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In order to use classical molecular dynamics to complement experiments accurately, it is important to use robust descriptions of the system. The interactions between biomolecules, like aspartic and glutamic acid, and dissolved ions are often studied using standard biomolecular force-fields, where the interactions between biomolecules and cations are often not parameterized explicitly. In this study, we have employed metadynamics simulations to investigate different interactions of Ca with aspartic and glutamic acid and constructed the free energy profiles of Ca2+–carboxylate association. Starting from a generally accepted, AMBER-based force field, the association was substantially over and under-estimated, depending on the choice of water model (TIP3P and SPC/fw, respectively). To rectify this discrepancy, we have replaced the default calcium parameters. Additionally, we modified the σij value in the hetero-atomic Lennard-Jones interaction by 0.5% to further improve the interaction between Ca and carboxylate, based on comparison with the experimentally determined association constant for Ca with the carboxylate group of L-aspartic acid. The corrected description retrieved the structural properties of the ion pair in agreement with the original biomolecule – Ca2+ interaction in AMBER, whilst also producing an association constant comparable to experimental observations. This refined force field was then used to investigate the interactions between amino acids, calcium and carbonate ions during biogenic and biomimetic calcium carbonate mineralisation.

Pseudorabies virus (PRV) is a porcine alphaherpesvirus that belongs to the Herpesviridae family. We showed earlier that infection of porcine epithelial cells with PRV triggers activation of the nuclear factor kappa B (NF-kappa B) pathway, a pivotal signaling axis in the early immune response. However, PRV-induced NF-kappa B activation does not lead to NF-kappa B-dependent gene expression. Here, using electrophoretic mobility shift assays (EMSAs), we show that PRV does not disrupt the ability of NF-kappa B to interact with its kappa B target sites. Assessing basal cellular transcriptional activity in PRV-infected cells by quantitation of prespliced transcripts of constitutively expressed genes uncovered a broad suppression of cellular transcription by PRV, which also affects the inducible expression of NF-kappa B target genes. Host cell transcription inhibition was rescued when viral genome replication was blocked using phosphonoacetic acid (PAA). Remarkably, we found that host gene expression shutoff in PRV-infected cells correlated with a substantial retention of the NF-kappa B subunit p65, the TATA box binding protein, and RNA polymerase II-essential factors required for (NF-kappa B-dependent) gene transcription-in expanding PRV replication centers in the nucleus and thereby away from the host chromatin. This study reveals a potent mechanism used by the alphaherpesvirus PRV to steer the protein production capacity of infected cells to viral proteins by preventing expression of host genes, including inducible genes involved in mounting antiviral responses. IMPORTANCE Herpesviruses are highly successful pathogens that cause lifelong persistent infections of their host. Modulation of the intracellular environment of infected cells is imperative for the success of virus infections. We reported earlier that a DNA damage response in epithelial cells infected with the alphaherpesvirus pseudorabies virus (PRV) results in activation of the hallmark proinflammatory NF-kappa B signaling axis but, remarkably, that this activation does not lead to NF-kappa B-induced (proinflammatory) gene expression. Here, we report that PRV-mediated inhibition of host gene expression stretches beyond NF-kappa B-dependent gene expression and in fact reflects a broad inhibition of host gene transcription, which correlates with a substantial recruitment of essential host transcription factors in viral replication compartments in the nucleus, away from the host chromatin. These data uncover a potent alphaherpesvirus mechanism to interfere with production of host proteins, including proteins involved in antiviral responses. Herpesviruses are highly successful pathogens that cause lifelong persistent infections of their host. Modulation of the intracellular environment of infected cells is imperative for the success of virus infections.

Mother cells recycle parental MCMs and simultaneously synthesize nascent MCMs, both of which are inherited by daughter cells, in which the former are preferentially used to form active replisomes and the latter adjust the pace of replisome movement to minimize errors during DNA replication.Minichromosome maintenance proteins (MCMs) are DNA-dependent ATPases that bind to replication origins and license them to support a single round of DNA replication. A large excess of MCM2-7 assembles on chromatin in G1 phase as pre-replication complexes (pre-RCs), of which only a fraction become the productive CDC45-MCM-GINS (CMG) helicases that are required for genome duplication(1-4). It remains unclear why cells generate this surplus of MCMs, how they manage to sustain it across multiple generations, and why even a mild reduction in the MCM pool compromises the integrity of replicating genomes(5,6). Here we show that, for daughter cells to sustain error-free DNA replication, their mother cells build up a nuclear pool of MCMs both by recycling chromatin-bound (parental) MCMs and by synthesizing new (nascent) MCMs. Although all MCMs can form pre-RCs, it is the parental pool that is inherently stable and preferentially matures into CMGs. By contrast, nascent MCM3-7 (but not MCM2) undergo rapid proteolysis in the cytoplasm, and their stabilization and nuclear translocation require interaction with minichromosome-maintenance complex-binding protein (MCMBP), a distant MCM paralogue(7,8). By chaperoning nascent MCMs, MCMBP safeguards replicating genomes by increasing chromatin coverage with pre-RCs that do not participate on replication origins but adjust the pace of replisome movement to minimize errors during DNA replication. Consequently, although the paucity of pre-RCs in MCMBP-deficient cells does not alter DNA synthesis overall, it increases the speed and asymmetry of individual replisomes, which leads to DNA damage. The surplus of MCMs therefore increases the robustness of genome duplication by restraining the speed at which eukaryotic cells replicate their DNA. Alterations in physiological fork speed might thus explain why even a minor reduction in MCM levels destabilizes the genome and predisposes to increased incidence of tumour formation.

