The Signaling State of Orange Carotenoid Protein

Orange carotenoid protein (OCP) is the photoactive protein that is responsible for high light tolerance in cyanobacteria. We studied the kinetics of the OCP photocycle by monitoring changes in its absorption spectrum, intrinsic fluorescence, and fluorescence of the Nile red dye bound to OCP. It was demonstrated that all of these three methods provide the same kinetic parameters of the photocycle, namely, the kinetics of OCP relaxation in darkness was biexponential with a ratio of two components equal to 2:1 independently of temperature. Whereas the changes of the absorption spectrum of OCP characterize the geometry and environment of its chromophore, the intrinsic fluorescence of OCP reveals changes in its tertiary structure, and the fluorescence properties of Nile red indicate the exposure of hydrophobic surface areas of OCP to the solvent following the photocycle. The results of molecular-dynamics studies indicated the presence of two metastable conformations of 3′-hydroxyechinenone, which is consistent with characteristic changes in the Raman spectra. We conclude that rotation of the β-ionylidene ring in the C-terminal domain of OCP could be one of the first conformational rearrangements that occur during photoactivation. The obtained results suggest that the photoactivated form of OCP represents a molten globule-like state that is characterized by increased mobility of tertiary structure elements and solvent accessibility.     

P2Y1 and P2Y13 purinergic receptors mediate Ca2+ signaling and proliferative responses in pulmonary artery vasa vasorum endothelial cells

Extracellular ATP and ADP have been shown to exhibit potent angiogenic effects on pulmonary artery adventitial vasa vasorum endothelial cells (VVEC). However, the molecular signaling mechanisms of extracellular nucleotide-mediated angiogenesis remain not fully elucidated. Since elevation of intracellular Ca(2+) concentration ([Ca(2+)](i)) is required for cell proliferation and occurs in response to extracellular nucleotides, this study was undertaken to delineate the purinergic receptor subtypes involved in Ca(2+) signaling and extracellular nucleotide-mediated mitogenic responses in VVEC. Our data indicate that stimulation of VVEC with extracellular ATP resulted in the elevation of [Ca(2+)](i) via Ca(2+) influx through plasma membrane channels as well as Ca(2+) mobilization from intracellular stores. Moreover, extracellular ATP induced simultaneous Ca(2+) responses in both cytosolic and nuclear compartments. An increase in [Ca(2+)](i) was observed in response to a wide range of purinergic receptor agonists, including ATP, ADP, ATPγS, ADPβS, UTP, UDP, 2-methylthio-ATP (MeSATP), 2-methylthio-ADP (MeSADP), and BzATP, but not adenosine, AMP, diadenosine tetraphosphate, αβMeATP, and βγMeATP. Using RT-PCR, we identified mRNA for the P2Y1, P2Y2, P2Y4, P2Y13, P2Y14, P2X2, P2X5, P2X7, A1, A2b, and A3 purinergic receptors in VVEC. Preincubation of VVEC with the P2Y1 selective antagonist MRS2179 and the P2Y13 selective antagonist MRS2211, as well as with pertussis toxin, attenuated at varying degrees agonist-induced intracellular Ca(2+) responses and activation of ERK1/2, Akt, and S6 ribosomal protein, indicating that P2Y1 and P2Y13 receptors play a major role in VVEC growth responses. Considering the broad physiological implications of purinergic signaling in the regulation of angiogenesis and vascular homeostasis, our findings suggest that P2Y1 and P2Y13 receptors may represent novel and specific targets for treatment of pathological vascular remodeling involving vasa vasorum expansion.     

