bulls (DM) were compared with those of 59 bulls of the same breed with normal conformation (N). DM showed superior carcass quality as revealed in increased dressing percentage, meat production yield, conformation grade, muscle/fat and muscle/bone ratios (all P < 0·001). Longissimus dorsi (LD) shear force values, drip and cooking losses at 8 days post mortem (pm) were significantly higher (P < 0·001) for DM, whereas sarcomere lengths were not different. Calpain 1 and calpastatin levels at 1 h and 24 h pm were tremendously decreased in DM as were also cathepsin B and L levels at 1 and 8 days pm (P < 0·001). As evident from semi-quantitative SDS-PAGE, these differences were accompanied by higher titin and lower 30 kDa levels (P < 0·001) in DM. Troponin-t levels were not different, but very low. Intramuscular collagen content was significantly lower in DM (P < 0·001). This suggests that lower background toughness in DM was compensated for by reduced post-mortem proteolytic tenderization. Discrepancy with literature reports regarding tenderness of DM might be related to the extreme muscularity of the Belgian Blue White breed, compared to other DM breeds. The results also suggest that reduced protein turnover might be involved in the muscle hypertrophy phenomenon within this breed, because of likely reduced levels of calpains and cathepsins in living DM animals.     

Synthesis methods of array antenna excitation laws

Standard numerical optimization methods become very computational time consuming when dealing with synthesis of array antenna excitation laws, especially when number of elements exceeds a few tenths. Array antenna designer needs a fast and efficient synthesis tool, since the design phase implies several reoptimizations within the definition phase, in order to satisfy tradeoffs on antagonistic requirements : performances, size, cost,… We propose the use of an efficient, from the computational time point of view, and secured, from the convergence point of view, synthesis method illustrated by two examples. The optimized solution satisfies a sta-tionarity condition, which leads to steady solutions in frequency but also with regard to errors (manufacturing, …). Based on analytical calculus performed before any numerical resolution and together with the use of fast Fourier transform algorithms, this method leads to reduced optimization times (in the order of a minute) for arrays of some tenths up to some hundred feeds, computations being performed on a pc. Two theoretical applications are presented and for each of them a computed example is also shown; moreover possible extensions are considered.