Significance Viruses that infect bacteria (phages) represent the most abundant living entities on the planet, and many aspects of our fundamental knowledge of phage–bacteria relationships have been derived in the context of exponentially growing bacteria. In the case of the prototypical Escherichia coli phage T7, specific inhibition of the housekeeping form of the RNA polymerase (Eσ 70 ) by a T7 protein, called Gp2, is essential for the development of viral progeny. We now reveal that T7 uses a second specific inhibitor that selectively inhibits the stationary phase RNA polymerase (Eσ S ), which enables T7 to develop well in exponentially growing and stationary phase bacteria. The results have broad implications for our understanding of phage–bacteria relationships and the therapeutic application of phages.

Heterotrimeric G proteins are pivotal mediators of cellular signal transduction in eukaryotic cells and abnormal G-protein signaling plays an important role in numerous diseases. During the last two decades it has become evident that the activation status of heterotrimeric G proteins is both highly localized and strongly regulated by a number of factors, including a receptor-independent activation pathway of heterotrimeric G proteins that does not involve the classical GDP/GTP exchange and relies on nucleoside diphosphate kinases (NDPKs). NDPKs are NTP/NDP transphosphorylases encoded by the nme/nm23 genes that are involved in a variety of cellular events such as proliferation, migration, and apoptosis. They therefore contribute, for example, to tumor metastasis, angiogenesis, retinopathy, and heart failure. Interestingly, NDPKs are translocated and/or upregulated in human heart failure. Here we describe recent advances in the current understanding of NDPK functions and how they have an impact on local regulation of G-protein signaling.

The coordination features and signaling of a L-lactate ion by a [Tb(bpcd)]+ (bpcd = N,N′-bis(2-pyridylmethyl)-trans-1,2-diaminocyclohexane-N,N′-diacetate) complex have been investigated by means of a combination of techniques, including total luminescence, calorimetry and circularly polarized luminescence. The L-lactate/[Tb(bpcd)]+ association constant, determined by both luminescence titration and isothermal titration calorimetry, indicates a weak interaction (log K = 1.3–1.45) between the analyte and both enantiomers of the complex. The theoretical DFT calculations suggest that the most likely coordination of L-lactate to the possible stereoisomers of the [Tb(S,S-bpcd)]+ complex (trans-O,O or trans-Npy,Npy) is one involving a hydroxyl group. The results of [Tb(rac-bpcd)]+ as a chiroptical luminescent probe of L-lactate underline the peculiar role of the chiral 1,2-diaminocyclohexane (DACH) backbone. Indeed, the target anion is capable of inducing CPL activity in the racemic mixture of Tb complexes containing DACH-based ligands. The same is not observed for the achiral analogue [Tb(bped)]+ (bped = N,N′-bis(2-pyridylmethyl)ethylenediamine-N,N′-diacetate) complex, likely because of the flexibility of the ethylenic group which allows an interconversion between different isomers which produces a null net CPL activity. Thanks to the differential quantum yield of the two diastereomeric species (R,R)-L and (S,S)-L, one can use the racemic complex to reveal L-lactate by measuring the induced CPL spectrum. Interestingly, this has been demonstrated in a commercial complex solution for medical use, containing several electrolytes, namely Ringer's lactate.

Long interspersed element-1 (LINE-1, L1) is a mobile genetic element comprising about 17% of the human genome. L1 utilizes an endonuclease to insert L1 cDNA into the target genomic DNA, which induces double-strand DNA breaks in the human genome and activates the DNA damage signaling pathway, resulting in the recruitment of DNA-repair proteins. This may facilitate or protect L1 integration into the human genome. Therefore, the host DNA repair machinery has pivotal roles in L1 mobility. In this study, we have, for the first time, demonstrated that the DNA repair protein, Rad18, restricts L1 mobility. Notably, overexpression of Rad18 strongly suppressed L1 retrotransposition as well as L1-mediated Alu retrotransposition. In contrast, L1 retrotransposition was enhanced in Rad18-deficient or knockdown cells. Furthermore, the Rad6 (E2 ubiquitin-conjugated enzyme)-binding domain, but not the Polη-binding domain, was required for the inhibition of L1 retrotransposition, suggesting that the E3 ubiquitin ligase activity of Rad18 is important in regulating L1 mobility. Accordingly, wild-type, but not the mutant Rad18-lacking Rad6-binding domain, bound with L1 ORF1p and sequestered with L1 ORF1p into the Rad18-nuclear foci. Altogether, Rad18 restricts L1 and Alu retrotransposition as a guardian of the human genome against endogenous retroelements.

Ammonium assimilation inE. coliis regulated by two paralogous proteins (GlnB and GlnK), which orchestrate interactions with regulators of gene expression, transport proteins and metabolic pathways. Yet how they conjointly modulate the activity of glutamine synthetase (GS), the key enzyme for nitrogen assimilation, is poorly understood. We combine experiments and theory to study the dynamic roles of GlnB and GlnK during nitrogen starvation and upshift. We measure time-resolvedin vivoconcentrations of metabolites, total and post-translationally modified proteins, and develop a concise biochemical model of GlnB and GlnK that incorporates competition for active and allosteric sites, as well as functional sequestration of GlnK. The model predicts the responses of GS, GlnB and GlnK under time-varying external ammonium level in the wild type and two genetic knock-outs. Our results show that GlnK is tightly regulated under nitrogen-rich conditions, yet it is expressed during ammonium run-out and starvation. This suggests a role for GlnK as a buffer of nitrogen shock after starvation, and provides a further functional link between nitrogen and carbon metabolisms.

