Dynamics of CD8+ T cell responses during acute and chronic lymphocytic choriomeningitis virus infection

Infection of mice with lymphocytic choriomeningitis virus (LCMV) is frequently used to study the underlying principles of viral infections and immune responses. We fit a mathematical model to recently published data characterizing Ag-specific CD8+ T cell responses during acute (Armstrong) and chronic (clone 13) LCMV infection. This allows us to analyze the differences in the dynamics of CD8+ T cell responses against different types of LCMV infections. For the four CD8+ T cell responses studied, we find that, compared with the responses against acute infection, responses against chronic infection are generally characterized by an earlier peak and a faster contraction phase thereafter. Furthermore, the model allows us to give a new interpretation of the effect of thymectomy on the dynamics of CD8+ T cell responses during chronic LCMV infection: a smaller number of naive precursor cells is sufficient to account for the observed differences in the responses in thymectomized mice. Finally, we compare data characterizing LCMV-specific CD8+ T cell responses from different laboratories. Although the data were derived from the same experimental model, we find quantitative differences that can be solved by introducing a scaling factor. Also, we find kinetic differences that are at least partly due to the infrequent measurements of CD8+ T cells in the different laboratories.     

Designing allosteric peptide ligands targeting a globular protein

Patented signal analytic algorithms applied to hydrophobically transformed, numerical amino acid sequences have previously been used to design short, protein-targeted, L or D retro-inverso peptides. These peptides have demonstrated allosteric and/or indirect agonist effects on a variety of G-protein and tyrosine kinase coupled membrane receptors with 30% to over 80% hit rates. Here we extend these approaches to a globular protein target. We designed eight peptide ligands targeting an ELISA antibody responsive protein, beta-galactosidase, betaGAL. Three of the eight 14mer peptides allosterically activated betaGAL with ELISA methodology. Using Bayesian statistics, this 38% hit rate would have occurred 2 x 10(-9) by chance. These peptides demonstrated binding site competitive or noncompetitive interactions, suggesting allosteric site multiplicity with respect to their betaGAL binding-mediated ELISA signal. Kinetic studies demonstrated the temperature dependence of the betaGAL peptide binding functions. Using the van't Hoff relation, we found evidence for enthalpy-entropy compensation. This relation is often found for hydrophobic interactions in aqueous media, and is consistent with the postulated hydrophobic series encoding underlying our protein-targeted, peptide design methods. It appears that our algorithmic, hydrophobic autocovariance eigenvector template approach to the design of allosteric peptides targeting membrane receptors may also be applicable to the design of peptide ligands targeting nonmembrane involved globular proteins.     

Selective inhibition of the interaction of C1q with immunoglobulins and the classical pathway of complement activation by steroids and triterpenoids sulfates

Since undesirable activation of the complement system through the classical pathway is associated with tissue damage and other pathologic proinflammatory consequences at ischemia/reperfusion injury, autoimmune diseases, and rejection of allo- and xenografts, creation of selective inhibitors of the classical pathway leaving the alternative pathway intact is of great importance. Classical pathway is triggered by binding of its recognizing unit, protein C1q, to a number of targets like antibodies, pentraxins, apoptotic cells, and others. In order to obtain inhibitors blocking the first step of the classical cascade, synthesis of sulfates of steroids (Delta(5)-3beta-hydroxycholenic, Delta(5)-3beta-hydroxyetiocholenic, deoxycholic, and cholic acids) and triterpenoids (betulin, 20,29-dihydro-20,29-dichloromethylenbetulin, betulinic, ursolic, and oleanolic acids) has been performed. Testing of the compounds in classical pathway inhibition assay has displayed derivatives of triterpenoid betulin (betulin disulfate and betulinic acid sulfate) to be the most potent inhibitors. Further studies of the two compounds established that their activity to inhibit the classical pathway had been due to their capability to block the interaction of C1q with antibodies. Betulin disulfate and betulinic acid sulfate have shown weak inhibition of the alternative route of activation, what makes them promising inhibitors for the selective suppression of the classical complement pathway at the earliest possible level as well as perspective agents for blocking the interaction of C1q with its other targets.     