Modulation of Hyaluronan Synthase Activity in Cellular Membrane Fractions

Hyaluronan (HA), the only non-sulfated glycosaminoglycan, is involved in morphogenesis, wound healing, inflammation, angiogenesis, and cancer. In mammals, HA is synthesized by three homologous HA synthases, HAS1, HAS2, and HAS3, that polymerize the HA chain using UDP-glucuronic acid and UDP-N-acetylglucosamine as precursors. Since the amount of HA is critical in several pathophysiological conditions, we developed a non-radioactive assay for measuring the activity of HA synthases (HASs) in eukaryotic cells and addressed the question of HAS activity during intracellular protein trafficking. We prepared three cellular fractions: plasma membrane, cytosol (containing membrane proteins mainly from the endoplasmic reticulum and Golgi), and nuclei. After incubation with UDP-sugar precursors, newly synthesized HA was quantified by polyacrylamide gel electrophoresis of fluorophore-labeled saccharides and high performance liquid chromatography. This new method measured HAS activity not only in the plasma membrane fraction but also in the cytosolic membranes. This new technique was used to evaluate the effects of 4-methylumbeliferone, phorbol 12-myristate 13-acetate, interleukin 1β, platelet-derived growth factor BB, and tunicamycin on HAS activities. We found that HAS activity can be modulated by post-translational modification, such as phosphorylation and N-glycosylation. Interestingly, we detected a significant increase in HAS activity in the cytosolic membrane fraction after tunicamycin treatment. Since this compound is known to induce HA cable structures, this result links HAS activity alteration with the capability of the cell to promote HA cable formation.Hyaluronan (HA)³ is the only non-sulfated linear polymer belonging to the family of glycosaminoglycans (GAGs). HA is an unbranched polymer of alternating GlcNAc and GlcUA residues linked by alternate β(1→4) and β(1→3) bonds. Native HA is typically larger than other GAGs, reaching molecular mass values between 10⁶ and 10⁷ Da.HA is a major component of extracellular matrices and in pericellular spaces, particularly in tissues with rapid cell proliferation and cell migration (1). Through interactions with cell surface receptors, notably CD44 and RHAMM (receptor for HA-mediated motility), HA has important roles in regulating cell behavior, including signal transduction, cell adhesion, proliferation, migration, and differentiation (2). Recently, novel interactions involving HA and Toll-like receptors 4 and 2 have been described that have important roles in inflammation (3, 4). Moreover, HA has been implicated in morphogenesis (5–8), wound healing (9), angiogenesis (10), malignancies, cancer growth, and tumor invasion (11).In mammals, HA is normally synthesized at the plasma membrane and extruded directly into the extracellular space by three isoforms of HA synthases (HASs), HAS1, -2, and -3. The three HAS isoforms differ in tissue distribution, regulation, and enzymatic properties (12); nevertheless, they are similar in amino acid sequences and molecular structures.HA biosynthesis is under the control of a wide variety of cytokines and growth factors (13). The changes in HA synthesis can be related to HAS mRNA expression (14), to availability of the UDP-sugar precursors (15, 16), or to modulation by phosphorylation of HAS (17–19) in response to cytokines and growth factors. Moreover, HA chain synthesis can be controlled by additional mechanisms, such as cell type, intracellular environment, or HAS accessory proteins (20). Cultures of smooth muscle cells isolated from human colon increase synthesis of HA after treatment with a viral mimetic molecule (poly(I-C)) (21). The HA is organized into novel cable-like structures, and their synthesis may be initiated in the perinuclear and/or the endoplasmic reticulum (ER) membranes (22). Furthermore, HA interstitial deposition is correlated with inflammatory processes (23, 24) in which HA-CD44 interactions stimulate leukocyte adhesion in order to generate an inflammatory response (25).Cytokines and growth factors, such as IL-1β and platelet-derived growth factor BB (PDGF-BB), as well as 4-methylumbeliferone (4-MU) and the tumor promoter phorbol 12-myristate 13-acetate (PMA), also modulate HA synthesis (26–29). In order to elucidate how these different effectors affect HAS activity, it is important to purify and solubilize the HAS enzymes as previously underlined in studies on eukaryotic cell lines (30). In this context, Itano and Kimata (31) used a mammalian transient expression system to characterize the three different HAS isoforms in either cells or cellular membrane extracts. On the other hand, Spicer (32) described three relatively simple procedures for the detection of HA synthase activity in cultured mammalian cell lines. In all of these studies, the enzyme activity was measured by incubating cellular membrane extracts with radiolabeled UDP-sugar precursors, and the final analysis of the products was done by liquid scintillation counting. Various other strategies and methods can be used to determine the HA biosynthetic capacity of cells, although they are always based on the use of radiolabeled UDP-sugar precursors (33–35).In our previous studies, we described methods of polyacrylamide gel electrophoresis of fluorophore-labeled saccharides (PAGEFS) and high performance liquid chromatography (HPLC) for the analysis of disaccharides derived from HA and chondroitin sulfate (33–38). In order to improve the sensitivity of this method, a derivatization with 2-aminoacridone (AMAC) was done, followed by fluorescence detection (39). In this study, we modified this method to address the question of localization of HAS activity during intracellular trafficking, since HA has been detected inside cells in previous studies (40–42). This new non-radioactive method was used to quantify HAS activity on cell membranes fractionated by sucrose gradient methods. To test the robustness of our approach, we analyzed the effect of 4-MU, PMA, IL-1β, PDGF-BB, and tunicamycin on cell cultures. In particular, we found that tunicamycin induced an increase of HA synthesis in both plasma and internal cell membranes in EVC cells, whereas it increased HA synthesis only in the internal cell membranes in the OVCAR-3 cells. The results suggest that post-translational modulation of HAS activity is responsible for the increased HA synthesis inside the cells. Moreover, since tunicamycin induced HA cable structures in the OVCAR-3 cells, we correlated the altered intracellular HAS activity with the capability to promote HA cable formation.     