Herein, the synthesis of amylose-coated, temperature-responsive poly(N-vinylcaprolactam) (VCL)-based copolymer microgels by enzyme-catalyzed grafting-from polymerization with phosphorylase b from rabbit muscle is reported. The phosphorylase is able to recognize the oligosaccharide maltoheptaose as primer and attach glucose units from the monomer glucose-1-phosphate to it, thereby forming amylose chains while releasing inorganic phosphate. Therefore, to enable the phosphorylase-catalyzed grafting-from polymerization of glucose-1-phosphate from the PVCL-based microgels, the maltoheptaose primer is covalently attached to the microgel in the first synthesis step. This is realized by adding N-(2-aminoethyl)methacrylamide (AEMAA) as a comonomer to the PVCL microgel to integrate primary amino groups and subsequent coupling of maltoheptaonolactone. Both the PVCL/AEMAA microgel as well as the obtained microgel-maltoheptaose construct are characterized in detail by dynamic light scattering, electrophoretic mobility measurements, IR spectroscopy, and atomic force microscopy. From the microgel-maltoheptaose construct, the grafting-from polymerization of glucose-1-phosphate is performed by the addition of phosphorylase b. Atomic force microscopy images clearly demonstrate the formation of an amylose shell around the microgels. The developed amylose-coated microgels open up promising application possibilities, for example, as colloidal scavengers, since amylose helices can serve as host molecules for inclusion of hydrophobic guest molecules.

Supramolecular polymers with monomers bound together by secondary interactions, such as polyrotaxanes (PRXs), consisting of alpha cyclodextrin (αCD) threaded onto poly(ethylene glycol) (PEG), have attracted interest as a result of their ability to overcome physical limitations present in conventional, covalently structured polymers. Herein, we describe the formation of pH-responsive supramolecular assemblies from carboxyethylester bearing αCD and PEG PRXs. These PRXs were formed using PEG of Mw 20 kDa and a threading degree of 28%. Upon charge neutralisation the threaded αCDs co-localise, resulting in aggregation of the PRXs and the formation of a suspension by self-assembly. This process is shown to be reversible and possible via the mobility of CDs along the PEG guest chain. As a result of the inherent properties of PRXs, such as enhanced multivalent interactions and degradation, these responsive supramolecular polymers are expected to be of interest in fields where PRX-based materials have already found application, including paints, self-healing materials, surface coatings, and polymer therapeutics. Refereed/Peer-reviewed

Good’s buffer ionic liquids (GB-ILs) are new class of ILs with self-buffering capacity at the physiological pH range for biological research. GB-ILs are formed by the combination of Good’s buffers as anions and various organic bases as counter ions. In this work, the complexation of europium(III) ion with tricine and tricine-based GB-ILs, tetramethylammonium tricinate, tetraethylammonium tricinate, tetrabutylammonium tricinate, cholinium tricinate, and 1-ethyl-3-methylimidazolium tricinate in aqueous solution were determined potentiometrically at T = 298.2 K and ionic strength I = 0.1 mol · dm−3 NaNO3. The protonation constants of the studied ligands (L) and their overall stability constants ( lg β ) with Eu(III) were determined. The best model that fit the potentiometric data was consisted of six main species, EuL 2 + , EuL 2 + , EuL 3 , EuH - 1 L + , EuH - 2 L 2 - , and EuH - 3 L 3 3 - . The lg β Eu ( tricine ) , lg β Eu ( tricine ) 2 , and lg β Eu ( tricine ) 3 are 5.75, 9.51, and 12.79, respectively. The overall stability constants ( lg β ) of tricine-based GB-ILs were found to be greater than those of tricine. The species distribution diagrams of these complexes were calculated and discussed in terms of percent Eu(III) and pH. We present a density functional theory (DFT) study to understand tricine chelating to Eu(III).

International audience; Twelve structurally related pyridyl and meso-N-methylpyridylporphyrin derivatives are investigated electrochemically in different nonaqueous media. The UV/Vis spectrum of each newly investigated porphyrin was measured before and after electro-reduction and, based on this data, the site of electron transfer is proposed. An interaction occurs between the meso-pyridyl or meso-N-alkyl-4-pyridyl substituents and the porphyrin p-ring system, the magnitude of which depends upon the number of linked pyridyl or N-alkyl-4-pyridyl groups in the compound, the solvent, the supporting electrolyte, and/or other anions added to the solution.

Granulocyte–macrophage colony-stimulating factor (GM-CSF) is a cytokine used in the treatment of serious conditions resulting from chemotherapy and bone marrow transplantation such as neutropenia and aplastic anemia. Despite these effects, GM-CSF has a very short biological half-life, and it requires frequent injection during the treatment. Therefore, the cytokine production is possible in the body with plasmid-encoded GM-CSF (pGM-CSF) coding for cytokine administered to the body. However, the selection of the proper delivery system for the plasmid is important. In this study, two different delivery systems, encapsulated plasmid such as fucoidan–chitosan (fucosphere) and chitosan microspheres, were prepared and the particle physicochemical properties evaluated. Fucospheres and chitosan microspheres size ranges are 151–401 and 376–681 nm. The zeta potential values of the microspheres were changed between 8.3–17.1 mV (fucosphere) and +21.9–28.9 mV (chitosan microspheres). The encapsulation capacity of fucospheres changed between 84.2% and 94.7% depending on the chitosan molecular weight used in the formulation. In vitro plasmid DNA release from both delivery systems exhibited slower profiles of approximately 90–140 days. Integrity of released samples was checked by agarose gel electrophoresis, and any additional band was not seen. All formulations were analyzed kinetically. The calculated regression coefficients showed a higher r 2 value with zero-order kinetics. In conclusion, the characterizations of the microspheres can be modulated by changing the formulation variables, and it can be concluded that fucospheres might be a potential carrier system for the controlled delivery of GM-CSF encoding plasmid DNA.

