The footprint of antibody bound to pig cells: evidence of complex surface topology

The disaccharide Gal(alpha)1-3Gal is found on more than 45 different molecules on the endothelium of porcine cells and has recently attracted considerable interest, being the major target recognized by xenoreactive antibodies. In this study, the distribution and topology of Gal(alpha)1-3Gal on porcine endothelial cells was examined to access whether some Gal(alpha)1-3Gal-containing molecules might be preferentially recognized by antibodies binding to Gal(alpha)1-3Gal. Thirteen percent of the Gal(alpha)1-3Gal was found on glycolipid and 87% on glycoproteins. Of all the glycoproteins and glycolipids containing Gal(alpha)1-3Gal, two molecules, fibronectin and the integrin beta1 subunit, were most intensely labeled by galactose oxidase, suggesting that these molecules may be preferentially exposed on the apical surface of the endothelium. Binding of anti-Gal(alpha)1-3Gal antibodies to endothelial cell surfaces significantly diminished labeling of fibronectin and the integrin beta1 subunit by galactose oxidase, indicating that these glycoproteins are targets for the antibodies when binding to intact porcine cells.     

A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis

For tightly linked loci, cosegregation may lead to nonrandom associations between alleles in a population. Because of its evolutionary relationship with linkage, this phenomenon is called linkage disequilibrium. Today, linkage disequilibrium-based mapping has become a major focus of recent genome research into mapping complex traits. In this article, we present a new statistical method for mapping quantitative trait loci (QTL) of additive, dominant, and epistatic effects in equilibrium natural populations. Our method is based on haplotype analysis of multilocus linkage disequilibrium and exhibits two significant advantages over current disequilibrium mapping methods. First, we have derived closed-form solutions for estimating the marker-QTL haplotype frequencies within the maximum-likelihood framework implemented by the EM algorithm. The allele frequencies of putative QTL and their linkage disequilibria with the markers are estimated by solving a system of regular equations. This procedure has significantly improved the computational efficiency and the precision of parameter estimation. Second, our method can detect marker-QTL disequilibria of different orders and QTL epistatic interactions of various kinds on the basis of a multilocus analysis. This can not only enhance the precision of parameter estimation, but also make it possible to perform whole-genome association studies. We carried out extensive simulation studies to examine the robustness and statistical performance of our method. The application of the new method was validated using a case study from humans, in which we successfully detected significant QTL affecting human body heights. Finally, we discuss the implications of our method for genome projects and its extension to a broader circumstance. The computer program for the method proposed in this article is available at the webpage http://www.ifasstat.ufl.edu/genome/~LD.     

GIPC and GAIP form a complex with TrkA: a putative link between G protein and receptor tyrosine kinase pathways

NGF initiates the majority of its neurotrophic effects by promoting the activation of the tyrosine kinase receptor TrkA. Here we describe a novel interaction between TrkA and GIPC, a PDZ domain protein. GIPC binds to the juxtamembrane region of TrkA through its PDZ domain. The PDZ domain of GIPC also interacts with GAIP, an RGS (regulators of G protein signaling) protein. GIPC and GAIP are components of a G protein-coupled signaling complex thought to be involved in vesicular trafficking. In transfected HEK 293T cells GIPC, GAIP, and TrkA form a coprecipitable protein complex. Both TrkA and GAIP bind to the PDZ domain of GIPC, but their binding sites within the PDZ domain are different. The association of endogenous GIPC with the TrkA receptor was confirmed by coimmunoprecipitation in PC12 (615) cells stably expressing TrkA. By immunofluorescence GIPC colocalizes with phosphorylated TrkA receptors in retrograde transport vesicles located in the neurites and cell bodies of differentiated PC12 (615) cells. These results suggest that GIPC, like other PDZ domain proteins, serves to cluster transmembrane receptors with signaling molecules. When GIPC is overexpressed in PC12 (615) cells, NGF-induced phosphorylation of mitogen-activated protein (MAP) kinase (Erk1/2) decreases; however, there is no effect on phosphorylation of Akt, phospholipase C-gamma1, or Shc. The association of TrkA receptors with GIPC and GAIP plus the inhibition of MAP kinase by GIPC suggests that GIPC may provide a link between TrkA and G protein signaling pathways.     

Three-dimensional ultrastructural analysis of RNA distribution within germinal granules of Xenopus.

The germ plasm is a specialized region of oocyte cytoplasm that contains determinants of germ cell fate. In Xenopus oocytes, the germ plasm is a part of the METRO region of mitochondrial cloud. It contains the germinal granules and a variety of coding and noncoding RNAs that include Xcat2, Xlsirts, Xdazl, DEADSouth, Xpat, Xwnt11, fatVg, B7/Fingers, C10/XFACS, and mitochondrial large and small rRNA. We analyzed the distribution of these 11 different RNAs within the various compartments of germ plasm during Xenopus oogenesis and development by using whole-mount electron microscopy in situ hybridization. Serial EM sections were used to reconstruct a three-dimensional image of germinal granule distribution within the METRO region of the cloud and the distribution of RNAs on the granules in oocytes and embryos. We found that, in the oocytes, the majority of RNAs were associated either with the precursor of germinal granules or with the germ plasm matrix. Only Xcat2, Xpat, and DEADSouth RNAs were associated with the mature germinal granules in oocytes, while only Xcat2 and Xpat were associated with germinal granules in embryos. However, Xcat2 was the only RNA that was consistently sequestered inside the germinal granules, while the others were located on the periphery. Xdazl, which functions in germ cell migration/formation, was detected on the matrix between granules. Later in development, Xcat2 mRNA was released from the germinal granules. This coincides with the timing of its translational derepression. These results demonstrate that there is a dynamic three-dimensional architecture to the germinal granules that changes during oogenesis and development. They also indicate that association of specific RNAs with the germinal granules is not a prerequisite for their serving a germ cell function; however, it may be related to their state of translational repression.     

