Antigenic heterogeneity of the hepatitis C virus NS4 protein as modeled with synthetic peptides.
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The effect of sequence heterogeneity on the immunologic properties of two strong antigenic regions of the hepatitis C virus (HCV) NS4 protein was studied by using a set of 443 overlapping 20-mer synthetic peptides. One antigenic region comprising the cleavage site between NS4a and NS4b (region 5-1-1) was modeled with peptides derived from 73 different known sequences, representing HCV genotypes 1-6. The other antigenic region, designated region 59 and located at the C-terminus of the NS4b protein, was modeled with peptides from 7 known sequences representing genotypes 1-3. All peptides were tested for antigenic reactivity by enzyme immunoassay with a panel of anti-HCV-positive serum specimens representing genotypes 1-5. The data demonstrated that immunoreactive peptides fell into two groups. One group, represented by N-terminal peptides, demonstrated genotype-independent immunoreactivity; the other group, from the central part of region 5-1-1, showed strict genotype specificity. Nineteen peptides from the genotype-independent group strongly immunoreacted with a wide range of serum samples containing antibodies to all 5 HCV genotypes. Twenty-five peptides from the genotype-specific group were found to strongly react with serum containing antibodies only to the genotype from which the peptides were derived. Similar to the N-terminal part of region 5-1-1, peptides derived from region 59 did not show genotype-specific immunoreactivity. Some peptides derived from the central part of region 59 showed very strong and broad antigenic reactivity. Thus, after examining two antigenic regions of the NS4 protein, we identified short sequences that can be used for the efficient detection of either genotype-independent or genotype-specific HCV antibodies. (+info)
Virus phenotype switching and disease progression in HIV-1 infection.
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One of the phenotypic distinctions between different strains of human immunodeficiency virus type 1 (HIV-1) has to do with the ability to cause target cells to form large multinucleate bodies known as syncytia. There are two phenotypes according to this characterization: syncytium-inducing (SI) and non-syncytium-inducing (NSI). NSI strains are usually present throughout infection, while SI strains are typically seen at the beginning of the infection and near the onset of AIDS. The late emergence of SI strains is referred to as phenotype switching. In this paper we analyse the factors that lead to phenotype switching and contribute to the dynamics of disease progression. We show that a strong immune system selects for NSI strains while a weak immune system favours SI strains. The model explicitly accounts for the fact that CD4+ cells are both targets of HIV infection and crucial for activating immune responses against HIV In such a model, SI strains can emerge after a long and variable period of NSI dominated infection. Furthermore, versions of the model which do not explicitly account for HIV-specific, activated CD4+ cells do not exhibit phenotype switching, emphasizing the critical importance of this pool of cells. (+info)
Role of the adenomatous polyposis coli gene product in human cardiac development and disease.
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Expressed sequence tag (EST) and digital Northern analyses of human fetal, adult, and hypertrophic heart cDNA libraries revealed ESTs with high homology to adenomatosis polyposis coli (APC) and its associated protein, beta-catenin, as well as their differential expression. Thus, we hypothesize that the APC/beta-catenin pathway may play a role in cardiac development and disease. Reverse transcriptase-polymerase chain reaction analysis exhibited a higher APC expression in adult compared with fetal and hypertrophic heart but no significant difference in beta-catenin mRNA level. However, beta-catenin protein level was higher in fetal and hypertrophic heart compared with adult heart, suggesting the post-translational regulation of beta-catenin by APC in the cardiovascular system. In vitro antisense inhibition of APC resulted a higher beta-catenin protein expression leading to an incomplete myotube formation, suggesting APC/beta-catenin pathway involvement in myotube development. Western blot analysis further reveals three novel isoforms, APC-F, APC-A, and APC-D, ubiquitously expressed in fetal, adult, and hypertrophic heart, respectively. Isoform switching during development and disease pathogenesis suggests functionally distinct roles for each isoform. These data (i) demonstrate the usefulness of genome-based expression analysis for rapid discovery of differentially expressed genes, (ii) implicate the APC/beta-catenin pathway in the cardiovascular development, and (iii) demonstrate APC isoform switching during cardiac development and disease. (+info)
Identification and characterization of KLK-L4, a new kallikrein-like gene that appears to be down-regulated in breast cancer tissues.
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Kallikreins are a subgroup of serine proteases and these proteolytic enzymes have diverse physiological functions in many tissues. Growing evidence suggests that many kallikreins are implicated in carcinogenesis. In rodents, kallikreins constitute a large multigene family, but in humans, only three genes were identified. By using the positional candidate gene approach, we were able to identify a new kallikrein-like gene, tentatively named KLK-L4 (for kallikrein-like gene 4). This new gene maps to chromosome 19q13. 3-q13.4, is formed of five coding exons and four introns, and shows structural similarity to other kallikreins and kallikrein-like genes. KLK-L4 is expressed in a variety of tissues including prostate, salivary gland, breast, and testis. Our preliminary results show that KLK-L4 is down-regulated, at the mRNA level, in breast cancer tissues and breast cancer cell lines. Its expression is regulated by steroid hormones in the breast cancer cell line BT-474. This gene may be involved in the pathogenesis and/or progression of breast cancer and may find applicability as a novel cancer biomarker. (+info)
Interstitial flow through the internal elastic lamina affects shear stress on arterial smooth muscle cells.