The interactions of three heavy metal-containing compounds, cisplatin (CDDP), arsenic trioxide (As2O3), and mercury dichloride (HgCl2), with the multidrug resistance transporters MRP1 and MRP2 and the involvement of glutathione (GSH)-related processes herein were investigated. In Madin-Darby canine kidney cells stably expressing MRP1 or MRP2, viability, GSH content, calcein efflux and polarized GSH efflux were measured as a function of exposure to CDDP, As2O3 and HgCl2. In isolated Sf9-MRP1 and Sf9-MRP2 membrane vesicles, the interaction with MRP-associated ATPase activity was measured. In the latter model system adduct formation with GSH is not an issue. The data show that (1) CDDP interacts with both MRP1 and MRP2, and GSH appears to play no major role in this process, (2) As2O3 interacts with MRP1 and MRP2 in which process GSH seems to be essential, and (3) HgCl2 interacts with MRP1 and MRP2, either alone and/or as a metal-GSH complex. © 2008 Elsevier B.V. All rights reserved.

Item does not contain fulltext This review focuses on the tumour types and symptoms associated with non-islet cell tumour-induced hypoglycaemia (NICTH) as well as the pathogenesis, diagnosis and treatment of this rare paraneoplastic phenomenon. In addition, we report two illustrative cases of patients suffering from NICTH caused by a solid fibrous tumour and a haemangiopericytoma respectively. In the first case, NICTH resolved following complete resection of the tumour, but in the second case the patient needed long-term treatment aimed at controlling hypoglycaemia because of non-resectable metastases. Many tumour types have been associated with NICTH. The crucial event in the development of NICTH seems to be overexpression of the IGF-II gene by the tumour. NICTH is characterised by recurrent fasting hypoglycaemia and is associated with the secretion of incompletely processed precursors of IGF-II ('big'-IGF-II) by the tumour. This induces dramatic secondary changes in the circulating levels of insulin, GH, IGF-I and IGF-binding proteins, resulting in an insulin-like hypoglycaemic activity of 'big'-IGF-II.

This review focuses on the tumour types and symptoms associated with non-islet cell tumour-induced hypoglycaemia (NICTH) as well as the pathogenesis, diagnosis and treatment of this rare paraneoplastic phenomenon. In addition, we report two illustrative cases of patients suffering from NICTH caused by a solid fibrous tumour and a haemangiopericytoma respectively. In the first case, NICTH resolved following complete resection of the tumour, but in the second case the patient needed long-term treatment aimed at controlling hypoglycaemia because of non-resectable metastases. Many tumour types have been associated with NICTH. The crucial event in the development of NICTH seems to be overexpression of the IGF-II gene by the tumour. NICTH is characterised by recurrent fasting hypoglycaemia and is associated with the secretion of incompletely processed precursors of IGF-II ('big'-IGF-II) by the tumour. This induces dramatic secondary changes in the circulating levels of insulin, GH, IGF-I and IGF-binding proteins, resulting in an insulin-like hypoglycaemic activity of 'big'-IGF-II.

A dataset of experimentally characterized, human Golgi GlyTs with type II membrane topology was created. Based on the experimentally observed acceptor substrate preferences, the GlyTs were classified into five functional categories: biosynthesis of blood group antigens, glycolipids, N-glycans, O-glycans and glycosaminoglycans. The cytoplasmic, transmembrane and stem (CTS) regions were predicted and their length and composition were analyzed. The stem region of GlyTs involved in the biosynthesis of glycolipids and blood group antigens appear to have a shorter stem region compared to those GlyTs which participate in the biosynthesis of N- and O-linked glycans and glycosaminoglycans. The stem regions of all the GlyTs, irrespective of the functional category to which they belong, were found to be rich in disorder-promoting amino acid residues. Thus, the stem region is largely devoid of any regular secondary structure thereby facilitating its tethering role. A higher frequency of occurrence of basic amino acids is observed towards the N-terminus of the transmembrane domain and this is suggested to be important for topogenesis of these enzymes.

Cyclodextrins (CD) are often proposed as potential vehicles in targeted drug delivery. However, if the membrane structure is disrupted by CD, then it cannot be considered to be a good drug delivery vehicle. When an extrinsic fluorescence probe is used to monitor such interactions, there are no less than three possible equilibria that can operate simultaneously: surfactant-cyclodextrin, surfactant fluorophore and cyclodextrin fluorophore. The fluorescence intensity/lifetime might be affected by all these and so, the results depend strongly on the fluorophore used as well as the nature of the surfactant. This aspect highlights the importance of the suitability of the. fluorescence probe to be used to study complicated systems and interaction. In the present work, chlorin p(6), prepared from chlorophyll from spinach leaves, has been used as the fluorescence probe to investigate the interaction between alpha-CD and beta-CD with the neutral surfactants Triton X 100 (TX 100) and cetyl trimethyl ammonium bromide (CTAB). The fluorophore is found to be a sensitive one for the study of the interaction of alpha, beta and gamma-CD with the surfactants TX 100 and CTAB. It is found that contrary to earlier reports, a complex between alpha-CD and TX 100 is formed, even though the binding constant is not very high. This observation can be obtained with chlorin p(6), which does not bind to the CDs, but not with a fluorophore, which binds to the CD as well and thus complicates the situation as the binding with CD is stronger than that between TX 100 and alpha-CD as compared to that between TNS and CD.

Diets high in red meat and low in green vegetables are associated with an increased risk of colon cancer. In rats, dietary heme, mimicking red meat, increases colonic cytotoxicity and proliferation of the colonocytes, whereas addition of chlorophyll from green vegetables inhibits these heme-induced effects. Chlorophyllin is a water-soluble hydrolysis product of chlorophyll that inhibits the toxicity of many planar aromatic compounds. The present study investigated whether chlorophyllins could inhibit the heme-induced luminal cytotoxicity and colonic hyperproliferation as natural chlorophyll does. Rats were fed a purified control diet, the control diet supplemented with heme, or a heme diet with 1.2 mmol/kg diet of chlorophyllin, copper chlorophyllin, or natural chlorophyll for 14 d (n = 8/group). The cytotoxicity of fecal water was determined with an erythrocyte bioassay and colonic epithelial cell proliferation was quantified in vivo by [methyl-(3)H]thymidine incorporation into newly synthesized DNA. Exfoliation of colonocytes was measured as the amount of rat DNA in feces using quantitative PCR analysis. Heme caused a >50-fold increase in the cytotoxicity of the fecal water, a nearly 100% increase in proliferation, and almost total inhibition of exfoliation of the colonocytes. Furthermore, the addition of heme increased TBARS in fecal water. Chlorophyll, but not the chlorophyllins, completely prevented these heme-induced effects. In conclusion, inhibition of the heme-induced colonic cytotoxicity and epithelial cell turnover is specific for natural chlorophyll and cannot be mimicked by water-soluble chlorophyllins.