Glycosaminoglycans: key players in cancer cell biology and treatment

Glycosaminoglycans are natural heteropolysaccharides that are present in every mammalian tissue. They are composed of repeating disaccharide units that consist of either sulfated or non-sulfated monosaccharides. Their molecular size and the sulfation type vary depending on the tissue, and their state either as part of proteoglycan or as free chains. In this regard, glycosaminoglycans play important roles in physiological and pathological conditions. During recent years, cell biology studies have revealed that glycosaminoglycans are among the key macromolecules that affect cell properties and functions, acting directly on cell receptors or via interactions with growth factors. The accumulated knowledge regarding the altered structure of glycosaminoglycans in several diseases indicates their importance as biomarkers for disease diagnosis and progression, as well as pharmacological targets. This review summarizes how the fine structural characteristics of glycosaminoglycans, and enzymes involved in their biosynthesis and degradation, are involved in cell signaling, cell function and cancer progression. Prospects for glycosaminoglycan-based therapeutic targeting in cancer are also discussed.     

Evaluation of the Possible Transmission of BSE and Scrapie to Gilthead Sea Bream (Sparus aurata)

In transmissible spongiform encephalopathies (TSEs), a group of fatal neurodegenerative disorders affecting many species, the key event in disease pathogenesis is the accumulation of an abnormal conformational isoform (PrP^Sc) of the host-encoded cellular prion protein (PrP^C). While the precise mechanism of the PrP^C to PrP^Sc conversion is not understood, it is clear that host PrP^C expression is a prerequisite for effective infectious prion propagation. Although there have been many studies on TSEs in mammalian species, little is known about TSE pathogenesis in fish. Here we show that while gilthead sea bream (Sparus aurata) orally challenged with brain homogenates prepared either from a BSE infected cow or from scrapie infected sheep developed no clinical prion disease, the brains of TSE-fed fish sampled two years after challenge did show signs of neurodegeneration and accumulation of deposits that reacted positively with antibodies raised against sea bream PrP. The control groups, fed with brains from uninfected animals, showed no such signs. Remarkably, the deposits developed much more rapidly and extensively in fish inoculated with BSE-infected material than in the ones challenged with the scrapie-infected brain homogenate, with numerous deposits being proteinase K-resistant. These plaque-like aggregates exhibited congophilia and birefringence in polarized light, consistent with an amyloid-like component. The neurodegeneration and abnormal deposition in the brains of fish challenged with prion, especially BSE, raises concerns about the potential risk to public health. As fish aquaculture is an economically important industry providing high protein nutrition for humans and other mammalian species, the prospect of farmed fish being contaminated with infectious mammalian PrP^Sc, or of a prion disease developing in farmed fish is alarming and requires further evaluation.     

