'98 Escherichia coli SWISS-2DPAGE database update

The combination of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), computer image analysis and several protein identification techniques allowed the Escherichia coli SWISS-2DPAGE database to be established. This is part of the ExPASy molecular biology server accessible through the WWW at the URL address http://www.expasy.ch/ch2d/ch2d-top.html . Here we report recent progress in the development of the E. coli SWISS-2DPAGE database. Proteins were separated with immobilized pH gradients in the first dimension and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. To increase the resolution of the separation and thus the number of identified proteins, a variety of wide and narrow range immobilized pH gradients were used in the first dimension. Micropreparative gels were electroblotted onto polyvinylidene difluoride membranes and spots were visualized by amido black staining. Protein identification techniques such as amino acid composition analysis, gel comparison and microsequencing were used, as well as a recently described Edman "sequence tag" approach. Some of the above identification techniques were coupled with database searching tools. Currently 231 polypeptides are identified on the E. coli SWISS-2DPAGE map: 64 have been identified by N-terminal microsequencing, 39 by amino acid composition, and 82 by sequence tag. Of 153 proteins putatively identified by gel comparison, 65 have been confirmed. Many proteins have been identified using more than one technique. Faster progress in the E. coli proteome project will now be possible with advances in biochemical methodology and with the completion of the entire E. coli genome.     

The microsomal triglyceride transfer protein catalyzes the post-translational assembly of apolipoprotein B-100 very low density lipoprotein in McA-RH7777 cells

In cells in which the lipoprotein assembly process had been inactivated by brefeldin A (BFA), membrane-associated apoB-100 disappeared without forming lipoproteins or being secreted, indicating that it was degraded. Reactivation of the assembly process by chasing the cells in the absence of BFA, gave rise to a quantitative recovery of the membrane-associated apoB-100 in the very low density lipoprotein (VLDL) fraction in the medium. These results indicate that the membrane-associated apoB-100 can be converted to VLDL. A new method was developed by which the major amount (88%) of microsomal apoB-100 but not integral membrane proteins could be extracted. The major effect of this method was to increase the recovery of apoB-100 that banded in the LDL and HDL density regions, suggesting that the membrane-associated form of apoB-100 is partially lipidated. We also investigated the role of the microsomal triglyceride transfer protein (MTP) in the assembly of apoB-100 VLDL using a photoactivatable MTP inhibitor (BMS-192951). This compound strongly inhibited the assembly and secretion of apoB-100 VLDL when present during the translation of the protein. To investigate the importance of MTP during the later stages in the assembly process, the cells were preincubated with BFA (to reversibly inhibit the assembly of apoB-100 VLDL) and pulse-labeled (+BFA) and chased (+BFA) for 30 min to obtain full-length apoB-100 associated with the microsomal membrane. Inhibition of MTP after the 30-min chase blocked assembly of VLDL. This indicates that MTP is important for the conversion of full-length apoB-100 into VLDL. Results from experiments in which a second chase (-BFA) was introduced before the inactivation of MTP indicated that only early events in this conversion of full-length apoB-100 into VLDL were blocked by the MTP inhibitor. Together these results indicate that there is a MTP-dependent "window" in the VLDL assembly process that occurs after the completion of apoB-100 but before the major amount of lipids is added to the VLDL particle. Thus the assembly of apoB-100 VLDL from membrane-associated apoB-100 involves an early MTP-dependent phase and a late MTP-independent phase, during which the major amount of lipid is added.     

Addressing the tertiary structure of human parathyroid hormone-(1-34)

Parathyroid hormone (PTH) regulates mineral metabolism and bone turnover by activating specific receptors located on osteoblastic and renal tubular cells and is fully functional as the N-terminal 1-34 fragment, PTH-(1-34). Previously, a "U-shaped" conformation with N- and C-terminal helices brought in close proximity by a turn has been postulated. The general acceptance of this hypothesis, despite limited experimental evidence, has altered the direction of the design of PTH-analogs. Examining the structure of human PTH-(1-34) under conditions that encompass the different environments the hormone may experience in the approach to and interaction with the G-protein-coupled receptor (including benign aqueous and saline solutions and in the presence of dodecylphosphocholine), we observe no evidence for a U-shape conformation or any tertiary structure. Instead, the N- and C-terminal helical domains, which vary in length and stability depending on the conditions, are separated by a highly flexible region of undefined conformation. These observations are in complete accord with recent conformational studies of PTH-related protein analogs containing lactams (Mierke, D. F., Maretto, S., Schievano, E. , DeLuca, D., Bisello, A., Mammi, S., Rosenblatt, M., Peggion, E., and Chorev, M. (1997) Biochemistry 36, 10372-10383) or a model amphiphilic alpha-helix (Pellegrini, M., Bisello, A., Rosenblatt, M., Chorev, M., and Mierke, D. F. (1997) J. Med. Chem. 40, 3025-3031). Reliable structural data from different environmental conditions are absolutely requisite for the next step in the design of non-peptide PTH analogs.     