In the present study, we analysed the expression and localization of p21(Waf1/Cip1) in normal and malignant haematopoietic cells. We demonstrate that in normal monocytic cells, protein kinase C (PKC)-induced p21 gene activation, which is nuclear factor-kappaB (NF-kappaB) independent, results in predominantly cytoplasmic localized p21 protein. In acute monocytic leukaemia (M4, M5), monocytic blasts (N = 12) show constitutive cytoplasmic p21 expression in 75% of the cases, while in myeloid leukaemic blasts (N = 10), low nuclear and cytoplasmic localization of p21 could be detected, which is also PKC dependent. Constitutive p21 expression in monocytic leukaemia might have important antiapoptotic functions. This is supported by the finding that in U937 cells overexpressing p21, VP16-induced apoptosis is significantly reduced (20.0+/-0.9 vs 55.8+/-3.8%, P

Cationic lipids are widely used for gene transfection, but their mechanism of action is still poorly understood. To improve this knowledge, a structure-function study was carried out with two pyridinium-based lipid analogs with identical headgroups but differing in alkyl chain (un)saturation, i.e., SAINT-2 (diC18:1) and SAINT-5 (diC18:0). Although both amphiphiles display transfection activity per se, DOPE strongly promotes SAINT-2-mediated transfection, but not that of SAINT-5, despite the fact that DOPE effectively facilitates plasmid dissociation from either lipoplex. This difference appears to correlate with membrane stiffness, dictated by the cationic lipid packing in the donor liposomes, which governs the kinetics of lipid recruitment by the plasmid upon lipoplex assembly. Because of its interaction with the relatively rigid SAINT-5 membranes, the plasmid becomes inappropriately condensed, which results in formation of structurally deformed lipoplexes. This structural deformation does not affect its cellular uptake but, rather, hampers plasmid translocation across endosomal and/or nuclear membranes. This is inferred from the observation that both lipoplexes effectively translocate much smaller oligonucleotides into cells. In fact, SAINT-5/DOPE-mediated transfection is greatly improved when, before lipoplex assembly, the plasmid is stabilized by condensation with polylysine. The results emphasize a role of the structural shape of the plasmid in gaining cytosolic/nuclear access. Moreover, it has been proposed that such a translocation is promoted when the lipoplex adopts the hexagonal phase, and data are presented that demonstrate that the lamellar SAINT-5/DOPE lipoplex adopts such a phase after its interaction with acidic phospholipid-containing membranes.

We report that fluorescently tagged arabinogalactan glycosyltransferases target not only the Golgi apparatus but also uncharacterized smaller compartments when transiently expressed in Nicotiana benthamiana. Approximately 80% of AtGALT31A [Arabidopsis thaliana galactosyltransferase from family 31 (At1g32930)] was found in the small compartments, of which, 45 and 40% of AtGALT29A [Arabidopsis thaliana galactosyltransferase from family 29 (At1g08280)] and AtGlcAT14A [Arabidopsis thaliana glucuronosyltransferase from family 14 (At5g39990)] colocalized with AtGALT31A, respectively; in contrast, N-glycosylation enzymes rarely colocalized (3-18%), implicating a role of the small compartments in a part of arabinogalactan (O-glycan) biosynthesis rather than N-glycan processing. The dual localization of AtGALT31A was also observed for fluorescently tagged AtGALT31A stably expressed in an Arabidopsis atgalt31a mutant background. Further, site-directed mutagenesis of a phosphorylation site of AtGALT29A (Y144) increased the frequency of the protein being targeted to the AtGALT31A-localized small compartments, suggesting a role of Y144 in subcellular targeting. The AtGALT31A localized to the small compartments were colocalized with neither SYP61 (syntaxin of plants 61), a marker for trans-Golgi network (TGN), nor FM4-64-stained endosomes. However, 41% colocalized with EXO70E2 (Arabidopsis thaliana exocyst protein Exo70 homolog 2), a marker for exocyst-positive organelles, and least affected by Brefeldin A and Wortmannin. Taken together, AtGALT31A localized to small compartments that are distinct from the Golgi apparatus, the SYP61-localized TGN, FM4-64-stained endosomes and Wortmannin-vacuolated prevacuolar compartments, but may be part of an unconventional protein secretory pathway represented by EXO70E2 in plants.

Drug-induced phospholipidosis (PLD) is characterized by accumulation of phospholipids, the inducing drugs and lamellar inclusion bodies in the lysosomes of affected tissues. These side effects must be considered as early as possible during drug discovery, and, in fact, numerous in silico models designed to predict PLD have been published. However, the quality of any in silico model cannot be better than the quality of the experimental data set used to build it. The present paper reports an overview of the difficulties and errors encountered in the generation of databases used for the published PLD models. A new database of 466 compounds was constructed from seven literature sources, containing only publicly available compounds. A comparison of the PLD assignations in selected databases proved useful in revealing some inconsistencies and raised doubts about the previously assigned PLD+ and PLD- classifications for some chemicals. Finally, a Partial Least Squares Discriminant Analysis (PLS-DA) approach was also applied, revealing further anomalies and clearly showing that metabolism as well as data quality must be taken into account when generating accurate methods for predicting the likelihood that a compound will induce PLD. A new curated database of 331 compounds is proposed.