Combined therapy with cyclophosphamide and DNA preparation inhibits the tumor growth in mice

Background

When cyclophosphamide and preparations of fragmented exogenous genomic double stranded DNA were administered in sequence, the regressive effect on the tumor was synergic: this combined treatment had a more pronounced effect than cyclophosphamide alone. Our further studies demonstrated that exogenous DNA stimulated the maturation and specific activities of dendritic cells. This suggests that cyclophosphamide, combined with DNA, leads to an immune response to the tumors that were grafted into the subjects post treatment.

Methods

Three-month old CBA/Lac mice were used in the experiments. The mice were injected with cyclosphamide (200 mkg per 1 kg body weight) and genomic DNA (of human, mouse or salmon sperm origin). The DNA was administered intraperitoneally or subcutaneously. After 23 to 60 days, one million tumor cells were intramuscularly grafted into the mice. In the final experiment, the mice were pre-immunized by subcutaneous injections of 20 million repeatedly thawed and frozen tumor cells. Changes in tumor growth were determined by multiplying the three perpendicular diameters (measured by caliper). Students' t-tests were used to determine the difference between tumor growth and average survival rate between the mouse groups and the controls.

Results

An analysis of varying treatments with cyclophosphamide and exogenous DNA, followed by tumor grafting, provided evidence that this combined treatment had an immunizing effect. This inhibitory effect in mice was analyzed in an experiment with the classical immunization of a tumor homogenate. The strongest inhibitory action on a transplanted graft was created through the following steps: cyclophosphamide at 200 mg/kg of body weight administered as a pretreatment; 6 mg fragmented exogenous DNA administered over the course of 3 days; tumor homogenate grafted 10 days following the final DNA injection.

Conclusion

Fragmented exogenous DNA injected with cyclophosphamide inhibits the growth of tumors that are grafted to mice after this combined treatment.     

Applications of InterPro in protein annotation and genome analysis

The applications of InterPro span a range of biologically important areas that includes automatic annotation of protein sequences and genome analysis. In automatic annotation of protein sequences InterPro has been utilised to provide reliable characterisation of sequences, identifying them as candidates for functional annotation. Rules based on the InterPro characterisation are stored and operated through a database called RuleBase. RuleBase is used as the main tool in the sequence database group at the EBI to apply automatic annotation to unknown sequences. The annotated sequences are stored and distributed in the TrEMBL protein sequence database. InterPro also provides a means to carry out statistical and comparative analyses of whole genomes. In the Proteome Analysis Database, InterPro analyses have been combined with other analyses based on CluSTr, the Gene Ontology (GO) and structural information on the proteins.     

Metal-enhanced fluorescence: an emerging tool in biotechnology

Over the past 15 years, fluorescence has become the dominant detection/sensing technology in medical diagnostics and biotechnology. Although fluorescence is a highly sensitive technique, where single molecules can readily be detected, there is still a drive for reduced detection limits. The detection of a fluorophore is usually limited by its quantum yield, autofluorescence of the samples and/or the photostability of the fluorophores; however, there has been a recent explosion in the use of metallic nanostructures to favorably modify the spectral properties of fluorophores and to alleviate some of these fluorophore photophysical constraints. The use of fluorophore-metal interactions has been termed radiative decay engineering, metal-enhanced fluorescence or surface-enhanced fluorescence.