Accuracy and efficacy of chest radiography in the intensive care unit

264 patients with cancer of larynx, 21 female and 234 male, had a testosterone and sex hormone binding globulin (SHBG) before the treatment in serum estimated. Because of dependence of levels of hormones the group of patients was divided into three following groups: "lower than standard", "standard", "higher than standard". The correlation between these groups and sex, age, localization of tumor, organs' advances, stage of morphological malignancy and type of cancer was reported. Anomalous values of testosterone were in male group more frequently reported. Anomalous values of SHBG were similar in male and female groups, but in the female group there was a significant majority of "lower than standard" values reported. The majority of abnormal values of testosterone and SHBG was described in groups of age higher than 50 years. There were no differences in testosterone and SHBG levels in different localization of tumors in larynx. In advanced stage T3 and T4 there were more frequent lower mean values of testosterone levels and higher values of SHBG levels in comparison to T2 stages. In tumors in G1 and G2 stages of histological malignancy higher levels of SHBG and higher mean levels of testosterone. The tumors in stage G3 the hormone levels were lowers were observed. The levels of SHBG in groups of carcinoma planoepitheliale keratodes were in 66% higher than in a group of carcinoma planoepitheliale akeratodes but in both groups the levels of testosterone were nearing the same. In group of patients with larynx cancer the negative correlation between the levels of testosterone and SHBG was not observed. Higher SHBG levels were not always accompanied by lower testosterone levels.     

Wavefront raycasting using larger filter kernels for on-the-fly GPU gradient reconstruction

The quality of images generated by volume rendering strongly depends on the accuracy of gradient estimation. However, the most commonly used techniques for on-the-fly gradient reconstruction are still very simple, such as central differences; they generally gather only limited neighbourhood information and thus ultimately produce rather poor quality images. While there are many higher-order reconstruction methods, such as 3×3×3 or 5×5×5 filters, which can improve the quality, their excessive sampling costs have meant that they are generally used only for pre-computed gradients, which are then quantized and stored for later runtime re-interpolation. This may introduce further errors and, significantly, may consume valuable texture memory. In this paper, we address these issues by proposing a CUDA-based rendering framework that uses larger filter kernels for on-the-fly gradient computation in real-time raycasting applications. By using adaptive wavefront tracing, our approach can dramatically reduce the memory bandwidth requirements related to larger neighbour samples. To further ensure that samples are consumed wisely, we have devised a novel adaptive sampling scheme and a customized 3D mipmapping technique in the CUDA environment to sample at a proper level of detail as the ray recedes into the distance. We compared our technique with two previous state-of-the-art GPU raycasting algorithms and found that it achieves higher quality imaging and faster rendering performance across a variety of data sets than the previous methods.     

Superquadric glyphs for symmetric second-order tensors

Symmetric second-order tensor fields play a central role in scientific and biomedical studies as well as in image analysis and feature-extraction methods. The utility of displaying tensor field samples has driven the development of visualization techniques that encode the tensor shape and orientation into the geometry of a tensor glyph. With some exceptions, these methods work only for positive-definite tensors (i.e. having positive eigenvalues, such as diffusion tensors). We expand the scope of tensor glyphs to all symmetric second-order tensors in two and three dimensions, gracefully and unambiguously depicting any combination of positive and negative eigenvalues. We generalize a previous method of superquadric glyphs for positive-definite tensors by drawing upon a larger portion of the superquadric shape space, supplemented with a coloring that indicates the quadratic form (including eigenvalue sign). We show that encoding arbitrary eigenvalue magnitudes requires design choices that differ fundamentally from those in previous work on traceless tensors that arise in the study of liquid crystals. Our method starts with a design of 2-D tensor glyphs guided by principles of scale-preservation and symmetry, and creates 3-D glyphs that include the 2-D glyphs in their axis-aligned cross-sections. A key ingredient of our method is a novel way of mapping from the shape space of three-dimensional symmetric second-order tensors to the unit square. We apply our new glyphs to stress tensors from mechanics, geometry tensors and Hessians from image analysis, and rate-of-deformation tensors in computational fluid dynamics.     

High strain electromechanical actuators based on electrodeposited polypyrrole doped with di-(2-ethylhexyl)sulfosuccinate

The low-voltage electromechanical actuation of polypyrrole (PPy) doped with di-(2-ethylhexyl)sulfosuccinate (DEHS) has been investigated. The PPy-DEHS has been prepared both chemically (cast as films from solution) and by more conventional electrochemical polymerization. Very large strains of ∼30% were obtained during slow-scan redox cycling of the electrochemically prepared PPy-DEHS films. In constrast, PPy-DEHS films cast from solutions of the chemically polymerized polymer gave actuation strains of ∼2.5%. The polymerization method was also found to have a significant effect on the structure, conductivity and mechanical properties of the PPy-DEHS materials. The conductivity of the electrochemically polymerized PPy-DEHS was 75 S cm⁻¹, considerably higher than that found for the chemically derived polymer (7 S cm⁻¹). The structure of the PPy-DEHS was further elucidated from UV-vis, Raman and FT-IR spectral studies which indicated that the conjugation length of the PPy could be increased significantly by varying the polymerization method. Films obtained by casting chemically prepared PPy-DEHS showed higher modulus (2.3 GPa) than electropolymerized PPy-DEHS (0.6 GPa), but were more brittle. Both materials were electroactive in acetonitrile/water electrolyte. The higher actuation strain observed in the electrochemically prepared films was attributed to a more open molecular structure (as indicated by the lower modulus) allowing for easier ion diffusion and a higher conductivity allowing easier charge transfer.