Two citric acid crosslinked gamma-cyclodextrin oligomers (p gamma-CyD) with a MW of 21-33 kDa and 10-15 gamma-CyD units per molecule were prepared by following green chemistry methods and were fully characterized. The non-covalent association of doxorubicin (DOX) with these macromolecules was investigated in neutral aqueous medium by means of circular dichroism (CD), UV-vis absorption and fluorescence. Global analysis of multiwavelength spectroscopic CD and fluorescence titration data, taking into account the DOX monomer-dimer equilibrium, evidenced the formation of 1 : 1 and 1 : 2 p gamma-CyD unit-DOX complexes. The binding constants are 1-2 orders of magnitude higher than those obtained for gamma-CyD and depend on the characteristics of the oligomer batch used. The concentration profiles of the species in solution evidence the progressive monomerization of DOX with increasing oligomer concentration. Confocal fluorescence imaging and spectral imaging showed a similar drug distribution within the MCF-7 cell line incubated with either DOX complexed to p gamma-CyD or free DOX. In both cases DOX is taken up into the cell nucleus without any degradation.

The dense phases of the CO2-CCl4 (I) and CO2-CS2 (II) mixtures have been studied by Raman spectroscopy. Mixture I is found almost ideal and II strongly non-ideal. At high CS2 concentration in II, the local structure of CS2 is preserved suggesting a nano-segregation of the liquid phase without demixing whereas in CO2 concentrated mixtures a diversity of species are present. Thermodynamical considerations together with spectroscopic results show that a subtle interplay between attractive and repulsive interactions leads to this non-ideal behaviour. The connection of these results with the liquid-liquid demixing reported for CO2-CS2 at lower temperature is discussed. (C) 2013 Elsevier B. V. All rights reserved.

Isothermal titration microcalorimetry has been applied to investigate the interactions between hydrophobically-modified water-soluble polymers and surfactants. The following polymers were used in this study: poly(sodium acrylate-co-n-alkyl methacrylate) (A), where n-alkyl = C9H19, C12H25, and C18H37 (percentage of n-alkyl methacrylate to total monomer content ranging from 0 to 8), and poly(acrylamide-co-n-alkyl methacrylate) (B), where n-alkyl = C12H25 (percentage of lauryl methacrylate to total monomer content ranging from 0 to 5). The surfactants were a cyclic (mono-) n-dodecyl sodium phosphate (1) (CMP), a cyclic di-n-dodecyl sodium phosphate (2) (CDP), n-dodecyltrimethylammonium bromide (3) (DTAB), and di-n-dodecyldimethylammonium bromide (4) (DDAB). The following factors were found to influence the interactions between polymers and surfactants: electrostatic forces, polymer hydrophobicity (both the length of the hydrophobic moiety and the degree of hydrophobic modification), and the aggregational states of the amphiphilic molecules, which are micellar for the single-tailed surfactants and vesicular for the double-tailed amphiphiles. We provide evidence that, in the case of the single-tailed surfactants, individual amphiphilic molecules adsorb onto existing polymeric microdomains. This is in strong contrast with 'classical' polymer-surfactant interactions, where cooperative aggregation of single-tailed amphiphiles in the presence of homopolymers like poly(ethylene oxide) or poly(propylene oxide) was found at concentrations lower than the critical micelle concentration in pure water. In the case of vesicle-forming surfactants, the hydrophobic side chain of the polymer anchors into the bilayers of the vesicles. Non-hydrophobically-modified polymers do not interact at all with the vesicle bilayers. Interestingly, the interactions between single-tailed surfactants and hydrophobically-modified polymers are governed by different factors than the binding of hydrophobically-modified polymers to vesicular bilayers. In the former case, the number and strength of existing (inter)polymeric associations is of importance, and it is particularly the length of the hydrophobic moieties that is decisive. However, for favorable polymer-bilayer interactions it is sufficient that the hydrophobic moieties are long enough to be able to anchor. If this is the case, the number of hydrophobic anchors per polymer molecule further determines the effectiveness of the interaction. Finally, it appears that electrostatic repulsions can be easily overcome by hydrophobic interactions, but added salt facilitates the interactions between equally charged polymers and surfactants.

In the Arabidopsis multiparent recombinant inbred line mapping population, a limited number of plants were detected that lacked axillary buds in most of the axils of the cauline (stem) leaves, but formed such buds in almost all rosette axils. Genetic analysis showed that polymorphisms in at least three loci together constitute this phenotype, which only occurs in late-flowering plants. Early flowering is epistatic to two of these loci, called REDUCED SHOOT BRANCHING1 (RSB1) and RSB2, which themselves do not affect flowering time. Map-based cloning and confirmation by transformation with genes from the region where RSB1 was identified by fine-mapping showed that a specific allele of AGAMOUS-Like6 from accession C24 conferred reduced branching in the cauline leaves. Site-directed mutagenesis in the Columbia allele revealed the causal amino acid substitution, which behaved as dominant negative, as was concluded from a loss-of-function mutation that showed the same phenotype in the late-flowering genetic background. This causal allele occurs at a frequency of 15% in the resequenced Arabidopsis thaliana accessions and correlated with reduced stem branching only in late-flowering accessions. The data show the importance of natural variation and epistatic interactions in revealing gene function.

