Vitamin binding

Abstract: Receptor-mediated endocytosis is an essential mechanism for the transport of a variety of macromolecules into cells as well as across epithelia (Mukherjee et al. 1997). Clathrin-mediated endocytosis is the predominant pathway for macromolecule uptake along epithelia (Mukherjee et al. 1997; Schmid, 1997; Marshansky et al. 1997; Christensen & Birn, 2002). An example of clathrin-mediated endocytosis is the uptake of filtered proteins by renal proximal tubular cells (Gekle et al. 1997; Gekle, 1998; Christensen & Birn, 2002). Renal proximal tubular protein reabsorption is of major importance because it prevents the loss of vitamins, hormones and amino acids (Christensen & Willnow, 1999), but at the same time it can induce tubulointerstitial inflammation and fibrosis (Burton & Harris, 1996; Jerums et al. 1997; Gekle, 1998). The mechanisms leading to protein-induced inflammation and fibrosis involve the expression of mediators such as RANTES, monocyte chemoattractant protein-1 (MCP-1), nuclear factor-κB (NF-κB) and mitogenic pathways (Burton & Harris, 1996; Dixon & Brunskill, 1999; Wang et al. 1999; Guijarro & Egido, 2001). One of the major receptors for proximal tubular protein endocytosis is the megalin- cubilin complex, which serves as a scavenger receptor (Christensen & Willnow, 1999) and includes reabsorption of albumin (Birn et al. 2000; Zhai et al. 2000; Verroust & Kozyraki, 2001), which binds to cubilin and megalin. Thus, the megalin-cubilin pathway can be monitored using albumin. The megalin-cubilin complex accepts a variety of ligands other than albumin (Christensen & Willnow, 1999; Nykjaer et al. 1999, 2001), including vitamin binding proteins, hormone binding proteins, hormones and light chains. In the case of vitamin D this pathway seems to be necessary for the final activation of the vitamin (Christensen & Willnow, 1999). Consequently, impairment of the megalin-cubilin pathway could lead to the urinary excretion of these proteins. Reduced megalin expression has been reported for Dent's disease, autosomal-dominant polycystic kidney disease and following exposure to aristocholic acid as reviewed by Verroust et al. (2002). The proximal-tubule-derived opossum kidney (OK) cell line has been shown to be a suitable model system for the study of megalin-cubilin-mediated, clathrin-dependent endocytosis of albumin (Dixon & Brunskill, 1999; Gekle et al. 1999; Zhai et al. 2000). As we have shown before, albumin endocytosis in OK cells can be inhibited by ligands for megalin (receptor-associated protein; RAP), cubilin (intrinsic factor) as well as by anti-megalin and anti-cubilin antibodies (Zhai et al. 2000). Thus, we used this cell line in order to determine the potential impact of TGF-β1 exposure on megalin-cubilin-mediated endocytosis. TGF-β1 is a member of a superfamily of multifunctional cytokines involved in a wide array of biological activities, such as development and blood vessel modelling (Schiffer et al. 2000). In addition, TGF-β1 plays an important role in pathological processes, such as induction of extracellular matrix protein synthesis, compensatory renal growth, proximal tubular hypertrophy and epithelial- mesenchymal transdifferentiation (Kanda et al. 1993; Wolf et al. 1993; Border & Noble, 1994; Eickelberg et al. 1999). Epithelial- mesenchymal transdifferentiation can lead to a loss of typical epithelial features such as reabsorption or secretory transport and therefore not only support fibrosis but also decrease tubular function. Enhanced levels of TGF-β1 in pathophysiological conditions derive, for example, from upregulated synthesis in proximal tubular cells exposed to nephritogenic conditions (Van Kooten et al. 1999; Wolf et al. 2001) or from infiltrating macrophages. Various studies have shown that enhanced levels of TGF-β1 correlate positively with the amount of urinary protein excretion, i.e. proteinuria and albuminuria (Bottinger & Bitzer, 2002). Interestingly, a gene expression profiling approach revealed that TGF-β1 can affect the expression of several genes (either induction or repression) involved in endocytosis (Zavadil et al. 2001). Proximal tubular cells are responsive to TGF-β1 (Wolf et al. 1993; Park et al. 2001). It has also been shown that proximal tubular cells produce TGF-β1 (Van Kooten et al. 1999; Wolf et al. 2001). Thus, the entire signalling cascade for TGF-β1 is present in the proximal tubule. Although altered TGF-β1 homeostasis is associated with renal diseases that lead to proteinuria and, furthermore, enhanced proximal tubular protein load can induce TGF-β1 formation in proximal tubular cells, it is not clear whether TGF-β1per se can affect proximal tubular protein endocytosis (Abbate & Remuzzi, 1999; Van Kooten et al. 1999). The aim of our present study was to determine whether exposure to TGF-β1 has an effect on megalin-cubilin-mediated protein uptake in a suitable cell culture system devoid of systemic factors.