Translation initiation factor 4E blocks endoplasmic reticulum-mediated apoptosis

Eukaryotic translation initiation factor 4E (eIF4E) is the mRNA cap-binding protein required for translation of cellular mRNAs utilizing the 5' cap structure. The rate-limiting factor for mRNA recruitment to ribosomes, eIF4E is a major target for regulation of translation by growth factors, hormones, and other extracellular stimuli. When overexpressed, eIF4E exerts profound effects on cell growth and survival, leading to suppression of oncogene-dependent apoptosis, causing malignant transformation and conferring tumors with multiple drug resistance. We found previously that overexpressed eIF4E interdicts the apoptotic pathway induced by growth factor withdrawal and cytotoxic drugs by selectively activating the expression of Bcl-X(L), thus preventing mitochondrial release of cytochrome c. In this study, we examined the impact of ectopic eIF4E expression on apoptosis mediated by the endoplasmic reticulum (ER). Here we show that eIF4E rescued cells from the ER stressors brefeldin A, tunicamycin, thapsigargin, and the Ca(2+) ionophore A23187. In addition, we found that cells rescued from Ca(2+) ionophore-triggered apoptosis did not release calcium from their ER nor did they translocate caspase-12 from the ER to the cytoplasm. These data lend strong support to the concept that eIF4E functions as a pleiotropic regulator of cell viability and that integration of critical organelle-mediated checkpoints for apoptosis can be controlled by the cap-dependent translation apparatus.     

Automatic registration of microarray images. II. Hexagonal grid

MOTIVATION: In the first part of this paper the author presented an efficient, robust and completely automated algorithm for spot and block indexing in microarray images with rectangular grids. Although the rectangular grid is currently the most common type of grouping the probes on microarray slides, there is another microarray technology based on bundles of optical fibers where the probes are packed in hexagonal grids. The hexagonal grid provides both advantages and drawbacks over the standard rectangular packing and of course requires adaptation and/or modification of the algorithm of spot indexing presented in the first part of the paper. RESULTS: In the second part of the paper the author presents a version of the spot indexing algorithm adapted for microarray images with spots packed in hexagonal structures. The algorithm is completely automated, works with hexagonal grids of different types and with different parameters of grid spacing and rotation as well as spot sizes. It can successfully trace the local and global distortions of the grid, including non-orthogonal transformations. Similar to the algorithm from part I, it scales linearly with the grid size, the time complexity is O(M), where M is total number of grid points in hexagonal grid. The algorithm has been tested both on CCD and scanned images with spot expression rates as low as 2%. The processing time of an image with about 50 000 hex grid points was less than a second. For images with high expression rates ( approximately 90%) the registration time is even smaller, around a quarter of a second. Supplementary information: http://fleece.ucsd.edu/~vit/Registration_Supplement.pdf     

A biomechanical model of sagittal tongue bending

The human tongue is a structurally complex and extremely flexible organ. In order to better understand the mechanical basis for lingual deformations, we modeled a primitive movement of the tongue, sagittal tongue bending. We hypothesized that sagittal bending is a synergistic deformation derived from co-contraction of the longitudinalis and transversus muscles. Our model of tongue bending was based on classical bimetal strip theory, in which curvature is produced when one muscle layer contracts more so than another. Contraction was modulated via mismatched thermal expansion coefficients and temperature change (to simulate muscular contraction). Our results demonstrated that synergistic contraction produced curvature and strain results which were in better correspondence to empirical results derived from tagging MRI than were the results of contraction of the longitudinalis muscle alone. This fundamental reliance of tongue bending on the synergistic contraction of its intrinsic fibers supports the muscular hydrostat theory of tongue function.     

Spectroscopic evidence for site-specific cellular activity in the tubular gland in human intestine

The intestinal crypts contain mucus-secreting goblet cells in large numbers. In the tubular gland (crypt), the cells are generated at the bottom and end their life cycle at the top. Recently, FTIR microspectroscopy (FTIR-MC) has been applied in biology and medicine. The characterization of various cellular types using FTIR-MC and its subsequent application for the diagnosis of cancer is becoming a reality. In this report, we investigate the differential cellular activity in the normal tubular gland using FTIR-MC. Our results indicate that the absorbance for the cells in the bottom of the crypt is always higher than those in the upper portion. There are spectral pattern changes and frequency shifts for cells at the bottom and top sites of the normal crypt. Also, the comparison of a normal crypt with a malignant one has been made. This is the first spectroscopic evidence in the literature showing the difference in the cellular activity at different sites in the tubular gland. The reasons for our observations and their implications are discussed.     

Recognition of cell-specific binding of phage display derived peptides using an acoustic wave sensor

ASSLNIA, a peptide selected for murine myofibers using phage display technology, was immobilized onto an acoustic wave sensor. The sensor responded to murine and feline muscle homogenates indicating crosspieces interactions. Kidney, liver, and brain preparations produced insignificant responses.