Influenza viruses are the cause of yearly epidemics and occasional pandemics that represent a significant challenge to public health. Current control strategies are imperfect and there is an unmet need for new antiviral therapies. Here, we report the identification of small molecule compounds able to effectively and specifically inhibit growth of influenza A and B viruses in cultured cells through targeting an assembly interface of the viral RNA-dependent RNA polymerase. Using an existing crystal structure of the primary protein–protein interface between the PB1 and PA subunits of the influenza A virus polymerase, we conducted an in silico screen to identify potential small molecule inhibitors. Selected compounds were then screened for their ability to inhibit the interaction between PB1 and PA in vitro using an ELISA-based assay and in cells, to inhibit nuclear import of a binary PB1–PA complex as well as transcription by the full viral ribonucleoprotein complex. Two compounds emerged as effective inhibitors with IC 50 values in the low micromolar range and negligible cytotoxicity. Of these, one compound also acted as a potent replication inhibitor of a variety of influenza A virus strains in Madin-Darby canine kidney (MDCK) cells, including H3N2 and H1N1 seasonal and 2009 pandemic strains. Importantly, this included an oseltamivir-resistant isolate. Furthermore, potent inhibition of influenza B viruses but not other RNA or DNA viruses was seen. Overall, these compounds provide a foundation for the development of a new generation of therapeutic agents exhibiting high specificity to influenza A and B viruses.

The association of doxorubicin (DOX) with gamma-cyclodextrin (gamma-CyD) was studied in phosphate buffer of pH 7.4, at 22 degrees C by performing titration experiments monitored with circular dichroism (CD), UV-vis absorption, and fluorescence. Global analysis of multiwavelength spectroscopic data obtained at different DOX concentrations was performed by taking into account the DOX monomer-dimer equilibrium. Formation of gamma-CyD: DOX 1 : 1, 2 : 1, 1 : 2 and 2 : 2 complexes was evidenced. The stability constants and the absolute CD, UV-vis absorption and fluorescence spectra of all the complexes were determined. gamma-CyD did not prove to be able to disrupt the DOX dimer when the latter is the predominant form in solution. The triplet state absorption and kinetic properties of DOX in the presence of gamma-CyD and in ethanol were also determined by laser flash photolysis. The excited singlet and the triplet features indicated the environment experienced by DOX in the CyD complexes is ethanol-like. The structure of the gamma-CyD: DOX 1 : 1 complex was investigated by Molecular Mechanics (MM) and Molecular Dynamics (MD) for both the neutral and the positively charged (-NH3+ in the daunosamine moiety) DOX forms. The possibility of interaction of both the aglycone and the daunosamine parts with the gamma-CyD cavity was evidenced.

International audience; The activating transcription factor 4 (ATF4) promotes transcriptional upregulation of specific target genes in response to cellular stress. ATF4 expression is regulated at the translational level by two short open reading frames (uORFs) in its 5′-untranslated region (5′-UTR). Here, we describe a mechanism regulating ATF4 expression in translation termination-deficient human cells. Using microarray analysis of total RNA and polysome-associated mRNAs, we show that depletion of the eucaryotic release factor 3a (eRF3a) induces upregulation of ATF4 and of ATF4 target genes. We show that eRF3a depletion modifies ATF4 translational control at regulatory uORFs increasing ATF4 ORF translation. Finally, we show that the increase of REDD1 expression, one of the upregulated targets of ATF4, is responsible for the mTOR pathway inhibition in eRF3a-depleted cells. Our results shed light on the molecular mechanisms connecting eRF3a depletion to mammalian target of rapamycin (mTOR) pathway inhibition and give an example of ATF4 activation that bypasses the signal transduction cascade leading to the phosphorylation of eIF2α. We propose that in mammals, in which the 5′-UTR regulatory elements of ATF4 mRNA are strictly conserved, variations in translation termination efficiency allow the modulation of the ATF4 response.

N,N'-dioxide ligands such as 2, 2'-bipyridine-N,N-dioxide (BPDO-I) and 4, 4'-bipyridine-N,N-dioxide (BPDO-II) were used to trap the hydrated dimethyltin cations under controlled hydrolysis. The use of the chelating ligand BPDO-I leads to the isolation of the discrete monocation [Me2Sn(BPDO-I)(OH2)(NO3)]+[NO3] (2), whereas the linear ligand BPDO-II directs the construction of cationic polymers, [{Me2Sn(OH2)2(mu-BPDO-II)}2+{NO3}2 center dot 2H2O]n (3 center dot 2H2O) and [{Me2Sn(mu-OH)(BPDO-II)}22+{NO3}2 center dot H2O]n (4 center dot H2O) under different reaction conditions.

Melittin, a membrane-active peptide with antimicrobial activity, was investigated at the interface formed between two immiscible electrolyte solutions (ITIES) supported on a metallic electrode. Ion-transfer voltammetry showed well-defined semi-reversible transfer peaks along with adsorptive peaks. The reversible adsorption of melittin at the liquid-liquid interface is qualitatively discussed from voltammetric data and experimentally confirmed by real-time image analysis of video snapshots. It is also demonstrated that polarization of the water/1,2-DCE interface results in drastic drop shape variations caused by large variations of the interfacial tension. The experimental data also confirmed that maximum adsorption occurs near the ion transfer potential. Finally, the interaction of melittin with a monolayer of L-alpha-dipalmitoyl phosphatidylcholine (DPPC) was also investigated showing that melittin destabilizes the lipidic monolayer facilitating its desorption. The non-covalent complex formation between melittin and DPPC was confirmed by mass spectrometry.