Abstract: Chromium (Cr) being multifarious industrial used element, is considered a potential environmental threat. Cr found to be a prospective water and soil pollutant, and thus it is a current area of concern. Oilseed rape (Brassica napus L.) is well known as a major source of edible oil around the globe. Due to its higher growth, larger biomass and capability to uptake toxic materials B. napus is considered a potential candidate plant against unfavorable conditions. To date, no study has been done that described the Cr and GSH mechanism at RNA-Seq level. Both digital gene expression (DGE) and transcriptome profile analysis (TPA) approaches had opened new insights to uncover the several number of genes related to Cr stress and GSH alleviating mechanism in two leading cultivars (ZS 758 and Zheda 622) of B. napus plants. Data showed that Cr inhibited KEGG pathways i.e. stilbenoid, diarlyheptanoid and gingerol biosynthesis; limonene and pentose degradation and glutathione metabolism in ZS 758; and ribosome and glucosinolate biosynthesis in Zheda-622. On the other hand, vitamin B6, tryptophan, sulfur, nitrogen and fructose and manose metabolisms were induced in ZS 758, and zeatin biosynthesis, linoleic acid metabolism, arginine and proline metabolism, and alanine, asparate and glutamate metabolism pathways in Zheda 622. Cr increased the TFs that were related to hydralase activity, antioxidant activity, catalytic activity phosphatase and pyrophosphatase activity in ZS 758, and vitamin binding and oxidoreductase activity in Zheda 622. Cr also up-regulated the promising proteins related to intracellular membrane bounded organelles, nitrile hyrdatase activity, cytoskeleton protein binding and stress response. It also uncovered, a novel Cr-responsive protein (CL2535.Contig1_All) that was statistically increased as compared to control and GSH treated plants. Exogenously applied GSH successfully not only recovered the changes in metabolic pathways but also induced cysteine and methionine metabolism in ZS 758 and ubiquinone and other terpenoid-quinone biosynthesis pathways in Zheda 622. Furthermore, GSH increased the level of TFs i.e. the gene expression of antioxidant and catalytic activities, iron ion binding and hydrolase activity as compared with Cr. Moreover, results pointed out a novel GSH responsive protein (CL827.Contig3_All) whose expression was found to be significantly increased when compared than Cr stress. Results further delineated that GSH induced TFs such as glutathione disulphide oxidoreducatse and aminoacyl-tRNA ligase activity, and beta glucosidase activity in ZS 758. Similarly in Zheda 622, GSH induced the TFs for instance DNA binding and protein dimerization activity. GSH also highlighted the proteins that were involved in transportation, photosynthesis process, RNA polymerase activity, and against the metal toxicity. These results indicated that cultivar ZS 758 had better metabolism and showed higher tolerance against Cr toxicity. The responses of ZS 758 and Zheda 622 differed considerably at both physiological and transcriptional level. Moreover, RNA-Seq method explored the hazardous behavior of Cr as well as GSH up-regulating mechanism by activating plant metabolism, stress responsive genes, TFs and protein encyclopedia.

Abstract: Introduction This egg type is, to us, a familiar and hence seemingly prosaic structure suitable for the breakfast table. It is, in reality, the most marvelous single ‘invention’ in the whole history of vertebrate life. Alfred S. Romer (1968, p. 183) The relationship between the nutrient content of the material diet and egg production and hatchability has been studied for many nutrients in the domestic fowl ( Gallus gallus ) (Beer, 1969; Naber, 1979; Anon, 1979). The confounding influence of various strains, interacting nutrients, antibiotics, husbandry, and a host of other variables on this relationship continues to be the focus of research papers. There are thousands of birds and egg-laying reptiles, however, for which there is virtually no such information and on which there is little chance of doing the appropriate dietary studies. Some of these species are endangered, and our only hope for their continued survival may be through captive breeding programs where successful reproduction may depend upon manufactured and supplemented diets. To what extent can nutritional knowledge of a few domestic species be applied to the variety of species that exist? As yet, this question cannot be answered. However, this review will argue that a knowledge of the evolutionarily conserved processes that link maternal diet with egg quality, can provide a basis for evaluating the diverse nutritional needs of other species even when few individuals are available for study. In particular, there are a number of proteins whose function is to transport specific nutrients to the oocyte; these protein-nutrient complexes become yolk constituents for later use by the embryo. The amounts, and relative saturation, of these proteins may indicate the specific nutrient needs of the embryo and the nutrient status of the mother respectively.

Abstract: Vitamins are typical ligands that play critical roles in various metabolic processes. The accurate identification of the vitamin-binding residues solely based on a protein sequence is of significant importance for the functional annotation of proteins, especially in the post-genomic era, when large volumes of protein sequences are accumulating quickly without being functionally annotated. In this paper, a new predictor called TargetVita is designed and implemented for predicting protein-vitamin binding residues using protein sequences. In TargetVita, features derived from the position-specific scoring matrix (PSSM), predicted protein secondary structure, and vitamin binding propensity are combined to form the original feature space; then, several feature subspaces are selected by performing different feature selection methods. Finally, based on the selected feature subspaces, heterogeneous SVMs are trained and then ensembled for performing prediction. The experimental results obtained with four separate vitamin-binding benchmark datasets demonstrate that the proposed TargetVita is superior to the state-of-the-art vitamin-specific predictor, and an average improvement of 10% in terms of the Matthews correlation coefficient (MCC) was achieved over independent validation tests. The TargetVita web server and the datasets used are freely available for academic use at http://csbio.njust.edu.cn/bioinf/TargetVita or http://www.csbio.sjtu.edu.cn/bioinf/TargetVita .