Analysis of genetic effects of major genes and polygenes on quantitative traits. II. Genetic models for seed traits of crops

Genetic models for quantitative seed traits with effects of several major genes and polygenes, as well as their GE interaction, were proposed. Mixed linear model approaches were suggested for analyzing the genetic models. Monte Carlo simulations were conducted to evaluate unbiasedness and efficiency for estimating fixed effects and variance components of the embryo and the endosperm models, including effects of a major gene from an unbalanced modified diallel mating design with nine parents, respectively. Simulation results showed that estimates of generalized least squares (GLS) were unbiased and efficient, while those of ordinary least squares (OLS) were almost as good as GLS. Minimum norm quadratic unbiased estimation (MINQUE) could obtain unbiased estimates of the variance components. It was also suggested that precision of MINQUE estimation would be improved with augmentation of experimental size. Data from a modified diallel design in upland cotton ( Gossypium hirsutum L.) were used as a worked example to illustrate the parameter estimation.     

Analysis of genetic effects of major genes and polygenes on quantitative traits I. Genetic model for diploid plants and animals

A genetic model was proposed to simultaneously investigate genetic effects of both polygenes and several single genes for quantitative traits of diploid plants and animals. Mixed linear model approaches were employed for statistical analysis. Based on two mating designs, a full diallel cross and a modified diallel cross including F₂, Monte Carlo simulations were conducted to evaluate the unbiasedness and efficiency of the estimation of generalized least squares (GLS) and ordinary least squares (OLS) for fixed effects and of minimum norm quadratic unbiased estimation (MINQUE) and Henderson III for variance components. Estimates of MINQUE (1) were unbiased and efficient in both reduced and full genetic models. Henderson III could have a large bias when used to analyze the full genetic model. Simulation results also showed that GLS and OLS were good methods to estimate fixed effects in the genetic models. Data on Drosophila melanogaster from Gilbert were used as a worked example to demonstrate the parameter estimation. Received: 11 November 2000 / Accepted: 2 May 2001     

The dopamine D1 receptor is a critical mediator for cocaine-induced gene expression

The dopamine D1 receptor plays a major role in mediating behavioral responses to cocaine administration. The time course for the acquisition and the relative stability for the expression of behavioral responses suggest the involvement of enduring neuroadaptations in response to repeated cocaine exposure. Changes in gene expression through the D1 receptors may accompany and mediate the development of such neuroadaptations to repeated cocaine stimulation. To test this possibility, we systematically compared the expression of the fos and Jun family immediate early genes in the nucleus accumbens and caudoputamen in D1 receptor mutant and wild-type control mice after acute and repeated cocaine exposure. Moreover, we compared the expression of three molecules that have been implicated in mediating the actions of cocaine, Galphaolf, beta-catenin and brain-derived neurotrophic factor, in the two groups of mice before and after cocaine administration. We found that there is a lack of induction of c-Fos, FosB, Fra-2 and JunB by acute cocaine exposure, and of DeltaFosB by repeated cocaine administration in both the NAc and CPu of D1 receptor mutant mice compared with wild-type control mice. Moreover, the D1 receptor is differentially required for mediating Galphaolf, beta-catenin and BDNF expression in the NAc and CPu upon cocaine exposure. These results suggest that the D1 receptor is a critical mediator for cocaine-induced expression of these genes.     

cAMP inhibition of Akt is mediated by activated and phosphorylated Rap1b

Rap1b has been implicated in the transduction of the cAMP mitogenic signal. Rap1b is phosphorylated and activated by cAMP, and its expression in cells where cAMP is mitogenic leads to an increase in G(1)/S phase entry and tumor formation. The PCCL3 thyroid follicular cells represent a differentiated and physiologically relevant system that requires thyrotropin (TSH), acting via cAMP, for a full mitogenic response. In this model system, cAMP stimulation of DNA synthesis requires activation and phosphorylation of Rap1b by the cAMP-dependent protein kinase A (PKA). This scenario presents the challenge of identifying biochemical processes involved in the phosphorylation-dependent Rap1b mitogenic action. In thyroid cells, Akt has been implicated in the stimulation of cell proliferation by TSH and cAMP. However, the mechanism(s) by which cAMP regulates Akt activity remains unclear. In this study we show that in PCCL3 cells 1) TSH inhibits Akt activity via cAMP and PKA; 2) Rap1b is required for cAMP inhibition of Akt; and 3) transduction of the cAMP signal into Akt requires activation as well as phosphorylation of Rap1b by PKA.     

Molecular determinants of the hanatoxin binding in voltage-gated K+-channel drk1

The carboxyl terminus of S3 segment (S3(C)) in voltage-gated potassium channels was proposed to bear the binding site for gating modifier toxins like Hanatoxin and a helical secondary structural arrangement was suggested. Due to the lack of complete structure in high resolution for such a channel molecule, no further direct experimental data to elucidate the mechanism for their binding conformations could thus far be derived. In order to examine the putative three-dimensional structure of S3(C) and to illustrate the residues required for Hanatoxin binding, molecular simulation and docking were performed, based on the solution structure of Hanatoxin and the structural information from lysine-scanning results for S3(C) fragment. From our results, it is indicated that both hydrophobic and electrostatic interactions are utilized to stabilize the toxin binding. Detailed docking residues and appropriate orientation for binding regarding hydrophobic/-philic environments are also described. Compared with the functional data proposed by previous studies, the helical structural arrangement for the C-terminus of S3 segment in voltage-gated potassium channels can therefore be further emphasized.