Interactions between cyclomaltoheptaose (β-cyclodextrin, βCD) and p-toluenesulfonyl chloride (TsCl) were investigated using MD simulations, both in vacuum, approximating the hydrophobic environment of the CD cavity, and with water as a solvent. In both cases, the minimum energy adiabatic paths, and the mean force potentials (MFP) for the insertion of TsCl along a reaction coordinate perpendicular to the CD plane, were calculated for the two possible orientations of TsCl. The results show a preferred entry of TsCl in the CD cavity with the sulfonyl chloride group pointing to the primary hydroxyls rim. In each orientation, two energy minima for the complex are detected in vacuum that reflect the H-H contacts between host and guest observed by NMR spectroscopy (ROESY, NOESY). These separate minima collapsed into a single broader minimum, when the solvent was introduced in the simulations. The resulting association constant between TsCl and βCD (Ka ≈ 100 M-1) is in good agreement with the NMR results (Ka = 102 ± 12 M-1) in deuterated water solution at 298 K. Advantage has been taken of the dynamics of the reagent inclusion to set up a one step process involving a transient Cu2+ chelate at the secondary hydroxyls rim position for the electrophilic monoactivation of βCD at the primary hydroxyls rim using water as solvent. © 2011 American Chemical Society., This project was supported by the Spanish Ministerio de Ciencia e Innovacion (MICINN, contract No. CTQ2009-14551-C02-01/BQU and CTQ2010-15848), the Junta de Andalucia (P07-FQM2774), the CSIC and the CNRS. We also acknowledge financial support from FEDER funds.

9 páginas, 7 figuras, 1 tabla, 2 esquemas.-- et al., Lipoplexes constituted by calf-thymus DNA (CT-DNA) and mixed cationic liposomes consisting of varying proportions of the cationic lipid 3β-[N-(N′,N′-dimethylaminoethane)-carbamoyl]cholesterol hydrochloride (DC-Chol) and the zwitterionic lipid, 1,2-dioleoyl-sn-glycero-3-phosphoetanolamine (DOPE) have been analyzed by means of electrophoretic mobility, SAXS, and fluorescence anisotropy experiments, as well as by theoretically calculated phase diagrams. Both experimental and theoretical studies have been run at several liposome and lipoplex compositions, defined in terms of cationic lipid molar fraction, α, and either the mass or charge ratios of the lipoplex, respectively. The experimental electrochemical results indicate that DC-Chol/DOPE liposomes, with a mean hydrodynamic diameter of around (120 ± 10) nm, compact and condense DNA fragments at their cationic surfaces by means of a strong entropically driven electrostatic interaction. Furthermore, the positive charges of cationic liposomes are compensated by the negative charges of DNA phosphate groups at the isoneutrality L/D ratio, (L/D), which decreases with the cationic lipid content of the mixed liposome, for a given DNA concentration. This inversion of sign process has been also studied by means of the phase diagrams calculated with the theoretical model, which confirms all the experimental results. SAXS diffractograms, run at several lipoplex compositions, reveal that, irrespectively of the lipoplex charge ratio, DC-Chol/DOPE-DNA lipoplexes show a lamellar structure, Lα, when the cationic lipid content on the mixed liposomes α ≥ 0.4, while for a lower content (α = 0.2) the lipoplexes show an inverted hexagonal structure, HII, usually related with improved cell transfection efficiency. A similar conclusion is reached from fluorescence anisotropy results, which indicate that the fluidity on liposome and lipoplexes membrane, also related with better transfection results, increases as long as the cationic lipid content decreases., The authors thank MICINN of Spain (Projects Nos. CTQ2009-10002BQU and UCMA05-33-010) and to the Comunidad Autónoma of Madrid (Project No. S-SAL- 0249-2006). A.N. thanks MICINN of Spain (Project No. MAT2008-03232) and CSIC (Project No. PIE200750-I021). A.M.-M. thanks the Ministerio de Ciencia e Innovación (Project MAT2009-13155-C04-04) and Junta de Andalucía (Projects P07-FQM-02517 and P09-FQM-4698).

Background The genetic control of floral organ specification is currently being investigated by various approaches, both experimentally and through modeling. Models and simulations have mostly involved boolean or related methods, and so far a quantitative, continuous-time approach has not been explored. Results We propose an ordinary differential equation (ODE) model that describes the gene expression dynamics of a gene regulatory network that controls floral organ formation in the model plant Arabidopsis thaliana. In this model, the dimerization of MADS-box transcription factors is incorporated explicitly. The unknown parameters are estimated from (known) experimental expression data. The model is validated by simulation studies of known mutant plants. Conclusions The proposed model gives realistic predictions with respect to independent mutation data. A simulation study is carried out to predict the effects of a new type of mutation that has so far not been made in Arabidopsis, but that could be used as a severe test of the validity of the model. According to our predictions, the role of dimers is surprisingly important. Moreover, the functional loss of any dimer leads to one or more phenotypic alterations.

Background Failure of sperm differentiation is one of the major causes of male sterility. During spermiogenesis, spermatids undergo a complex metamorphosis, including chromatin condensation and cell elongation. Although the resulting sperm morphology and property can vary depending on the species, these processes are fundamental in many organisms. Studying genes involved in such processes can thus provide important information for a better understanding of spermatogenesis, which might be universally applied to many other organisms. Results In a screen for genes that have gonad-specific expression we isolated an elav-like gene, melav2, from Macrostomum lignano, containing the three RNA recognition motifs characteristic of elav-like genes. We found that melav2 mRNA was expressed exclusively in the testis, as opposed to the known elav genes, which are expressed in the nervous system. The RNAi phenotype of melav2 was characterized by an aberrant spermatid morphology, where sperm elongation often failed, and an empty seminal vesicle. Melav2 RNAi treated worms were thus male-sterile. Further analysis revealed that in melav2 RNAi treated worms precocious chromatin condensation occurred during spermatid differentiation, resulting in an abnormally tightly condensed chromatin and large vacuoles in round spermatids. In addition, immunostaining using an early-spermatid specific antibody revealed that melav2 RNAi treated worms had a larger amount of signal positive cells, suggesting that many cells failed the transition from early spermatid stage. Conclusion We characterize a new function for elav-like genes, showing that melav2 plays a crucial role during spermatid differentiation, especially in the regulation of chromatin condensation and/or cell elongation.