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Interstitial flow through the tunica media of an artery wall in the presence of the internal elastic lamina (IEL), which separates it from the subendothelial intima, has been studied numerically. A two-dimensional analysis applying the Brinkman model as the governing equation for the porous media flow field was performed. In the numerical simulation, the IEL was modeled as an impermeable barrier to water flux, except for the fenestral pores, which were uniformly distributed over the IEL. The tunica media was modeled as a heterogeneous medium composed of a periodic array of cylindrical smooth muscle cells (SMCs) embedded in a fiber matrix simulating the interstitial proteoglycan and collagen fibers. A series of calculations was conducted by varying the physical parameters describing the problem: the area fraction of the fenestral pore (0. 001-0.036), the diameter of the fenestral pore (0.4-4.0 microm), and the distance between the IEL and the nearest SMC (0.2-0.8 microm). The results indicate that the value of the average shear stress around the circumference of the SMC in the immediate vicinity of the fenestral pore could be as much as 100 times greater than that around an SMC in the fully developed interstitial flow region away from the IEL. These high shear stresses can affect SMC physiological function. (+info)
Using database matches with for HMMGene for automated gene detection in Drosophila.
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The application of the gene finder HMMGene to the Adh region of the Drosophila melanogaster is described, and the prediction results are analyzed. HMMGene is based on a probabilistic model called a hidden Markov model, and the probabilistic framework facilitates the inclusion of database matches of varying degrees of certainty. It is shown that database matches clearly improve the performance of the gene finder. For instance, the sensitivity for coding exons predicted with both ends correct grows from 62% to 70% on a high-quality test set, when matches to proteins, cDNAs, repeats, and transposons are included. The specificity drops more than the sensitivity increases when ESTs are used. This is due to the high noise level in EST matches, and it is discussed in more detail why this is and how it might be improved. (+info)
Advection and diffusion of substances in biological tissues with complex vascular networks.
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For highly diffusive solutes the kinetics of blood-tissue exchange is only poorly represented by a model consisting of sets of independent parallel capillary-tissue units. We constructed a more realistic multicapillary network model conforming statistically to morphometric data. Flows through the tortuous paths in the network were calculated based on constant resistance per unit length throughout the network and the resulting advective intracapillary velocity field was used as a framework for describing the extravascular diffusion of a substance for which there is no barrier or permeability limitation. Simulated impulse responses from the system, analogous to tracer water outflow dilution curves, showed flow-limited behavior over a range of flows from about 2 to 5 ml min(-1) g(-1), as is observed for water in the heart in vivo. The present model serves as a reference standard against which to evaluate computationally simpler, less physically realistic models. The simulated outflow curves from the network model, like experimental water curves, were matched to outflow curves from the commonly used axially distributed models only by setting the capillary wall permeability-surface area (PS) to a value so artifactually low that it is incompatible with the experimental observations that transport is flow limited. However, simple axially distributed models with appropriately high PSs will fit water outflow dilution curves if axial diffusion coefficients are set at high enough values to account for enhanced dispersion due to the complex geometry of the capillary network. Without incorporating this enhanced dispersion, when applied to experimental curves over a range of flows, the simpler models give a false inference that there is recruitment of capillary surface area with increasing flow. Thus distributed models must account for diffusional as well as permeation processes to provide physiologically appropriate parameter estimates. (+info)
Facilitated diffusion and membrane permeation of fatty acid in albumin solutions.
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Facilitated transport is characteristic of most living systems, and usually involves a series of consecutive adjacent transfer regions, each having different transport properties. As a first step in the analysis of the multiregional problem, we consider in a single unstirred layer the facilitated diffusion of fatty acid (F) in albumin (A) solution under conditions of slow versus rapid association-dissociation, accounting for differing diffusivities of the albumin-fatty acid complex (AF). Diffusion gradients become established in an unstirred layer between a source of constant concentration of A, AF, and F in equilibrium, and a membrane permeable to F. The posited system does not reduce to a thin- or thick-layer approximation. The transient state is prolonged by slower on/off binding rates and by increasing the thickness of the unstirred layer. Solutions to transient and steady state depend upon the choice of boundary conditions, especially for thin regions. When there are two regions (each with its specific binding protein) separated by a permeable membrane, the steady-state fluxes and concentration profiles depend on the rates of association and dissociation reactions, on the diffusion coefficients, local consumption rates, and on the membrane permeability. Sensitivity analysis reveals the relative importance of these mechanisms. (+info)